@article{sohn_kibbe_dioli_hector_bai_garrard_muddiman_2024, title={A statistical approach to system suitability testing for mass spectrometry imaging}, volume={38}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9725}, abstractNote={RationaleMass spectrometry imaging (MSI) elevates the power of conventional mass spectrometry (MS) to multidimensional space, elucidating both chemical composition and localization. However, the field lacks any robust quality control (QC) and/or system suitability testing (SST) protocols to monitor inconsistencies during data acquisition, both of which are integral to ensure the validity of experimental results. To satisfy this demand in the community, we propose an adaptable QC/SST approach with five analyte options amendable to various ionization MSI platforms (e.g., desorption electrospray ionization, matrix‐assisted laser desorption/ionization [MALDI], MALDI‐2, and infrared matrix‐assisted laser desorption electrospray ionization [IR‐MALDESI]).MethodsA novel QC mix was sprayed across glass slides to collect QC/SST regions‐of‐interest (ROIs). Data were collected under optimal conditions and on a compromised instrument to construct and refine the principal component analysis (PCA) model in R. Metrics, including mass measurement accuracy and spectral accuracy, were evaluated, yielding an individual suitability score for each compound. The average of these scores is utilized to inform if troubleshooting is necessary.ResultsThe PCA‐based SST model was applied to data collected when the instrument was compromised. The resultant SST scores were used to determine a statistically significant threshold, which was defined as 0.93 for IR‐MALDESI‐MSI analyses. This minimizes the type‐I error rate, where the QC/SST would report the platform to be in working condition when cleaning is actually necessary. Further, data scored after a partial cleaning demonstrate the importance of QC and frequent full instrument cleaning.ConclusionsThis study is the starting point for addressing an important issue and will undergo future development to improve the efficiency of the protocol. Ultimately, this work is the first of its kind and proposes this approach as a proof of concept to develop and implement universal QC/SST protocols for a variety of MSI platforms.}, number={9}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Sohn, Alexandria L. and Kibbe, Russell R. and Dioli, Olivia E. and Hector, Emily C. and Bai, Hongxia and Garrard, Kenneth P. and Muddiman, David C.}, year={2024}, month={May} }
 @article{eisenberg_muddiman_2024, title={Improved detection in untargeted lipidomics through silver-doped infrared matrix-assisted laser desorption electrospray ionization}, volume={38}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9832}, abstractNote={Silver doping of electrospray is known to increase the abundance of olefinic compounds detected by mass spectrometry. While demonstrated in targeted experiments, this has yet to be investigated in an untargeted study. Utilizing infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging (IR-MALDESI-MSI), an untargeted lipidomics experiment on mouse liver was performed to evaluate the advantages of silver-doped electrospray.}, number={15}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Eisenberg, Seth M. and Muddiman, David C.}, year={2024}, month={Aug} }
 @article{ashbacher_mills_sohn_xie_muddiman_2024, title={Incorporation of Three Different Optical Trains into the IR-MALDESI Mass Spectrometry Imaging Platform to Characterize <i>Artemisia annua</i>}, volume={35}, ISSN={["1879-1123"]}, url={https://doi.org/10.1021/jasms.4c00060}, DOI={10.1021/jasms.4c00060}, abstractNote={Artemisinin is the leading medication for the treatment of malaria and is only produced naturally in Artemisia annua. The localization of artemisinin in both the glandular and non-glandular trichomes of the plant makes it an ideal candidate for mass spectrometry imaging (MSI) as a model system for method development. Infrared matrix-assisted laser desorption electrospray ionization MSI (IR-MALDESI-MSI) has the capability to detect hundreds to thousands of analytes simultaneously, providing abundance information in conjunction with species localization throughout a sample. The development of several new optical trains and their application to the IR-MALDESI-MSI platform has improved data quality in previous proof-of-concept experiments but has not yet been applied to analysis of native biological samples, especially the MSI analysis of plants. This study aimed to develop a workflow and optimize MSI parameters, specifically the laser optical train, for the analysis of Artemisia annua with the NextGen IR-MALDESI platform coupled to an Orbitrap Exploris 240 mass spectrometer. Two laser optics were compared to the conventional set up, of which include a Schwarzschild-like reflective objective and a diffractive optical element (DOE). These optics, respectively, enhance the spatial resolution of imaging experiments or create a square spot shape for top-hat imaging. Ultimately, we incorporated and characterized three different optical trains into our analysis of Artemisia annua to study metabolites in the artemisinin pathway. These improvements in our workflow, resulted in high spatial resolution and improved ion abundance from previous work, which will allow us to address many different questions in plant biology beyond this model system.}, number={6}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Ashbacher, Sarah M. and Mills, Quinn and Sohn, Alexandria L. and Xie, De-Yu and Muddiman, David C.}, year={2024}, month={Apr}, pages={1245–1252} }
 @article{palomino_muddiman_2024, title={Mass spectrometry imaging of <i>N</i>-linked glycans: Fundamentals and recent advances}, volume={6}, ISSN={["1098-2787"]}, DOI={10.1002/mas.21895}, abstractNote={Abstract With implications in several medical conditions, N ‐linked glycosylation is one of the most important posttranslation modifications present in all living organisms. Due to their nontemplate synthesis, glycan structures are extraordinarily complex and require multiple analytical techniques for complete structural elucidation. Mass spectrometry is the most common way to investigate N ‐linked glycans; however, with techniques such as liquid‐chromatography mass spectrometry, there is complete loss of spatial information. Mass spectrometry imaging is a transformative analytical technique that can visualize the spatial distribution of ions within a biological sample and has been shown to be a powerful tool to investigate N ‐linked glycosylation. This review covers the fundamentals of mass spectrometry imaging and N ‐linked glycosylation and highlights important findings of recent key studies aimed at expanding and improving the glycomics imaging field.}, journal={MASS SPECTROMETRY REVIEWS}, author={Palomino, Tana V. and Muddiman, David C.}, year={2024}, month={Jun} }
 @article{wang_ouyang_segura_muddiman_2024, title={Optimizing neurotransmitter pathway detection by IR-MALDESI-MSI in mouse brain}, volume={6}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-024-05354-1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Wang, Mary F. and Ouyang, Yunxin and Segura, Tatiana and Muddiman, David C.}, year={2024}, month={Jun} }
 @article{kibbe_muddiman_2024, title={Quantitative mass spectrometry imaging (qMSI): A tutorial}, volume={59}, ISSN={["1096-9888"]}, DOI={10.1002/jms.5009}, abstractNote={AbstractMass spectrometry imaging (MSI) is an analytical technique that enables the simultaneous detection of hundreds to thousands of chemical species while retaining their spatial information; usually, MSI is applied to biological tissues. Combining these elements can create ion images, which allows for the identification and localization of multiple chemical species within the sample. Being able to produce molecular images of biological tissues has already impacted the study of health and disease; however, the next logical step is being able to combine MSI with quantitative mass spectrometry methods to both quantify and determine the localization of disease progression or drug action. In this tutorial, we will detail the main factors to consider when designing a qMSI experiment and highlight the methods that have been developed to overcome these added complexities, specifically for those newer to the field of MSI.}, number={4}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Kibbe, Russell R. and Muddiman, David C.}, year={2024}, month={Apr} }
 @article{holman_langley_muddiman_novak-mitchell_2024, title={RCM protocols: improving reproducibility in the field of mass spectrometry}, volume={1}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9677}, abstractNote={Rapid Communications in Mass SpectrometryVolume 38, Issue S1 e9677 EDITORIAL RCM protocols: improving reproducibility in the field of mass spectrometry Stephen W. Holman, Stephen W. Holman Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UKSearch for more papers by this authorG. John Langley, G. John Langley Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UKSearch for more papers by this authorDavid C. Muddiman, David C. Muddiman FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USASearch for more papers by this authorCalum Novak-Mitchell, Calum Novak-Mitchell John Wiley & Sons, Inc., Oxford, UKSearch for more papers by this author Stephen W. Holman, Stephen W. Holman Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, UKSearch for more papers by this authorG. John Langley, G. John Langley Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UKSearch for more papers by this authorDavid C. Muddiman, David C. Muddiman FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USASearch for more papers by this authorCalum Novak-Mitchell, Calum Novak-Mitchell John Wiley & Sons, Inc., Oxford, UKSearch for more papers by this author First published: 02 January 2024 https://doi.org/10.1002/rcm.9677 [Correction added on 28 February 2024, after the first online publication. Publication month and year for this article was corrected to January 2024] Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. REFERENCES 1Baker M. 1,500 scientists lift the lid on reproducibility. Nature. 2016; 533(7604): 452-454. doi:10.1038/533452a 10.1038/533452a CASPubMedWeb of Science®Google Scholar 2Miyakawa T. No raw data, no science: Another possible source of the reproducibility crisis. Mol Brain. 2020; 13(1): 24. doi:10.1186/s13041-020-0552-2 10.1186/s13041-020-0552-2 PubMedWeb of Science®Google Scholar 3Oakden-Rayner L, Beam AL, Palmer LJ. Medical journals should embrace preprints to address the reproducibility crisis. Int J Epidemiol. 2018; 47(5): 1363-1365. doi:10.1093/ije/dyy105 10.1093/ije/dyy105 PubMedWeb of Science®Google Scholar 4Sayre F, Riegelman A. The reproducibility crisis and academic libraries. Coll Res Libr. 2018; 79(1): 2-9. doi:10.5860/crl.79.1.2 10.5860/crl.79.1.2 Web of Science®Google Scholar 5Treves A. "Best available science" and the reproducibility crisis. Front Ecol Environ. 2022; 20(9): 495. doi:10.1002/fee.2568 10.1002/fee.2568 Web of Science®Google Scholar 6Twa MD. Scientific integrity and the reproducibility crisis. Optom vis Sci. 2019; 96(1): 1-2. doi:10.1097/OPX.0000000000001339 10.1097/OPX.0000000000001339 PubMedWeb of Science®Google Scholar 7Oransky I. Retractions are increasing, but not enough. Nature. 2022; 608(7921): 9. doi:10.1038/d41586-022-02071-6 10.1038/d41586-022-02071-6 CASPubMedWeb of Science®Google Scholar Volume38, IssueS1Supplement: New Protocols for RCMJanuary 2024e9677 ReferencesRelatedInformation}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Holman, Stephen W. and Langley, G. John and Muddiman, David C. and Novak-Mitchell, Calum}, year={2024}, month={Jan} }
 @article{muddiman_hittle_2024, title={Rigorous scientific inquiry guided by creativity, curiosity and support: One of the last Renaissance scientists of our time}, volume={7}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-024-05417-3}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Muddiman, David C. and Hittle, Lucinda R.}, year={2024}, month={Jul} }
 @article{palomino_muddiman_2023, title={Achieving Cross-Ring Fragmentation of <i>N</i>-Linked Glycans by IR-MALDESI}, volume={35}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00283}, abstractNote={Glycans are complex structures that require MS/MS for detailed structural elucidation. Incorporating metals can provide more structural information by inhibiting glycosidic cleavage and enhancing cross-ring fragmentation. A direct analysis was performed using lithium doping and IR-MALDESI to induce cross-ring fragmentation of glycans. The protonated and lithiated versions of the two glycans were isolated and subjected to HCD. For protonated glycans, only glycosidic cleavages were observed. Using lithium doping, MS/MS consisted of abundant cross-ring fragments. Seventeen cross-ring fragments were detected across both glycans using lithium-doped ESI. This is the first incorporation of metal doping in IR-MALDESI to achieve cross-ring fragments in MS/MS analysis.}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Palomino, Tana V. and Muddiman, David C.}, year={2023}, month={Dec}, pages={166–171} }
 @article{kibbe_muddiman_2023, title={Achieving Sub-Parts-per-Million Mass Measurement Accuracy on an Orbitrap Mass Spectrometry Imaging Platform without Automatic Gain Control}, volume={4}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00004}, abstractNote={The collection of profile data is standard practice within the field of mass spectrometry (MS). However, profile data collection often results in large data files that require extensive processing times, especially in mass spectrometry imaging (MSI) studies where thousands of high-resolution scans are recorded. Natively collecting centroid MS data is an alternative that effectively reduces both the resulting file size and the data processing time. Herein, high-resolution accurate mass (HRAM) Orbitrap MSI data on mouse liver tissue sections without automatic gain control (AGC) were natively collected in both profile and centroid modes and compared based on the file size and processing time. Additionally, centroid data were evaluated against the profile data with regard to the spectra integrity, mass measurement accuracy (MMA), and the number of lipid annotations to ensure that centroid data did not compromise the data quality. For both native and postacquisition centroided data, the variation in mass measurement accuracy decreased relative to the profile data collection. Furthermore, centroid data collection increased the number of METASPACE database annotations indicating higher sensitivity and greater accuracy for lipid annotation compared to native profile data collection. Profile MSI data was shown to have a higher likelihood of false positive identifications due to an increased number of data points on either side of the peaks, whereas the same trend was not observed in data collected in native centroid data collection. This publication explores and explains the importance in properly centroiding MSI data, either natively or by adequate centroiding methods, to obtain the most accurate information and come to the best conclusions. These data support that natively collecting centroid data significantly improves MMA to sub-ppm levels without AGC and reduces false positive annotations.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Kibbe, Russell R. and Muddiman, David C.}, year={2023}, month={Apr} }
 @article{xi_knizner_garrard_muddiman_2023, title={Automatic z-Axis Correction for IR-MALDESI Mass Spectrometry Imaging of Uneven Surfaces}, volume={6}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00151}, abstractNote={Two-dimensional mass spectrometry imaging (2D MSI) experiments mainly involve samples with a flat surface and constant thickness, but some samples are challenging to section due to the texture and topography. Herein, we present an MSI method that automatically corrects for discernible height differences across surfaces during imaging experiments. A chromatic confocal sensor was incorporated into the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) system to measure the sample surface height at the location of each analytical scan. The height profile is subsequently used for adjusting the z-axis position of the sample during MSI data acquisition. We evaluated this method using a tilted mouse liver section and an unsectioned Prilosec tablet due to their exterior quasi-homogeneity and height differences of approximately ∼250 μm. MSI with automatic z-axis correction showed consistent ablated spot sizes and shapes, revealing the measured ion spatial distribution across a mouse liver section and a Prilosec tablet. Conversely, irregular spots and reduced signals with large variability were observed when no z-axis correction was applied.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Xi, Ying and Knizner, Kevan T. T. and Garrard, Kenneth P. P. and Muddiman, David C. C.}, year={2023}, month={Jun} }
 @article{wang_ritter_kullman_muddiman_2023, title={Comparative analysis of sucrose-embedding for whole-body zebrafish MSI by IR-MALDESI}, volume={8}, ISSN={["1618-2650"]}, url={https://doi.org/10.1007/s00216-023-04914-1}, DOI={10.1007/s00216-023-04914-1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Wang, Mary F. and Ritter, Morgan M. and Kullman, Seth W. and Muddiman, David C.}, year={2023}, month={Aug} }
 @article{eisenberg_knizner_muddiman_2023, title={Development of an object-based image analysis tool for mass spectrometry imaging ion classification}, volume={5}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-023-04764-x}, abstractNote={Mass spectrometry imaging (MSI) is an analytical technique that can detect and visualize thousands of m/z values resolved in two- and three-dimensional space. These m/z values lead to hundreds of molecular annotations, including on-tissue and background ions. Discrimination of sample-related analytes from ambient ions conventionally involves manual investigation of each ion heatmap, which requires significant researcher time and effort (for a single tissue image, it can take an hour to determine on-tissue and off-tissue species). Moreover, manual investigation lends itself to subjectivity. Herein, we present the utility of an ion classification tool (ICT) developed using object-based image analysis in MATLAB. The ICT functions by segmenting ion heatmap images into on-tissue and off-tissue objects through binary conversion. The binary images are analyzed and within seconds used to classify the ions as on-tissue or background using a binning approach based on the number of detected objects. In a representative dataset with 50 randomly selected annotations, the ICT was able to accurately classify 45/50 ions as on-tissue or background.}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Eisenberg, Seth M. and Knizner, Kevan T. and Muddiman, David C.}, year={2023}, month={May} }
 @article{samal_palomino_chen_muddiman_segura_2023, title={Enhanced Detection of Charged N-Glycans in the Brain by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometric Imaging}, volume={95}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.3c00494}, abstractNote={N-linked glycosylation represents a structurally diverse, complex, co- and posttranslational protein modification that bridges metabolism and cellular signaling. Consequently, aberrant protein glycosylation is a hallmark of most pathological scenarios. Due to their complex nature and non-template-driven synthesis, the analysis of glycans is faced with several challenges, underlining the need for new and improved analytical technologies. Spatial profiling of N-glycans through direct imaging on tissue sections reveals the regio-specific and/or disease pathology correlating tissue N-glycans that serve as a disease glycoprint for diagnosis. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a soft hybrid ionization technique that has been used for diverse mass spectrometry imaging (MSI) applications. Here, we report the first spatial analysis of the brain N-linked glycans by IR-MALDESI MSI, leading to a significant increase in the detection of the brain N-sialoglycans. A formalin-fixed paraffin-embedded mouse brain tissue was analyzed in negative ionization mode after tissue washing, antigen retrieval, and pneumatic application of PNGase F for enzymatic digestion of N-linked glycans. We report a comparative analysis of section thickness on the N-glycan detection using IR-MALDESI. One hundred thirty-six unique N-linked glycans were confidently identified in the brain tissue (with an additional 132 unique N-glycans, not reported in GlyConnect), where more than 50% contained sialic acid residues, which is approximately 3-fold higher than the previous reports. This work demonstrates the first application of IR-MALDESI in N-linked glycan imaging of the brain tissue, leading to a 2.5-fold increase in the in situ total brain N-glycan detection compared to the current gold standard of positive-mode matrix-assisted laser desorption/ionization mass spectrometry imaging. This is also the first report of the application of the MSI toward the identification of sulfoglycans in the rodent brain. Overall, IR-MALDESI-MSI presents a sensitive glycan detection platform to identify tissue-specific and/or disease-specific glycosignature in the brain while preserving the sialoglycans without any chemical derivatization.}, number={29}, journal={ANALYTICAL CHEMISTRY}, author={Samal, Juhi and Palomino, Tana V. and Chen, Judy and Muddiman, David C. and Segura, Tatiana}, year={2023}, month={Jul}, pages={10913–10920} }
 @article{joignant_knizner_xi_muddiman_2023, title={Evaluating the optimal tissue thickness for mass spectrometry imaging using infrared matrix-assisted laser desorption electrospray ionization}, volume={37}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9638}, abstractNote={RationaleInfrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) utilizes a 2970 nm mid‐IR laser to desorb samples with depth resolutions (Z) on the order of micrometers. Conventionally, 5–20 μm thick tissue sections are used to characterize different applications of the IR‐MALDESI source, but an optimal thickness has not been systematically investigated.MethodsMouse liver was sectioned to various thicknesses and analyzed using IR‐MALDESI mass spectrometry imaging (MSI). Height profiles of tissue sections of various cryosectioned thicknesses were acquired to affirm tissue thickness. Tissue sections of each thickness were measured using a Keyence microscope. Paraffin wax was cryosectioned, mounted on microscope slides, and measured using a chromatic confocal sensor system to determine the cryostat sectioning accuracy.ResultsAnalyzing sectioned tissues at higher thickness (>10 μm) leads to lower ion abundance, a decrease in signal over long analysis times, and more frequent instrument cleaning. Additionally, increasing tissue thickness above the optimum (7 μm) does not result in a significant increase in lipid annotations.ConclusionsThis work defines an optimal sample thickness for IR‐MALDESI‐MSI and demonstrates the utility of optimizing tissue thickness for MSI platforms of comparable Z resolution.}, number={22}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Joignant, Alena N. and Knizner, Kevan T. and Xi, Ying and Muddiman, David C.}, year={2023}, month={Nov} }
 @article{joignant_xi_muddiman_2023, title={Impact of wavelength and spot size on laser depth of focus: Considerations for mass spectrometry imaging of non-flat samples}, volume={3}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4914}, abstractNote={AbstractBiospecimens with nearly flat surfaces on a flat stage are typically required for laser‐based mass spectrometry imaging (MSI) techniques. However, sampling stages are rarely perfectly level, and accounting for this and the need to accommodate non‐flat samples requires a deeper understanding of the laser beam depth of focus. In ablation‐based MSI methods, a laser is focused on top of the sample surface, ensuring that the sample is at the focal point or remains within depth of focus. In general, the depth of focus of a given laser is related to the beam quality (M2) and the wavelength (λ). However, because laser is applied on a biological sample, other variables can also impact the depth of focus, which could affect the robustness of the MSI techniques for diverse sample types. When the height of a sample ranges outside of the depth of focus, ablated area and the corresponding ion abundances may vary as well, increasing the variability of results. In this tutorial, we examine the parameters and equations that describe the depth of focus of a Gaussian laser beam. Additionally, we describe several approaches that account for surface roughness exceeding the depth of focus of the laser.}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Joignant, Alena N. N. and Xi, Ying and Muddiman, David C. C.}, year={2023}, month={Mar} }
 @article{wang_sohn_samal_erning_segura_muddiman_2023, title={Lipidomic Analysis of Mouse Brain to Evaluate the Efficacy and Preservation of Different Tissue Preparatory Techniques by IR-MALDESI-MSI}, volume={3}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.2c00353}, abstractNote={Numerous preparatory methods have been developed to preserve the cellular and structural integrity of various biological tissues for different -omics studies. Herein, two preparatory methods for mass spectrometry imaging (MSI) were evaluated, fresh-frozen and sucrose-embedded, paraformaldehyde (PFA) fixed, in terms of ion abundance, putative lipid identifications, and preservation of analyte spatial distributions. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)-MSI was utilized to compare the preparatory methods of interest with and without the use of the conventional ice matrix. There were 2.5-fold and 1.6-fold more lipid species putatively identified in positive- and negative-ion modes, respectively, for sucrose-embedded, PFA-fixed tissues without an ice matrix relative to the current IR-MALDESI-MSI gold-standard, fresh-frozen tissue preparation with an exogenous ice matrix. Furthermore, sucrose-embedded tissues demonstrated improved spatial distribution of ions resulting from the cryo-protective property of sucrose and paraformaldehyde fixation. Evidence from these investigations supports sucrose-embedding without ice matrix as an alternative preparatory technique for IR-MALDESI-MSI.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Wang, Mary F. and Sohn, Alexandria L. and Samal, Juhi and Erning, Kevin and Segura, Tatiana and Muddiman, David C.}, year={2023}, month={Mar} }
 @article{joignant_ritter_knizner_garrard_kullman_muddiman_2023, title={Maximized Spatial Information and Minimized Acquisition Time of Top-Hat IR-MALDESI-MSI of Zebrafish Using Nested Regions of Interest (nROIs)}, volume={8}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00210}, abstractNote={Increasing the spatial resolution of a mass spectrometry imaging (MSI) method results in a more defined heatmap of the spatial distribution of molecules across a sample, but it is also associated with the disadvantage of increased acquisition time. Decreasing the area of the region of interest to achieve shorter durations results in the loss of potentially valuable information in larger specimens. This work presents a novel MSI method to reduce the time of MSI data acquisition with variable step size imaging: nested regions of interest (nROIs). Using nROIs, a small ROI may be imaged at a higher spatial resolution while nested inside a lower-spatial-resolution peripheral ROI. This conserves the maximal spatial and chemical information generated from target regions while also decreasing the necessary acquisition time. In this work, the nROI method was characterized on mouse liver and applied to top-hat MSI of zebrafish using a novel optical train, which resulted in a significant improvement in both acquisition time and spatial detail of the zebrafish. The nROI method can be employed with any step size pairing and adapted to any method in which the acquisition time of larger high-resolution ROIs poses a practical challenge.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Joignant, Alena N. and Ritter, Morgan M. and Knizner, Kevan T. and Garrard, Kenneth P. and Kullman, Seth W. and Muddiman, David C.}, year={2023}, month={Aug} }
 @article{eisenberg_knizner_muddiman_2023, title={Metabolite Annotation Confidence Score (MACS): A Novel MSI Identification Scoring Tool}, volume={8}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00178}, abstractNote={Mass spectrometry imaging (MSI) is an analytical technique capable of measuring and visualizing the spatial distribution of thousands of ions across a sample. Measured ions can be putatively identified and annotated by comparing their mass-to-charge ratio (m/z) to a database of known compounds. For high-resolution, accurate mass (HRAM) imaging data sets, this is commonly performed by the annotation platform METASPACE. Annotations are reported with a metabolite-signal-match (MSM) score as a measure of the annotation's confidence level. However, the MSM scores reported by METASPACE often do not reflect a reasonable confidence level of an annotation and are not assigned consistently. The metabolite annotation confidence score (MACS) is an alternative scoring system based on fundamental mass spectrometry imaging metrics (mass measurement accuracy, spectral accuracy, and spatial distribution) to generate values that reflect the confidence of a specific annotation in HRAM-MSI data sets. Herein, the MACS system is characterized and compared to MSM scores from ions annotated by METASPACE.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Eisenberg, Seth M. and Knizner, Kevan T. and Muddiman, David C.}, year={2023}, month={Aug} }
 @article{muddiman_2023, title={On the importance of color in mass spectrometry imaging (vol 57, e4898, 2022)}, volume={58}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4921}, abstractNote={Knizner, KT, Kibbe, RR, Garrard, KP, Nuñez, JR, Anderton, CR, Muddiman, DC. On the importance of color in mass spectrometry imaging. J Mass Spectrom. 2022; 57(12):e4898. doi:10.1002/jms.4898 In the article by Knizner et al, the article type Research Article should be changed to Tutorial. We apologize for this error.}, number={5}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Muddiman, David C.}, year={2023}, month={May} }
 @article{palomino_muddiman_2023, title={Predicting Sialic Acid Content of N-Linked Glycans Using the Isotopic Pattern of Chlorine}, volume={6}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00100}, abstractNote={Sialic acids play several roles in both physiological and pathological processes; however, due to their labile nature, they are difficult to analyze using mass spectrometry. Previous work has shown that infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is able to detect intact sialylated N-linked glycans without the use of chemical derivatization. In this work, we describe a new rule that can predict the number of sialic acids on a glycan. Formalin-fixed paraffin-embedded human kidney tissue was prepared using previously established methods and analyzed using IR-MALDESI in negative-ion mode mass spectrometry. Using the experimental isotopic distribution of a detected glycan, we can predict the number of sialic acids on the glycan; #sialic acids is equal to the charge state minus the number of chlorine adducts, or z - #Cl-. This new rule grants confident glycan annotations and compositions beyond accurate mass measurements, thereby further improving the capability of IR-MALDESI to study sialylated N-linked glycans within biological tissues.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Palomino, Tana V. and Muddiman, David C.}, year={2023}, month={Jun} }
 @article{knizner_eisenberg_muddiman_2024, title={Prototyping an ionization source for non-engineers}, volume={59}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4995}, abstractNote={AbstractNovel mass spectrometry (MS) based analytical platforms have enabled scientists to detect and quantify molecules within biological and environmental samples more accurately. Novel MS instrumentation starts as a prototype and, after years of development, can become a commercial product to be used by the larger MS community. Without the initial prototype, many MS‐based instruments today would not be produced. Additionally, biotechnology companies are the main drivers for research, development, and production of novel instruments, but the tools for prototyping instrumentation have never been more accessible. Here, we present a tutorial on prototyping instrumentation through the case study of developing the Next Generation IR‐MALDESI source to show that an engineering degree is not required to design and construct a prototype instrument with modern hardware and software. We discuss the prototyping process, the necessary skills required for efficient prototyping, and information about common hardware and software used within initial prototypes.}, number={1}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Knizner, Kevan T. and Eisenberg, Seth M. and Muddiman, David C.}, year={2024}, month={Jan} }
 @article{arciniega_garrard_guymon_manni sr_apffel_fjeldsted_muddiman_2023, title={Quasi-continuous infrared matrix-assisted laser desorption electrospray ionization source coupled to a quadrupole time-of-flight mass spectrometer for direct analysis from well plates}, volume={58}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4902}, abstractNote={AbstractHigh‐throughput screening (HTS) is a technique mostly used by pharmaceutical companies to rapidly screen multiple libraries of compounds to find drug hits with biological or pharmaceutical activity. Mass spectrometry (MS) has become a popular option for HTS given that it can simultaneously resolve hundreds to thousands of compounds without additional chemical derivatization. For this application, it is convenient to do direct analysis from well plates. Herein, we present the development of an infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) source coupled directly to an Agilent 6545 for direct analysis from well plates. The source is coupled to a quadrupole time‐of‐flight (Q‐TOF) mass spectrometer to take advantage of the high acquisition rates without sacrificing resolving power as required with Orbitrap or Fourier‐transform ion cyclotron resonance (FTICR) instruments. The laser used for this source operates at 100 Hz, firing 1 pulse‐per‐burst, and delivers around 0.7 mJ per pulse. Continuously firing this laser for an extended duration makes it a quasi‐continuous ionization source. Additionally, a metal capillary was constructed to extend the inlet of the mass spectrometer, increase desolvation of electrospray charged droplets, improve ion transmission, and increase sensitivity. Its efficiency was compared with the conventional dielectric glass capillary by measured signal and demonstrated that the metal capillary increased ionization efficiency due to its more uniformly distributed temperature gradient. Finally, we present the functionality of the source by analyzing tune mix directly from well plates. This source is a proof of concept for HTS applications using IR‐MALDESI coupled to a different MS platform.}, number={1}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Arciniega, Cristina and Garrard, Kenneth P. and Guymon, Jacob P. and Manni Sr, Jeffrey G. and Apffel, Alex and Fjeldsted, John C. and Muddiman, David C.}, year={2023}, month={Jan} }
 @article{xi_sohn_joignant_cologna_prentice_muddiman_2023, title={SMART: A data reporting standard for mass spectrometry imaging}, volume={58}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4904}, abstractNote={AbstractMass spectrometry imaging (MSI) is an important analytical technique that simultaneously reports the spatial location and abundance of detected ions in biological, chemical, clinical, and pharmaceutical studies. As MSI grows in popularity, it has become evident that data reporting varies among different research groups and between techniques. The lack of consistency in data reporting inherently creates additional challenges in comparing intra‐ and inter‐laboratory MSI data. In this tutorial, we propose a unified data reporting system, SMART, based on the common features shared between techniques. While there are limitations to any reporting system, SMART was decided upon after significant discussion to more easily understand and benchmark MSI data. SMART is not intended to be comprehensive but rather capture essential baseline information for a given MSI study; this could be within a study (e.g., effect of spot size on the measured ion signals) or between two studies (e.g., different MSI platform technologies applied to the same tissue type). This tutorial does not attempt to address the confidence with which annotations are made nor does it deny the importance of other parameters that are not included in the current SMART format. Ultimately, the goal of this tutorial is to discuss the necessity of establishing a uniform reporting system to communicate MSI data in publications and presentations in a simple format to readily interpret the parameters and baseline outcomes of the data.}, number={2}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Xi, Ying and Sohn, Alexandria L. and Joignant, Alena N. and Cologna, Stephanie M. and Prentice, Boone M. and Muddiman, David C.}, year={2023}, month={Feb} }
 @article{muddiman_2023, title={Time of acquisition and high spatial resolution mass spectrometry imaging (vol 58, e4911, 2023)}, volume={58}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4922}, abstractNote={Wang, MF, Joignant, AN, Sohn, AL, Garrard, KP, Muddiman, DC. Time of acquisition and high spatial resolution mass spectrometry imaging. J Mass Spectrom. 2023;e4911. doi:10.1002/jms.4911 In the article by Wang et al, there are some errors found in Figure 3. The arbitrary region of interest (ROI) total area was adjusted from 350 mm2 to 250 mm2 to increase the accuracy of Figure 3. The te,i and te,o values were recalculated according to the corrected arbitrary ROI area. Additionally in the original figure, the te,i value for “Arbitrary ROI” was incorrectly calculated with an area of 350 mm2. The tr equation was corrected to use the new “Arbitrary ROI” area of 250 mm2, and the parentheses were removed from the final ratio of “450 mm2/250 mm2” as the squaring only applies to the units and had been incorrectly applied to both the units and the numeric values. The final ratio value for tr was corrected to a value of 1.8. We apologize for this error.}, number={5}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Muddiman, David C.}, year={2023}, month={May} }
 @article{barnes_rodriguez-zapata_juarez-nunez_gates_janzen_kur_wang_jensen_estevez-palmas_crow_et al._2022, title={An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time}, volume={119}, ISSN={["1091-6490"]}, url={http://dx.doi.org/10.1073/pnas.2100036119}, DOI={10.1073/pnas.2100036119}, abstractNote={Native Americans domesticated maize (Zea maysssp.mays) from lowland teosinteparviglumis(Zea maysssp.parviglumis)in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identifyHigh PhosphatidylCholine 1(HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation atHPC1,with the highlandHPC1allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maizeHPC1variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis ofHPC1via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highlandHPC1allele entered cultivated maize by introgression from the wild highland teosinteZea maysssp.mexicanaand has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus,HPC1introgressed from teosintemexicanaunderlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.}, number={27}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barnes, Allison C. and Rodriguez-Zapata, Fausto and Juarez-Nunez, Karla A. and Gates, Daniel J. and Janzen, Garrett M. and Kur, Andi and Wang, Li and Jensen, Sarah E. and Estevez-Palmas, Juan M. and Crow, Taylor M. and et al.}, year={2022}, month={Jul} }
 @article{joignant_bai_guymon_garrard_pankow_muddiman_2022, title={Developing transmission mode for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging}, volume={36}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9386}, abstractNote={RationaleThe development and characterization of the novel NextGen infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) source catalyzed new advancements in IR‐MALDESI instrumentation, including the development of a new analysis geometry.MethodsA vertically oriented transmission mode (tm)‐IR‐MALDESI setup was developed and optimized on thawed mouse tissue. In addition, glycerol was introduced as an alternative energy‐absorbing matrix for tm‐IR‐MALDESI because the new geometry does not currently allow for the formation of an ice matrix. The tm geom was evaluated against the optimized standard geometry for the NextGen source in reflection mode (rm).ResultsIt was found that tm‐IR‐MALDESI produces comparable results to rm‐IR‐MALDESI after optimization. The attempt to incorporate glycerol as an alternative matrix provided little improvement to tm‐IR‐MALDESI ion abundances.ConclusionsThis work has successfully demonstrated the adaptation of the NextGen IR‐MALDESI source through the feasibility of tm‐IR‐MALDESI mass spectrometry imaging on mammalian tissue, expanding future biological applications of the method.}, number={22}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Joignant, Alena N. and Bai, Hongxia and Guymon, Jacob P. and Garrard, Kenneth P. and Pankow, Mark and Muddiman, David C.}, year={2022}, month={Nov} }
 @article{enders_weed_griffith_muddiman_2022, title={Development and validation of a high resolving power absolute quantitative per- and polyfluoroalkyl substances method incorporating Skyline data processing}, volume={36}, ISSN={["1097-0231"]}, url={https://doi.org/10.1002/rcm.9295}, DOI={10.1002/rcm.9295}, abstractNote={RationaleThe ability to perform absolute quantitation and non‐targeted analysis on a single mass spectrometry instrument would be advantageous to many researchers studying per‐ and polyfluoroalkyl substances (PFAS). High‐resolution accurate mass (HRAM) instrumentation (typically deployed for non‐targeted work) carries several advantages over traditional triple quadrupole workflows when performing absolute quantitation. Processing this data using a vendor‐neutral software would promote collaboration for these environmental studies.MethodsLC‐MS (Orbitrap Exploris 240) was used for absolute quantitation of 45 PFAS using precursor (MS1) peak areas for quantitation, whereas isotope pattern matching and fragmentation (MS2) pattern matching were used for qualitative identification. In addition, a fluorinated chromatographic column achieved superior separation compared to the typical C18 columns typically used in PFAS analyses. This method was validated across eight different chemical classes using recommended guidelines found in EPA Method 537.1 and Skyline data processing software.ResultsThe validated limits of all 45 compounds, as well as metrics or accuracy and reproducibility, are reported. Most compounds achieved limits of quantitation in the range of 2‐50 ng/L. Four newly released Chemours‐specific compounds (PEPA, PFO3OA, PFO4DA, and PFO5DoA) were also validated. Aspects of data analysis specific to high resolving power absolute quantitation are reviewed as are the details of processing these data via Skyline.ConclusionsThis method shows the feasibility of performing reproducible absolute quantitation of PFAS on an HRAM platform and does so using an open‐source vendor‐neutral data processing software to facilitate sharing of data across labs and institutions.}, number={11}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Enders, Jeffrey R. and Weed, Rebecca A. and Griffith, Emily H. and Muddiman, David C.}, year={2022}, month={Jun} }
 @article{wu_wong_chiles_mellinger_bae_jung_peterson_wang_negrete_huang_et al._2022, title={Glycerate from intestinal fructose metabolism induces islet cell damage and glucose intolerance}, volume={34}, ISSN={["1932-7420"]}, DOI={10.1016/j.cmet.2022.05.007}, abstractNote={Dietary fructose, especially in the context of a high-fat western diet, has been linked to type 2 diabetes. Although the effect of fructose on liver metabolism has been extensively studied, a significant portion of the fructose is first metabolized in the small intestine. Here, we report that dietary fat enhances intestinal fructose metabolism, which releases glycerate into the blood. Chronic high systemic glycerate levels induce glucose intolerance by slowly damaging pancreatic islet cells and reducing islet sizes. Our findings provide a link between dietary fructose and diabetes that is modulated by dietary fat.}, number={7}, journal={CELL METABOLISM}, author={Wu, Yanru and Wong, Chi Wut and Chiles, Eric N. and Mellinger, Allyson L. and Bae, Hosung and Jung, Sunhee and Peterson, Ted and Wang, Jamie and Negrete, Marcos and Huang, Qiang and et al.}, year={2022}, month={Jul}, pages={1042-+} }
 @article{mellinger_muddiman_gamcsik_2022, title={Highlighting Functional Mass Spectrometry Imaging Methods in Bioanalysis}, volume={6}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.2c00220}, abstractNote={Most mass spectrometry imaging (MSI) methods provide a molecular map of tissue content but little information on tissue function. Mapping tissue function is possible using several well-known examples of "functional imaging" such as positron emission tomography and functional magnetic resonance imaging that can provide the spatial distribution of time-dependent biological processes. These functional imaging methods represent the net output of molecular networks influenced by local tissue environments that are difficult to predict from molecular/cellular content alone. However, for decades, MSI methods have also been demonstrated to provide functional imaging data on a variety of biological processes. In fact, MSI exceeds some of the classic functional imaging methods, demonstrating the ability to provide functional data from the nanoscale (subcellular) to whole tissue or organ level. This Perspective highlights several examples of how different MSI ionization and detection technologies can provide unprecedented detailed spatial maps of time-dependent biological processes, namely, nucleic acid synthesis, lipid metabolism, bioenergetics, and protein metabolism. By classifying various MSI methods under the umbrella of "functional MSI", we hope to draw attention to both the unique capabilities and accessibility with the aim of expanding this underappreciated field to include new approaches and applications.}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Mellinger, Allyson L. and Muddiman, David C. and Gamcsik, Michael P.}, year={2022}, month={Jun} }
 @article{joignant_bai_manni_muddiman_2022, title={Improved spatial resolution of infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging using a reflective objective}, volume={36}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9392}, abstractNote={RationaleThe level of visual detail of a mass spectrometry image is dependent on the spatial resolution with which it is acquired, which is largely determined by the focal diameter in infrared laser ablation‐based techniques. While the use of mid‐IR light for mass spectrometry imaging (MSI) has advantages, it results in a relatively large focal diameter and spatial resolution. The continual advancement of infrared matrix‐assisted electrospray ionization (IR‐MALDESI) for MSI warranted novel methods to decrease laser ablation areas and thus improve spatial resolution.MethodsIn this work, a Schwarzschild‐like reflective objective was incorporated into the novel NextGen IR‐MALDESI source and characterized on both burn paper and mammalian tissue using an ice matrix. Ablation areas, mass spectra, and annotations obtained using the objective were compared against the current optical train on the NextGen system without modification.ResultsThe effective resolution was determined to be 55 μm by decreasing the step size until oversampling was observed. Use of the objective improved the spatial resolution by a factor of three as compared against the focus lens.ConclusionsA Schwarzschild‐like reflective objective was successfully incorporated into the NextGen source and characterized on mammalian tissue using an ice matrix. The corresponding improvement in spatial resolution facilitates the future expansion of IR‐MALDESI applications to include those that require fine structural detail.}, number={23}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Joignant, Alena N. and Bai, Hongxia and Manni, Jeffrey G., Sr. and Muddiman, David C.}, year={2022}, month={Dec} }
 @article{sohn_ping_glass_seyfried_hector_muddiman_2022, title={Interrogating the Metabolomic Profile of Amyotrophic Lateral Sclerosis in the Post-Mortem Human Brain by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) Mass Spectrometry Imaging (MSI)}, volume={12}, ISSN={["2218-1989"]}, DOI={10.3390/metabo12111096}, abstractNote={Amyotrophic lateral sclerosis (ALS) is an idiopathic, fatal neurodegenerative disease characterized by progressive loss of motor function with an average survival time of 2–5 years after diagnosis. Due to the lack of signature biomarkers and heterogenous disease phenotypes, a definitive diagnosis of ALS can be challenging. Comprehensive investigation of this disease is imperative to discovering unique features to expedite the diagnostic process and improve diagnostic accuracy. Here, we present untargeted metabolomics by mass spectrometry imaging (MSI) for comparing sporadic ALS (sALS) and C9orf72 positive (C9Pos) post-mortem frontal cortex human brain tissues against a control cohort. The spatial distribution and relative abundance of metabolites were measured by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI for association to biological pathways. Proteomic studies on the same patients were completed via LC-MS/MS in a previous study, and results were integrated with imaging metabolomics results to enhance the breadth of molecular coverage. Utilizing METASPACE annotation platform and MSiPeakfinder, nearly 300 metabolites were identified across the sixteen samples, where 25 were identified as dysregulated between disease cohorts. The dysregulated metabolites were further examined for their relevance to alanine, aspartate, and glutamate metabolism, glutathione metabolism, and arginine and proline metabolism. The dysregulated pathways discussed are consistent with reports from other ALS studies. To our knowledge, this work is the first of its kind, reporting on the investigation of ALS post-mortem human brain tissue analyzed by multiomic MSI.}, number={11}, journal={METABOLITES}, author={Sohn, Alexandria L. and Ping, Lingyan and Glass, Jonathan D. and Seyfried, Nicholas T. and Hector, Emily C. and Muddiman, David C.}, year={2022}, month={Nov} }
 @article{mellinger_kibbe_rabbani_meritet_muddiman_gamcsik_2022, title={Mapping glycine uptake and its metabolic conversion to glutathione in mouse mammary tumors using functional mass spectrometry imaging}, volume={193}, ISSN={["1873-4596"]}, DOI={10.1016/j.freeradbiomed.2022.11.010}, abstractNote={Although glutathione plays a key role in cancer cell viability and therapy response there is no clear trend in relating the level of this antioxidant to clinical stage, histological grade, or therapy response in patient tumors. The likely reason is that static levels of glutathione are not a good indicator of how a tissue deals with oxidative stress. A better indicator is the functional capacity of the tissue to maintain glutathione levels in response to this stress. However, there are few methods to assess glutathione metabolic function in tissue. We have developed a novel functional mass spectrometry imaging (fMSI) method that can map the variations in the conversion of glycine to glutathione metabolic activity across tumor tissue sections by tracking the fate of three glycine isotopologues administered in a timed sequence to tumor-bearing anesthetized mice. This fMSI method generates multiple time point kinetic data for substrate uptake and glutathione production from each spatial location in the tissue. As expected, the fMSI data shows glutathione metabolic activity varies across the murine 4T1 mammary tumor. Although glutathione levels are highest at the tumor periphery there are regions of high content but low metabolic activity. The timed infusion method also detects variations in delivery of the glycine isotopologues thereby providing a measure of tissue perfusion, including evidence of intermittent perfusion, that contributes to the observed differences in metabolic activity. We believe this new approach will be an asset to linking molecular content to tissue function.}, journal={FREE RADICAL BIOLOGY AND MEDICINE}, author={Mellinger, Allyson L. and Kibbe, Russell R. and Rabbani, Zahid N. and Meritet, Danielle and Muddiman, David C. and Gamcsik, Michael P.}, year={2022}, month={Nov}, pages={677–684} }
 @article{knizner_guymon_garrard_bouvree_manni_hauschild_strupat_fort_earley_wouters_et al._2022, title={Next-Generation Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Source for Mass Spectrometry Imaging and High-Throughput Screening}, volume={9}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.2c00178}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a hybrid, ambient ionization source that combines the advantages of electrospray ionization and matrix-assisted laser desorption/ionization, making it a versatile tool for both high-throughput screening (HTS) and mass spectrometry imaging (MSI) studies. To expand the capabilities of the IR-MALDESI source, an entirely new architecture was designed to overcome the key limitations of the previous source. This next-generation (NextGen) IR-MALDESI source features a vertically mounted IR-laser, a planar translation stage with computerized sample height control, an aluminum enclosure, and a novel mass spectrometer interface plate. The NextGen IR-MALDESI source has improved user-friendliness, improved overall versatility, and can be coupled to numerous Orbitrap mass spectrometers to accommodate more research laboratories. In this work, we highlight the benefits of the NextGen IR-MALDESI source as an improved platform for MSI and direct analysis. We also optimize the NextGen MALDESI source component geometries to increase target ion abundances over a wide m/z range. Finally, documentation is provided for each NextGen IR-MALDESI part so that it can be replicated and incorporated into any lab space.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Knizner, Kevan T. and Guymon, Jacob P. and Garrard, Kenneth P. and Bouvree, Guy and Manni, Jeffrey and Hauschild, Jan-Peter and Strupat, Kerstin and Fort, Kyle L. and Earley, Lee and Wouters, Eloy R. and et al.}, year={2022}, month={Sep} }
 @article{knizner_bagley_pu_elsen_williams_muddiman_2022, title={Normalization techniques for high-throughput screening by infrared matrix-assisted laser desorption electrospray ionization mass spectrometry}, volume={57}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4869}, abstractNote={AbstractMass spectrometry (MS) is an effective analytical tool for high‐throughput screening (HTS) in the drug discovery field. Infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) MS is a high‐throughput platform that has achieved analysis times of sub‐seconds‐per‐sample. Due to the high‐throughput analysis speed, methods are needed to increase the analyte signal while decreasing the variability in IR‐MALDESI‐MS analyses to improve data quality and reduce false‐positive hits. The Z‐factor is used as a statistic of assay quality that can be improved by reducing the variation of target ion abundances or increasing signal. Herein we report optimal solvent compositions for increasing measured analyte abundances with direct analysis by IR‐MALDESI‐MS. We also evaluate normalization strategies, such as adding a normalization standard that is similar or dissimilar in structure to the model target drug, to reduce the variability of measured analyte abundances with direct analyses by IR‐MALDESI‐MS in both positive and negative ionization modes.}, number={6}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Knizner, Kevan T. and Bagley, Michael C. and Pu, Fan and Elsen, Nathaniel L. and Williams, Jon D. and Muddiman, David C.}, year={2022}, month={Jun} }
 @article{kibbe_mellinger_muddiman_2022, title={Novel matrix strategies for improved ionization and spatial resolution using IR-MALDESI mass spectrometry imaging}, volume={57}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4875}, abstractNote={AbstractIn mass spectrometry imaging (MSI) applications of infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI), an exogenous ice layer is the gold standard for an energy‐absorbing matrix. However, the formation of the ice matrix requires additional time and instrument hardware, so glycerol was investigated herein as an alternative to the ice matrix to potentially improve spatial resolution and ionization, while decreasing experiment time. Glycerol solutions of varying concentrations were sprayed over top of rat liver tissue sections for analysis by IR‐MALDESI and compared to the typical ice matrix condition. Additionally, we tested if combining the ice matrix and glycerol matrix would further improve analyses. Matrix conditions were evaluated by comparing ion abundance of six lipid species, the laser ablation spot diameter, and number of METASPACE annotations. The ion abundances were also normalized to the volume of tissue ablated to correct for lower abundance values due to less ablated tissue. It was observed that utilizing a 50% glycerol matrix without ice provides improved spatial resolution with lipid abundances and annotations comparable to the ice matrix standard, while decreasing the time required to complete an IR‐MALDESI tissue imaging experiment.}, number={8}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Kibbe, Russell R. and Mellinger, Allyson L. and Muddiman, David C.}, year={2022}, month={Aug} }
 @article{knizner_kibbe_garrard_nunez_anderton_muddiman_2022, title={On the importance of color in mass spectrometry imaging}, volume={57}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4898}, abstractNote={AbstractMass spectrometry imaging (MSI) data visualization relies on heatmaps to show the spatial distribution and measured abundances of molecules within a sample. Nonuniform color gradients such as jet are still commonly used to visualize MSI data, increasing the probability of data misinterpretation and false conclusions. Also, the use of nonuniform color gradients and the combination of hues used in common colormaps make it challenging for people with color vision deficiencies (CVDs) to visualize and accurately interpret data. Here we present best practices for choosing a colormap to accurately display MSI data, improve readability, and accommodate all CVDs. We also provide other resources on the misuse of color in the scientific field and resources on scientifically derived colormaps presented herein.}, number={12}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Knizner, Kevan T. and Kibbe, Russell R. and Garrard, Kenneth P. and Nunez, Jamie R. and Anderton, Christopher R. and Muddiman, David C.}, year={2022}, month={Dec} }
 @article{knizner_bagley_garrard_hauschild_pu_elsen_williams_muddiman_2022, title={Optimized C-Trap Timing of an Orbitrap 240 Mass Spectrometer for High-Throughput Screening and Native MS by IR-MALDESI}, volume={33}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.1c00319}, abstractNote={Infrared matrix-assisted laser desorption ionization (IR-MALDESI) is a hybrid mass spectrometry ionization source that combines the benefits of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) making it a great analytical tool for high-throughput screening (HTS) analyses. IR-MALDESI is coupled to an Orbitrap Exploris 240 mass spectrometer that utilizes a bent quadrupole (C-trap) to inject accumulated ions into the high-field Orbitrap mass analyzer. Here, we present a study on the optimized C-trap timing for HTS analyses by IR-MALDESI mass spectrometry. The timing between initial ion generation and the C-trap opening time was optimized to reduce unnecessary ambient ion accumulation in the mass spectrometer. The time in which the C-trap was held open, the ion accumulation time, was further optimized to maximize the accumulation of analyte ions generated using IR-MALDESI. The resulting C-trap opening scheme benefits small-molecule HTS analyses by IR-MALDESI by maximizing target ion abundances, minimizing ambient ion abundances, and minimizing the total analysis time per sample. The proposed C-trap timing scheme for HTS does not translate to large molecules; a NIST monoclonal antibody standard reference material was analyzed to demonstrate that larger analytes require longer ion accumulation times and that IR-MALDESI can measure intact antibodies in their native state.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Knizner, Kevan T. and Bagley, Michael C. and Garrard, Kenneth P. and Hauschild, Jan-Peter and Pu, Fan and Elsen, Nathaniel L. and Williams, Jon D. and Muddiman, David C.}, year={2022}, month={Feb}, pages={328–334} }
 @article{muthusamy_williams_o'toole_brudvig_adler_weimer_muddiman_ghashghaei_2022, title={Phosphorylation-dependent proteome of Marcks in ependyma during aging and behavioral homeostasis in the mouse forebrain}, volume={1}, ISSN={["2509-2723"]}, url={http://dx.doi.org/10.1007/s11357-022-00517-3}, DOI={10.1007/s11357-022-00517-3}, abstractNote={Ependymal cells (ECs) line the ventricular surfaces of the mammalian central nervous system (CNS) and their development is indispensable to structural integrity and functions of the CNS. We previously reported that EC-specific genetic deletion of the myristoylated alanine-rich protein kinase C substrate (Marcks) disrupts barrier functions and elevates oxidative stress and lipid droplet accumulation in ECs causing precocious cellular aging. However, little is known regarding the mechanisms that mediate these changes in ECs. To gain insight into Marcks-mediated mechanisms, we performed mass spectrometric analyses on Marcks-associated proteins in young and aged ECs in the mouse forebrain using an integrated approach. Network analysis on annotated proteins revealed that the identified Marcks-associated complexes are in part involved in protein transport mechanisms in young ECs. In fact, we found perturbed intracellular vesicular trafficking in cultured ECs with selective deletion of Marcks (Marcks-cKO mice), or upon pharmacological alteration to phosphorylation status of Marcks. In comparison, Marcks-associated protein complexes in aged ECs appear to be involved in regulation of lipid metabolism and responses to oxidative stress. Confirming this, we found elevated signatures of inflammation in the cerebral cortices and the hippocampi of young Marcks-cKO mice. Interestingly, behavioral testing using a water maze task indicated that spatial learning and memory is diminished in young Marcks-cKO mice similar to aged wildtype mice. Taken together, our study provides first line of evidence for potential mechanisms that may mediate differential Marcks functions in young and old ECs, and their effect on forebrain homeostasis during aging.}, number={4}, journal={GEROSCIENCE}, publisher={Springer Science and Business Media LLC}, author={Muthusamy, Nagendran and Williams, Taufika I and O'Toole, Ryan and Brudvig, Jon J. and Adler, Kenneth B. and Weimer, Jill M. and Muddiman, David C. and Ghashghaei, H. Troy}, year={2022}, month={Jan} }
 @article{bai_manni sr_muddiman_2023, title={Transforming a Mid-infrared Laser Profile from Gaussian to a Top- Hat with a Diffractive Optical Element for Mass Spectrometry Imaging}, volume={34}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.2c00203}, abstractNote={Many mass spectrometry imaging (MSI) applications such as infrared matrix-assisted electrospray ionization (IR-MALDESI) employ an infrared (IR) laser with a Gaussian profile where laser irradiance is highest in the center and decreases exponentially. To enable full ablation of a square region of interest, oversampling is often needed, which results in nonuniform ablation and leads to decreased image quality. A diffractive optical element (DOE) was integrated into the optical path to generate homogeneous intensity distributions while maintaining laser energy above the ablation threshold, to enable complete sample removal from laser pulses without oversampling. 2D and 3D imaging with the DOE inserted show clear and sharp ablation patterns with satisfactory biological signals gained. Further improvements will optimize the beam profile and generate a square top-hat laser beam for MSI application at higher spatial resolution.}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Bai, Hongxia and Manni Sr, Jeffrey G. and Muddiman, David C.}, year={2023}, month={Jan}, pages={10–16} }
 @article{xi_muddiman_2021, title={Enhancing Metabolomic Coverage in Positive Ionization Mode Using Dicationic Reagents by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization}, volume={11}, ISSN={["2218-1989"]}, DOI={10.3390/metabo11120810}, abstractNote={Mass spectrometry imaging is a powerful tool to analyze a large number of metabolites with their spatial coordinates collected throughout the sample. However, the significant differences in ionization efficiency pose a big challenge to metabolomic mass spectrometry imaging. To solve the challenge and obtain a complete data profile, researchers typically perform experiments in both positive and negative ionization modes, which is time-consuming. In this work, we evaluated the use of the dicationic reagent, 1,5-pentanediyl-bis(1-butylpyrrolidinium) difluoride (abbreviated to [C5(bpyr)2]F2) to detect a broad range of metabolites in the positive ionization mode by infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging (IR-MALDESI MSI). [C5(bpyr)2]F2 at 10 µM was doped in 50% MeOH/H2O (v/v) electrospray solvent to form +1 charged adducted ions with anionic species (−1 charged) through post-electrospray ionization. This method was demonstrated with sectioned rat liver and hen ovary. A total of 73 deprotonated metabolites from rat liver tissue sections were successfully adducted with [C5(bpyr)2]2+ and putatively identified in the adducted positive ionization polarity, along with 164 positively charged metabolite ions commonly seen in positive ionization mode, which resulted in 44% increased molecular coverage. In addition, we were able to generate images of hen ovary sections showing their morphological features. Following-up tandem mass spectrometry (MS/MS) indicated that this dicationic reagent [C5(bpyr)2]2+ could form ionic bonds with the headgroup of glycerophospholipid ions. The addition of the dicationic reagent [C5(bpyr)2]2+ in the electrospray solvent provides a rapid and effective way to enhance the detection of metabolites in positive ionization mode.}, number={12}, journal={METABOLITES}, author={Xi, Ying and Muddiman, David C.}, year={2021}, month={Dec} }
 @article{lin_sun_song_chen_shi_yang_liu_tunlaya-anukit_liu_loziuk_et al._2021, title={Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa}, volume={12}, ISSN={["1664-462X"]}, url={http://europepmc.org/abstract/med/34691108}, DOI={10.3389/fpls.2021.727932}, abstractNote={Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. InPopulus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation ofPtrHCTsreduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenicP. trichocarpa. The Ptr4CL/PtrHCT interactions were then validatedin vivousing biomolecular fluorescence complementation (BiFC) and protein pull-down assays inP. trichocarpaSDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation inP. trichocarpa.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Lin, Chien-Yuan and Sun, Yi and Song, Jina and Chen, Hsi-Chuan and Shi, Rui and Yang, Chenmin and Liu, Jie and Tunlaya-Anukit, Sermsawat and Liu, Baoguang and Loziuk, Philip L. and et al.}, year={2021}, month={Oct} }
 @article{kalmar_garrard_muddiman_2021, title={GlycoHunter: An Open-Source Software for the Detection and Relative Quantification of INLIGHT-Labeled N-Linked Glycans}, volume={20}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.0c00840}, abstractNote={Glycans are responsible for many biological activities; however, their structures are incredibly diverse and complex, often rendering the field of glycomics unsolvable by a single analytical technique. The development of multiple chemical derivatization strategies and bioinformatic software is responsible for some of the greatest analytical gains in the field of glycomics. The INLIGHT strategy is a chemical derivatization technique using hydrazide chemistry to derivatize the reducing end of N-linked glycans and incorporates either a natural (NAT, 12C6) or a stable-isotope label (SIL, 13C6) to carry out relative quantification. Here we present GlycoHunter, a user-friendly software created in MATLAB that enables researchers to accurately and efficiently process MS1 glycomics data where a NAT and SIL pair is generated for relative quantification, including but not limited to, INLIGHT. GlycoHunter accepts the commonly used data file formats imzML and mzXML and effectively identifies all peak pairs associated with NAT- and SIL-labeled N-linked glycans using MS1 data. It also includes the ability to tailor the search parameters and export the results for further analysis using Skyline or Excel.}, number={4}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Kalmar, Jaclyn Gowen and Garrard, Kenneth P. and Muddiman, David C.}, year={2021}, month={Apr}, pages={1855–1863} }
 @article{tu_garrard_said_muddiman_2021, title={In situ detection of fatty acid C=C positional isomers by coupling on-tissue mCPBA epoxidation with infrared matrix-assisted laser desorption electrospray ionization mass spectrometry}, volume={35}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9119}, abstractNote={RationaleUnsaturated fatty acids (UFAs) play vital roles in regulating cellular functions. In‐depth structural characterization of UFAs such as localizing carbon–carbon double bonds is fundamentally important but poses considerable challenges in mass spectrometry (MS) given that the most widely accessible ion activation method, low‐energy collision‐induced dissociation (CID), primarily generates uninformative fragments (e.g., neutral loss of CO2) that are not suggestive of the double‐bond positions.Methodsm‐Chloroperoxybenzoic acid (mCPBA) was uniformly deposited onto the sample slides using a TM Sprayer, converting the carbon–carbon double bonds into epoxides under ambient conditions. The epoxidation product was ionized in situ by infrared matrix‐assisted laser desorption electrospray ionization mass spectrometry (IR‐MALDESI‐MS), and subsequently cleaved via CID, generating a diagnostic ion pair associated with the double‐bond position. The reaction efficiency, sensitivity and relative quantification capability of the method were validated with five UFA standards dried on glass slides, and then this strategy was demonstrated on thin tissue sections of rat liver and human bladder.ResultsThe mCPBA reaction yielded conversion rates in the range of 44–60% in 10 min with high specificity and sensitivity. Further tandem mass spectrometry (MS/MS) of the mono‐epoxidized products generated informative fragment ions specific to the double‐bond positions, and relative quantification of positional isomers in binary mixtures was performed across a wide mole fraction from 0 to 1. An innovative spiral scan pattern was utilized during data acquisition, elucidating the major isomeric compositions of multiple UFAs from a tissue section in a single run.ConclusionsThe on‐tissue mCPBA epoxidation was implemented into an ambient MS imaging workflow to offer a rapid and simple way for in situ identification and relative quantification of double‐bond positional isomers without the requirement for instrument modification. The method can be readily implemented on many other MS platforms to reveal the role of double‐bond positional isomers in lipid biology and to discover potential biomarkers.}, number={13}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Tu, Anqi and Garrard, Kenneth P. and Said, Neveen and Muddiman, David C.}, year={2021}, month={Jul} }
 @article{bagley_muddiman_2021, title={Investigations of beta-carotene radical cation formation in infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={35}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9133}, abstractNote={RationaleRadical cationization of endogenous hydrocarbons in cherry tomatoes was previously reported using infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI), a mass spectrometry imaging technique that operates at ambient conditions and requires no sample derivatization. Due to the surprising nature of this odd‐electron ionization, subsequent experiments were performed on β‐carotene to determine the amount of radical cationization across different sampling conditions.Methodsβ‐Carotene was analyzed across a variety of sample states using IR‐MALDESI followed by Orbitrap mass spectrometric analysis: first, as a standard in ethanol in a well plate; second, as particulates on printer paper; and third, as particulates covered by an ice matrix. These techniques were also performed with a β‐carotene standard either in solution with a reducing agent (ascorbic acid) or with ascorbic acid in the electrospray solution.ResultsTandem mass spectrometry confirmed the presence of the radical cation of β‐carotene by comparing fragments against NIST and METLIN databases. It was always analyzed as a radical cation when sampled from solution, where ascorbic acid increased radical cation abundance when in solution with β‐carotene. Mixed‐mode ionization between radical cationization and proton adduction was observed from dried particulates using IR‐MALDESI.ConclusionsThere are several potential mechanisms for β‐carotene radical cationization prior to IR‐MALDESI analysis, with multiphoton ionization, thermal degradation, and/or reaction with oxygen appearing to be the most logical explanations. Furthermore, although not the primary cause, changing certain aspects of sample conditions can result in significant mixed‐mode ionization with competing protonation.}, number={16}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bagley, M. Caleb and Muddiman, David C.}, year={2021}, month={Aug} }
 @article{pace_angel_drake_muddiman_2022, title={Mass Spectrometry Imaging of N-Linked Glycans in a Formalin-Fixed Paraffin-Embedded Human Prostate by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization}, volume={21}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00822}, abstractNote={N-Linked glycans are structurally diverse polysaccharides that represent significant biological relevance due to their involvement in disease progression and cancer. Due to their complex nature, N-linked glycans pose many analytical challenges requiring the continued development of analytical technologies. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a hybrid ionization technique commonly used for mass spectrometry imaging (MSI) applications. Previous work demonstrated IR-MALDESI to significantly preserve sialic acid containing N-linked glycans that otherwise require chemical derivatization prior to detection. Here, we demonstrate the first analysis of N-linked glycans in situ by IR-MALDESI MSI. A formalin-fixed paraffin-embedded human prostate tissue was analyzed in negative ionization mode after tissue washing, antigen retrieval, and pneumatic application of PNGase F for enzymatic digestion of N-linked glycans. Fifty-three N-linked glycans were confidently identified in the prostate sample where more than 60% contained sialic acid residues. This work demonstrates the first steps in N-linked glycan imaging of biological tissues by IR-MALDESI MSI. Raw data files are available in MassIVE (identifier: MSV000088414).}, number={1}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Pace, Crystal L. and Angel, Peggi M. and Drake, Richard R. and Muddiman, David C.}, year={2022}, month={Jan}, pages={243–249} }
 @article{pace_simmons_kelly_muddiman_2022, title={Multimodal Mass Spectrometry Imaging of Rat Brain Using IR-MALDESI and NanoPOTS-LC-MS/MS}, volume={21}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00641}, abstractNote={Multimodal mass spectrometry imaging (MSI) is a critical technique used for deeply investigating biological systems by combining multiple MSI platforms in order to gain the maximum molecular information about a sample that would otherwise be limited by a single analytical technique. The aim of this work was to create a multimodal MSI approach that measures metabolomic and proteomic data from a single biological organ by combining infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) for metabolomic MSI and nanodroplet processing in one pot for trace samples (nanoPOTS) LC-MS/MS for spatially resolved proteome profiling. Adjacent tissue sections of rat brain were analyzed by each platform, and each data set was individually analyzed using previously optimized workflows. IR-MALDESI data sets were annotated by accurate mass and spectral accuracy using HMDB, METLIN, and LipidMaps databases, while nanoPOTS-LC-MS/MS data sets were searched against the rat proteome using the Sequest HT algorithm and filtered with a 1% FDR. The combined data revealed complementary molecular profiles distinguishing the corpus callosum against other sampled regions of the brain. A multiomic pathway integration showed a strong correlation between the two data sets when comparing average abundances of metabolites and corresponding enzymes in each brain region. This work demonstrates the first steps in the creation of a multimodal MSI technique that combines two highly sensitive and complementary imaging platforms. Raw data files are available in METASPACE (https://metaspace2020.eu/project/pace-2021) and MassIVE (identifier: MSV000088211).}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Pace, Crystal L. and Simmons, Jared and Kelly, Ryan T. and Muddiman, David C.}, year={2022}, month={Mar}, pages={713–720} }
 @article{mellinger_garrard_khodjaniyazova_rabbani_gamcsik_muddiman_2022, title={Multiple Infusion Start Time Mass Spectrometry Imaging of Dynamic SIL-Glutathione Biosynthesis Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization}, volume={21}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00636}, abstractNote={Due to the high association of glutathione metabolism perturbation with a variety of disease states, there is a dire need for analytical techniques to study glutathione kinetics. Additionally, the elucidation of microenvironmental effects on changes in glutathione metabolism would significantly improve our understanding of the role of glutathione in disease. We therefore present a study combining a multiple infusion start time protocol, stable isotope labeling technology, infrared matrix-assisted laser desorption electrospray ionization, and high-resolution accurate mass-mass spectrometry imaging to study spatial changes in glutathione kinetics across in sectioned mouse liver tissues. After injecting a mouse with the isotopologues [2-13C,15N]-glycine, [1,2-13C2]-glycine, and [1,2-13C2,15N]-glycine at three different time points, we were able to fully resolve and spatially map their metabolism into three isotopologues of glutathione and calculate their isotopic enrichment in glutathione. We created a tool in the open-source mass spectrometry imaging software MSiReader to accurately compute the percent isotope enrichment (PIE) of these labels in glutathione and visualize them in heat-maps of the tissue sections. In areas of high flux, we found that each label enriched an approximate median of 1.6%, 1.8%, and 1.5%, respectively, of the glutathione product pool measured in each voxel. This method may be adapted to study the heterogeneity of glutathione flux in diseased versus healthy tissues.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Mellinger, Allyson L. and Garrard, Kenneth P. and Khodjaniyazova, Sitora and Rabbani, Zahid N. and Gamcsik, Michael P. and Muddiman, David C.}, year={2022}, month={Mar}, pages={747–757} }
 @article{muddiman_maccoss_2021, title={Obituary Michael S. Bereman (1981-2021)}, volume={32}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.1c00129}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVObituaryNEXTMichael S. Bereman (1981–2021)David C. Muddiman*David C. MuddimanDepartment of Chemistry and Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States*Email: [email protected]More by David C. Muddiman and Michael J. MacCoss*Michael J. MacCossGenome Sciences, University of Washington, Box 355065, Foege S113 3720 15th Ave NE, Seattle, Washington 98195-5065, United States*Email: [email protected]More by Michael J. MacCossCite this: J. Am. Soc. Mass Spectrom. 2021, 32, 5, 1272–1274Publication Date (Web):May 5, 2021Publication History Received11 April 2021Accepted14 April 2021Revised13 April 2021Published online5 May 2021Published inissue 5 May 2021https://pubs.acs.org/doi/10.1021/jasms.1c00129https://doi.org/10.1021/jasms.1c00129obituaryACS PublicationsCopyright © 2021 American Society for Mass Spectrometry. Published by American Chemical Society. All rights reserved. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1904Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (1 MB) Get e-AlertscloseSUBJECTS:Diagnosis,Kinetics,Mass spectrometry,Proteomics,Students Get e-Alerts}, number={5}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Muddiman, David C. and MacCoss, Michael J.}, year={2021}, month={May}, pages={1272–1274} }
 @article{tu_said_muddiman_2021, title={Spatially resolved metabolomic characterization of muscle invasive bladder cancer by mass spectrometry imaging}, volume={17}, ISSN={["1573-3890"]}, DOI={10.1007/s11306-021-01819-x}, abstractNote={Muscle invasive bladder cancer (MIBC) is an advanced stage of bladder cancer which poses a severe threat to life. Cancer development is usually accompanied by remarkable alterations in cell metabolism, and hence deep insights into MIBC at the metabolomic level can facilitate the understanding of the biochemical mechanisms involved in the cancer development and progression.In this proof-of-concept study, the optimal cutting temperature (OCT)-embedded MIBC samples were first washed with pure water to remove the polymer compounds which could cause severe signal suppression during mass spectrometry. Further, the tissue sections were analyzed by infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging (IR-MALDESI MSI), providing an overview on the spatially resolved metabolomic profiles.The MSI data enabled the discrimination between not only the cancerous and normal tissues, but also the subregions within a tissue section associated with different disease states. Using t-Distributed Stochastic Neighbor Embedding (t-SNE), the hyperdimensional MSI data was mapped into a two-dimensional space to visualize the spectral similarity, providing evidence that metabolomic alterations might have occurred outside the histopathological tumor border. Least absolute shrinkage and selection operator (LASSO) was further employed to classify sample pathology in a pixel-wise manner, yielding excellent prediction sensitivity and specificity up to 96% based on the statistically characteristic spectral features.The results demonstrate great promise of IR-MALDESI MSI to identify molecular changes derived from cancer and unveil tumor heterogeneity, which can potentially promote the discovery of clinically relevant biomarkers and allow for applications in precision medicine.}, number={8}, journal={METABOLOMICS}, author={Tu, Anqi and Said, Neveen and Muddiman, David C.}, year={2021}, month={Aug} }
 @article{bagley_garrard_muddiman_2021, title={The development and application of matrix assisted laser desorption electrospray ionization: The teenage years}, volume={5}, ISSN={["1098-2787"]}, DOI={10.1002/mas.21696}, abstractNote={AbstractIn the past 15 years, ambient ionization techniques have witnessed a significant incursion into the field of mass spectrometry imaging, demonstrating their ability to provide complementary information to matrix‐assisted laser desorption ionization. Matrix‐assisted laser desorption electrospray ionization is one such technique that has evolved since its first demonstrations with ultraviolet lasers coupled to Fourier transform‐ion cyclotron resonance mass spectrometers to extensive use with infrared lasers coupled to orbitrap‐based mass spectrometers. Concurrently, there have been transformative developments of this imaging platform due to the high level of control the principal group has retained over the laser technology, data acquisition software (RastirX), instrument communication, and image processing software (MSiReader). This review will discuss the developments of MALDESI since its first laboratory demonstration in 2005 to the most recent advances in 2021.}, journal={MASS SPECTROMETRY REVIEWS}, author={Bagley, Michael Caleb and Garrard, Kenneth P. and Muddiman, David C.}, year={2021}, month={May} }
 @article{bai_linder_muddiman_2021, title={Three-dimensional (3D) imaging of lipids in skin tissues with infrared matrix-assisted laser desorption electrospray ionization (MALDESI) mass spectrometry}, volume={413}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-020-03105-6}, abstractNote={Three-dimensional (3D) mass spectrometry imaging (MSI) has become a growing frontier as it has the potential to provide a 3D representation of analytes in a label-free, untargeted, and chemically specific manner. The most common 3D MSI is accomplished by the reconstruction of 2D MSI from serial cryosections; however, this presents significant challenges in image alignment and registration. An alternative method would be to sequentially image a sample by consecutive ablation events to create a 3D image. In this study, we describe the use of infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) in ablation-based 3D MSI for analyses of lipids within fresh frozen skin tissue. Depth resolution using different laser energy levels was explored with a confocal laser scanning microscope to establish the imaging parameters for skin. The lowest and highest laser energy level resulted in a depth resolution of 7 μm and 18 μm, respectively. A total of 594 lipids were putatively detected and detailed lipid profiles across different skin layers were revealed in a 56-layer 3D imaging experiment. Correlated with histological information, the skin structure was characterized with differential lipid distributions with a lateral resolution of 50 μm and a z resolution of 7 μm.}, number={10}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Bai, Hongxia and Linder, Keith E. and Muddiman, David C.}, year={2021}, month={Apr}, pages={2793–2801} }
 @article{enders_grace m. o'neill_whitten_muddiman_2021, title={Understanding the electrospray ionization response factors of per- and poly-fluoroalkyl substances (PFAS)}, volume={7}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-021-03545-8}, abstractNote={Per- and polyfluoroalkyl substances (PFAS) are used extensively in commercial products. Their unusual solubility properties make them an ideal class of compounds for various applications. However, these same properties have led to significant contamination and bioaccumulation given their persistence in the environment. Development of analytical techniques to detect and quantify these compounds must take into account the potential for these properties to perturb these measurements, specifically the potential to bias the electrospray ionization (ESI) process. Direct injection ESI analysis of 23 different PFAS species revealed that hydrophobicity and PFAS class can predict the ESI overall response factors. In this study, a method for predicting the behavior of individual PFAS compounds, including relative retention order in chromatography, is presented which is simply based on the number of fluorine atoms in the molecule as well as the class of the compound (e.g., perfluroalkylcarboxylic acids) vs. computational estimations (e.g., non-polar surface area and logP).}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Enders, Jeffrey R. and Grace M. O'Neill and Whitten, Jerry L. and Muddiman, David C.}, year={2021}, month={Jul} }
 @article{butler_kalmar_muddiman_baker_2021, title={Utilizing liquid chromatography, ion mobility spectrometry, and mass spectrometry to assess INLIGHT (TM) derivatized N-linked glycans in biological samples}, volume={8}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-021-03570-7}, abstractNote={Glycosylation is a ubiquitous co- and post-translational modification involved in the sorting, folding, and trafficking of proteins in biological systems; in humans, >50% of gene products are glycosylated with the cellular machinery of glycosylation compromising ~2% of the genome. Perturbations in glycosylation have been implicated in a variety of diseases including neurodegenerative diseases and certain types of cancer. However, understanding the relationship between a glycan and its biological role is often difficult due to the numerous glycan isomers that exist. To address this challenge, nanoflow liquid chromatography, ion mobility spectrometry, and mass spectrometry (nLC-IMS-MS) were combined with the Individuality Normalization when Labeling with the Isotopic Glycan Hydrazide Tags (INLIGHT™) strategy to study a series of glycan standards and those enzymatically released from the glycoproteins horseradish peroxidase, fetuin, and pooled human plasma. The combination of IMS and the natural (NAT) and stable-isotope label (SIL) in the INLIGHT™ strategy provided additional confidence for each glycan identification due to the mobility aligned NAT- and SIL-labeled glycans and further capabilities for isomer examinations. Additionally, molecular trend lines based on the IMS and MS dimensions were investigated for the INLIGHT™ derivatized glycans, facilitating rapid identification of putative glycans in complex biological samples.}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Butler, Karen E. and Kalmar, Jaclyn Gowen and Muddiman, David C. and Baker, Erin S.}, year={2021}, month={Aug} }
 @article{jaiswal_yerke_bagley_ekelof_weber_haddad_fodor_muddiman_williams_2020, title={3D Imaging and metabolomic profiling reveal higher neuroactive kavalactone contents in lateral roots and crown root peels of Piper methysticum (kava)}, volume={9}, ISSN={["2047-217X"]}, DOI={10.1093/gigascience/giaa096}, abstractNote={Abstract
               
                  Background
                  Kava is an important neuroactive medicinal plant. While kava has a large global consumer footprint for its clinical and recreational use, factors related to its use lack standardization and the tissue-specific metabolite profile of its neuroactive constituents is not well understood.
               
               
                  Results
                  Here we characterized the metabolomic profile and spatio-temporal characteristics of tissues from the roots and stems using cross-platform metabolomics and a 3D imaging approach. Gas chromatography–mass spectrometry and liquid chromatography–mass spectrometry revealed the highest content of kavalactones in crown root peels and lateral roots. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging revealed a unique tissue-specific presence of each target kavalactone. X-ray micro-computed tomography analysis demonstrated that lateral roots have morphological characteristics suitable for synthesis of the highest content of kavalactones.
               
               
                  Conclusions
                  These results provide mechanistic insights into the social and clinical practice of the use of only peeled roots by linking specific tissue characteristics to concentrations of neuroactive compounds.
               }, number={9}, journal={GIGASCIENCE}, author={Jaiswal, Yogini S. and Yerke, Aaron M. and Bagley, M. Caleb and Ekelof, Mans and Weber, Daniel and Haddad, Daniel and Fodor, Anthony and Muddiman, David C. and Williams, Leonard L.}, year={2020}, month={Sep} }
 @article{garrard_ekelöf_khodjaniyazova_bagley_muddiman_2020, title={A Versatile Platform for Mass Spectrometry Imaging of Arbitrary Spatial Patterns}, volume={31}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1021/jasms.0c00128}, DOI={10.1021/jasms.0c00128}, abstractNote={A vision-system driven platform, RastirX, has been constructed for mass spectrometry imaging (MSI) of arbitrary two-dimensional patterns. The user identifies a region of interest (ROI) by drawing on a live video image of the sample with the computer mouse. Motion commands are automatically generated to move the sample to acquire scan data for the pixels in the ROI. Synchronization of sample stage motion with laser firing and mass spectrometer (MS) scan acquisition is fully automated. RastirX saves a co-registered optical image and the scan location information needed to convert raw MS data into imzML format. Imaging an arbitrarily shaped ROI instead of the minimal enclosing rectangle reduces contamination from off-sample material and significantly reduces acquisition time.}, number={12}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Garrard, Kenneth P. and Ekelöf, Måns and Khodjaniyazova, Sitora and Bagley, M. Caleb and Muddiman, David C.}, year={2020}, month={Jun}, pages={2547–2552} }
 @article{pace_horman_patisaul_muddiman_2020, title={Analysis of neurotransmitters in rat placenta exposed to flame retardants using IR-MALDESI mass spectrometry imaging}, volume={412}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-020-02626-4}, abstractNote={Chemical exposures can adversely impact fetal development. For many compounds, including common flame retardants, the mechanisms by which this occurs remain unclear, but emerging evidence suggests that disruption at the level of the placenta may play a role. Understanding how the placenta might be vulnerable to chemical exposures is challenging due to its complex structure. The primary objective of this study was to develop a method for detecting placental neurotransmitters and related metabolites without chemical derivatization so changes in the abundance and spatial distribution of neurotransmitters in rat placenta following chemical exposure could be determined using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging. Without chemical derivatization, 49 neurotransmitters and their related metabolites were putatively identified in untreated rat placenta sections using mass measurement accuracy and spectral accuracy. A few neurotransmitters were less abundant in placentas that were exposed to various flame retardants and were further investigated by KEGG metabolic pathway analysis. Many of these downregulated neurotransmitters shared the same enzyme responsible for metabolism, aromaticl-amino acid decarboxylase, suggesting a mechanistic role. These data constitute a new approach that could help identify novel mechanisms of toxicity in complex tissues. Graphical abstract.}, number={15}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Pace, Crystal L. and Horman, Brian and Patisaul, Heather and Muddiman, David C.}, year={2020}, month={Jun}, pages={3745–3752} }
 @article{kalmar_oh_dean_muddiman_2020, title={Comparative Proteomic Analysis of Wild Type and Mutant Lacking an SCF E3 Ligase F-Box Protein in Magnaporthe oryzae}, volume={19}, ISBN={1535-3907}, DOI={10.1021/acs.jproteome.0c00294}, abstractNote={Magnaporthe oryzae (M. oryzae) is a pathogenic, filamentous fungus that is a primary cause of rice blast disease. The M. oryzae protein MGG_13065, SCF E3 Ubiquitin Ligase complex F-box protein has been identified as playing a crucial role in the infection process, specifically, as part of the ubiquitin mediated proteolysis pathway. Proteins targeted by MGG_13065 E3 ligase are first phosphorylated and then ubiquitinated by E3 ligase. In this study, we used a label-free quantitative global proteomics technique to probe the role of ubiquitination and phosphorylation in the mechanism of how E3 ligase regulates change in virulence of M. oryzae. To do this, we compared the WT M.oryzae 70-15 strain with a gene knock out (E3 ligase KO) strain. After applying a ≥ 5 normalized spectral count cut off, a total of 4,432 unique proteins were identified comprised of 4,360 and 4,372 in the WT and E3 ligase KO samples, respectively. Eighty proteins drastically increased in abundance while 65 proteins decreased in abundance in the E3 ligase KO strain. Fifty-nine proteins were identified only in the WT strain; 13 of which had both phosphorylation and ubiquitination post-translational modifications. Seventy-one proteins were revealed to be only in the E3 ligase KO strain; 23 having both phosphorylation and ubiquitination post-translational modifications. Several of these proteins were associated with key biological processes. These data greatly assist in the selection of future genes for functional studies and enabling mechanistic insight related to virulence.}, number={9}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Kalmar, Jaclyn Gowen and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2020}, pages={3761–3768} }
 @article{ekelöf_dodds_khodjaniyazova_garrard_baker_muddiman_2020, title={Coupling IR-MALDESI with Drift Tube Ion Mobility-Mass Spectrometry for High-Throughput Screening and Imaging Applications}, volume={31}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1021/jasms.9b00081}, DOI={10.1021/jasms.9b00081}, abstractNote={Due to its high degree of selectivity and chemical resolution, mass spectrometry (MS) is rapidly becoming the analytical method of choice for high-throughput evaluations and clinical diagnostics. While advances in MS resolving power have increased by an order of magnitude over the past decade, advances in sample introduction are still needed for high-throughput screening applications where the timeframe of chromatographic separation would limit duty cycle. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is an ambient ionization source that has been shown to be applicable for direct analyses and mass spec-trometry imaging (MSI) of complex biological samples in a high-throughput manner. To increase a range of detectable features in IR-MALDESI experiments, we integrated the home-built ion source with a commercially available drift tube ion mobility spec-trometer-mass spectrometer (IMS-MS) and analyzed small polar molecules, lipids, carbohydrates as well as intact proteins. We also describe in detail how the pulsed ionization source was synchronized with IMS-MS.}, number={3}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Ekelöf, Måns and Dodds, James and Khodjaniyazova, Sitora and Garrard, Kenneth P. and Baker, Erin S. and Muddiman, David C.}, year={2020}, month={Jan}, pages={642–650} }
 @article{bagley_ekelof_muddiman_2020, title={Determination of Optimal Electrospray Parameters for Lipidomics in Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry Imaging}, volume={31}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.9b00063}, abstractNote={Infrared matrix-assisted laser desorption ionization (IR-MALDESI) is an ambient mass spectrometry imaging (MSI) technique that relies on electrospray ionization (ESI) for ion generation of desorbed neutrals. Although many mechanisms in IR-MALDESI have been studied in depth, there has not yet been a comprehensive study of how the ESI parameters change the profiles of tissue specific lipids. Acetonitrile (ACN)/water and methanol (MeOH)/water solvent systems and compositions were varied across a series of applied ESI voltages during IR-MALDESI analysis of rat liver tissue. Gradients of 12 min were run from 5 to 95% organic solvent in both positive and negative polarities across 11 voltages between 2.25 and 4.5 kV. These experiments informed longer gradients (25-30 min) across shorter solvent gradient ranges with fewer voltages. Optimal ESI parameters for lipidomics were determined by the number and abundance of detected lipids and the relative proportion of background ions. In positive polarity, the best solvent composition was 60-75% ACN/40-25% H2O with 0.2% formic acid at 3.2 kV applied voltage. The best parameters for negative polarity analysis are 45-55% ACN/55-45% H2O with 1 mM of acetic acid for voltages between 2.25 and 3.2 kV. Using these defined parameters, IR-MALDESI positive polarity lipidomics studies can increase lipid abundances 3-fold, with 15% greater coverage, while an abundance increase of 1.5-fold and 10% more coverage can be achieved relative to commonly used parameters in negative polarity.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Bagley, M. Caleb and Ekelof, Mans and Muddiman, David C.}, year={2020}, month={Feb}, pages={319–325} }
 @article{bagley_stepanova_ekelof_alonso_muddiman_2020, title={Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings}, volume={34}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.8616}, abstractNote={RationaleMass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due to numerous biological considerations, established methods for the relative quantification of analytes using infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) mass spectrometry imaging are not viable options. In this study, we report a method for the quantification of auxin‐related compounds using stable‐isotope‐labelled (SIL) indole‐3‐acetic acid (IAA) doped into agarose substrate.MethodsWild‐type Arabidopsis thaliana seedlings, sur2 and wei8 tar2 loss‐of‐function mutants, and YUC1 gain‐of‐function line were grown for 3 days in the dark in standard growth medium. SIL‐IAA was doped into a 1% low‐melting‐point agarose gel and seedlings were gently laid on top for IR‐MALDESI imaging with Orbitrap mass spectrometry analysis. Relative quantification was performed post‐acquisition by normalization of auxin‐related compounds to SIL‐IAA in the agarose. Amounts of auxin‐related compounds were compared between genotypes to distinguish the effects of the mutations on the accumulation of indolic metabolites of interest.ResultsIAA added to agarose was found to remain stable, with repeatability and abundance features of IAA comparable with those of other compounds used in other methods for relative quantification in IR‐MALDESI analyses. Indole‐3‐acetaldoxime was increased in sur2 mutants compared with wild‐type and other mutants. Other auxin‐related metabolites were either below the limits of quantification or successfully quantified but showing little difference among mutants.ConclusionsAgarose was shown to be an appropriate sampling surface for IR‐MALDESI mass spectrometry imaging of Arabidopsis seedlings. SIL‐IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations.}, number={6}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bagley, M. Caleb and Stepanova, Anna N. and Ekelof, Mans and Alonso, Jose M. and Muddiman, David C.}, year={2020}, month={Mar} }
 @article{pace_muddiman_2020, title={Direct Analysis of Native N-Linked Glycans by IR-MALDESI}, volume={31}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.0c00176}, abstractNote={Glycan analysis by mass spectrometry has rapidly progressed due to the role of glycans in disease and tumor progression. Glycans are complex molecules that pose analytical challenges due to their isomeric compositions, labile character, and ionization preferences. This study sought to demonstrate infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) as a novel approach for the direct analysis of N-linked glycans. The glycoprotein bovine fetuin was chosen for this analysis as its glycome is well characterized and heavily composed of sialylated glycans. Native N-linked glycans produced by enzymatic cleavage (via PNGase F) of bovine fetuin were analyzed directly by IR-MALDESI in both positive and negative ionization mode. In this study, we detected 11 N-linked glycans in negative mode and 4 N-linked glycans in positive mode, a significant increase in the amount of underivatized glycans detected by other ionization sources. Importantly, all N-linked glycans detected contained at least one sialic acid residue which are known to be labile. This work represents a critical first step for N-linked glycan analysis by IR-MALDESI with future efforts directed at mass spectrometry imaging.}, number={8}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Pace, Crystal L. and Muddiman, David C.}, year={2020}, month={Aug}, pages={1759–1762} }
 @article{rock_st armour_horman_phillips_ruis_stewart_jima_muddiman_stapleton_patisaul_2020, title={Effects of Prenatal Exposure to a Mixture of Organophosphhate Flame Ritardants on Placental Gene Expression and Serotonergic Innervaion in the Fetal Rat Brain}, volume={176}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfaa046}, abstractNote={AbstractThere is a growing need to understand the potential neurotoxicity of organophosphate flame retardants (OPFRs) and plasticizers because use and, consequently, human exposure, is rapidly expanding. We have previously shown in rats that developmental exposure to the commercial flame retardant mixture Firemaster 550 (FM 550), which contains OPFRs, results in sex-specific behavioral effects, and identified the placenta as a potential target of toxicity. The placenta is a critical coordinator of fetal growth and neurodevelopment, and a source of neurotransmitters for the developing brain. We have shown in rats and humans that flame retardants accumulate in placental tissue, and induce functional changes, including altered neurotransmitter production. Here, we sought to establish if OPFRs (triphenyl phosphate and a mixture of isopropylated triarylphosphate isomers) alter placental function and fetal forebrain development, with disruption of tryptophan metabolism as a primary pathway of interest. Wistar rat dams were orally exposed to OPFRs (0, 500, 1000, or 2000 μg/day) or a serotonin (5-HT) agonist 5-methoxytryptamine for 14 days during gestation and placenta and fetal forebrain tissues collected for analysis by transcriptomics and metabolomics. Relative abundance of genes responsible for the transport and synthesis of placental 5-HT were disrupted, and multiple neuroactive metabolites in the 5-HT and kynurenine metabolic pathways were upregulated. In addition, 5-HTergic projections were significantly longer in the fetal forebrains of exposed males. These findings suggest that OPFRs have the potential to impact the 5-HTergic system in the fetal forebrain by disrupting placental tryptophan metabolism.}, number={1}, journal={TOXICOLOGICAL SCIENCES}, author={Rock, Kylie D. and St Armour, Genevieve and Horman, Brian and Phillips, Allison and Ruis, Matthew and Stewart, Allison K. and Jima, Dereje and Muddiman, David C. and Stapleton, Heather M. and Patisaul, Heather B.}, year={2020}, month={Jul}, pages={203–223} }
 @article{kalmar_butler_baker_muddiman_2020, title={Enhanced protocol for quantitativeN-linked glycomics analysis using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)(TM)}, volume={412}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-020-02892-2}, abstractNote={The analysis of N-linked glycans using liquid chromatography and mass spectrometry (LC-MS) presents significant challenges, particularly owing to their hydrophilic nature. To address these difficulties, a variety of derivatization methods have been developed to facilitate improved ionization and detection sensitivity. One such method, the Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™ strategy for labeling glycans, has previously been utilized in the analysis of N- and O-linked glycans in biological samples. To assess the maximum sensitivity and separability of the INLIGHT™ preparation and analysis pipeline, several critical steps were investigated. First, recombinant and nonrecombinant sources of PNGase F were compared to assess variations in the released glycans. Second, modifications in the INLIGHT™ derivatization step were evaluated including temperature optimization, solvent composition changes, reaction condition length and tag concentration. Optimization of the modified method resulted in 20–100 times greater peak areas for the detected N-linked glycans in fetuin and horseradish peroxidase compared with the standard method. Furthermore, the identification of low-abundance glycans, such as (Fuc)1(Gal)2(GlcNAc)4(Man)3(NeuAc)1 and (Gal)3(GlcNAc)5(Man)3(NeuAc)3, was possible. Finally, the optimal LC setup for the INLIGHT™ derivatized N-linked glycan analyses was found to be a C18 reverse-phase (RP) column with mobile phases typical of RPLC.}, number={27}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Kalmar, Jaclyn Gowen and Butler, Karen E. and Baker, Erin S. and Muddiman, David C.}, year={2020}, month={Nov}, pages={7569–7579} }
 @article{bagley_pace_ekelof_muddiman_2020, title={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging analysis of endogenous metabolites in cherry tomatoes}, volume={145}, ISSN={["1364-5528"]}, DOI={10.1039/d0an00818d}, abstractNote={We report the spatially resolved metabolic profiling of cherry tomatoes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI); an ambient mass spectrometry imaging (MSI) technique that requires no sample derivatization.}, number={16}, journal={ANALYST}, author={Bagley, M. Caleb and Pace, Crystal L. and Ekelof, Mans and Muddiman, David C.}, year={2020}, month={Aug}, pages={5516–5523} }
 @article{xi_tu_muddiman_2020, title={Lipidomic profiling of single mammalian cells by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={412}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-020-02961-6}, abstractNote={To better understand cell-to-cell heterogeneity, advanced analytical tools are in a growing demand for elucidating chemical compositions of each cell within a population. However, the progress of single-cell chemical analysis has been restrained by the limitations of small cell volumes and minute cellular concentrations. Here, we present a rapid and sensitive method for investigating the lipid profiles of isolated single cells using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry (IR-MALDESI-MS). In this work, HeLa cells were dispersed onto a glass slide, and the cellular contents were ionized by IR-MALDESI and measured using a Q-Exactive HF-X mass spectrometer. Importantly, this approach does not require extraction and/or enrichment of analytes prior to MS analysis. Using this approach, 45 distinct lipid species, predominantly phospholipids, were detected and putatively annotated from the single HeLa cells. The proof-of-concept study demonstrates the feasibility and efficacy of IR-MALDESI-MS for rapid lipidomic profiling of single cells, which provides an important basis for future work on differentiation between normal and diseased cells at various developmental states, which can offer new insights into cellular metabolic pathways and pathological processes. Although not yet accomplished, we believe this approach can be readily used as an assessment tool to compare the number of identified species during source evolution and method optimization (intra-laboratory), and also disclose the complementary nature of different direct analytical approaches for the coverage of different types of endogenous analytes (inter-laboratory). Graphical abstract}, number={29}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Xi, Ying and Tu, Anqi and Muddiman, David C.}, year={2020}, month={Nov}, pages={8211–8222} }
 @article{bereman_kirkwood_sabaretnam_furlong_rowe_guillemin_mellinger_muddiman_2020, title={Metabolite Profiling Reveals Predictive Biomarkers and the Absence of beta-Methyl Amino-L-alanine in Plasma from Individuals Diagnosed with Amyotrophic Lateral Sclerosis}, volume={19}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.0c00216}, abstractNote={By employing chip-based capillary zone electrophoresis coupled to high resolution mass spectrometry, we profiled the plasma metabolome of 134 patients diagnosed with sporadic amyotrophic lateral sclerosis (81 males and 53 females) and 118 individuals deemed healthy (49 males; 69 females). The most significant markers (p﹤0.01) were creatine, which was 49% elevated, and creatinine and methylhistidine which were decreased by 20% and 24%, respectively, in ALS patients. The ratio of creatine versus creatinine increased 370% and 200% for male and female ALS patients, respectively. In addition, male ALS patients on average had 5-13% lower amounts of 7 essential amino acids while females did not significantly differ from healthy controls. We developed two models using the metabolite abundances: 1) A classification model for the separation of ALS and healthy samples; and 2) A classification model for the prediction of disease progression based on the ALS functional rating score. Utilizing a Monte Carlo cross-validation approach, a linear discriminant analysis model achieved a mean area under the receiver operating characteristic curve (AUC) of 0.85 (0.06) with a mean sensitivity of 80% (9%) and specificity of 78% (10%), for the separation of ALS and controls, respectively. A support vector machine classifier predicted progression categories with an AUC of 0.90 (0.06) with a mean sensitivity 73% (10%) and specificity 86% (5%). Lastly, using a previously reported assay with a stable isotope labeled (13C315N2) spike-in standard, we were unable to detect the exogenous neurotoxic metabolite, β-methylamino-L-alanine (BMAA), in the free or protein bound fraction of any of the 252 plasma samples.}, number={8}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Bereman, Michael S. and Kirkwood, Kaylie I and Sabaretnam, Tharani and Furlong, Sarah and Rowe, Dominic B. and Guillemin, Gilles J. and Mellinger, Allyson L. and Muddiman, David C.}, year={2020}, month={Aug}, pages={3276–3285} }
 @article{stutts_knuth_ekelöf_mahapatra_kullman_muddiman_2020, title={Methods for Cryosectioning and Mass Spectrometry Imaging of Whole-Body Zebrafish}, volume={31}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1021/jasms.9b00097}, DOI={10.1021/jasms.9b00097}, abstractNote={The zebrafish (Danio rerio) is an ideal model for whole animal studies of lipid metabolism and lipid-related disease. In this work, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging (MSI) was applied for direct visualization of lipid and metabolite distributions across various organs in whole-body zebrafish tissue sections. Detailed methods for overcoming the challenges of cryosectioning adult male zebrafish for MSI and complementary histological imaging are described. Representative two-dimensional ion maps demonstrated organ specific localization of lipid analytes allowing for visualization of areas of interest including the brain, liver, intestines, and skeletal muscle. A high resolving power mass spectrometer was utilized for accurate mass measurements, which permitted the use of open-source, web-based tools for MS1 annotations including METASPACE and METLIN. Whole-body MSI with IR-MALDESI allowed for broad lipid coverage with high spatial resolution, illustrating the potential of this technique for studying lipid-related diseases using zebrafish as a model organism.}, number={4}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Stutts, Whitney L. and Knuth, Megan M. and Ekelöf, Måns and Mahapatra, Debabrata and Kullman, Seth W. and Muddiman, David C.}, year={2020}, month={Feb}, pages={768–772} }
 @article{de leoz_duewer_fung_liu_yau_potter_staples_furuki_frenkel_hu_et al._2019, title={NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods}, volume={19}, ISSN={1535-9476 1535-9484}, url={http://dx.doi.org/10.1074/mcp.RA119.001677}, DOI={10.1074/mcp.RA119.001677}, abstractNote={A broad-based interlaboratory study of glycosylation profiles of a reference and modified IgG antibody involving 103 reports from 76 laboratories. Graphical Abstract Highlights A broad-based interlaboratory study of the glycosylation of a reference antibody: NISTmAb. 103 reports were received from 76 diverse laboratories worldwide. Analysis involved two samples, the NISTmAb and an enzymatically modified sample, enabling within-lab separation of random and systematic errors using the “Youden two-sample” method. Consensus values were derived and similar performance across all experimental methods was noted. Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.}, number={1}, journal={Molecular & Cellular Proteomics}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={De Leoz, Maria Lorna A. and Duewer, David L. and Fung, Adam and Liu, Lily and Yau, Hoi Kei and Potter, Oscar and Staples, Gregory O. and Furuki, Kenichiro and Frenkel, Ruth and Hu, Yunli and et al.}, year={2019}, month={Oct}, pages={11–30} }
 @article{judd_bagley_li_zhu_lei_yuzuak_ekelöf_pu_zhao_muddiman_et al._2019, title={Artemisinin Biosynthesis in Non-glandular Trichome Cells of Artemisia annua}, volume={12}, ISSN={1674-2052}, url={http://dx.doi.org/10.1016/j.molp.2019.02.011}, DOI={10.1016/j.molp.2019.02.011}, abstractNote={Artemisinin-based combination therapy (ACT) forms the first line of malaria treatment. However, the yield fluctuation of artemisinin has remained an unsolved problem in meeting the global demand for ACT. This problem is mainly caused by the glandular trichome (GT)-specific biosynthesis of artemisinin in all currently used Artemisia annua cultivars. Here, we report that non-GT cells of self-pollinated inbred A. annua plants can express the artemisinin biosynthetic pathway. Gene expression analysis demonstrated the transcription of six known pathway genes in GT-free leaves and calli of inbred A. annua plants. LC–qTOF–MS/MS analysis showed that these two types of GT-free materials produce artemisinin, artemisinic acid, and arteannuin B. Detailed IR-MALDESI image profiling revealed that these three metabolites and dihydroartemisinin are localized in non-GT cells of leaves of inbred A. annua plants. Moreover, we employed all the above approaches to examine artemisinin biosynthesis in the reported A. annua glandless (gl) mutant. The resulting data demonstrated that leaves of regenerated gl plantlets biosynthesize artemisinin. Collectively, these findings not only add new knowledge leading to a revision of the current dogma of artemisinin biosynthesis in A. annua but also may expedite innovation of novel metabolic engineering approaches for high and stable production of artemisinin in the future.}, number={5}, journal={Molecular Plant}, publisher={Elsevier BV}, author={Judd, Rika and Bagley, M. Caleb and Li, Mingzhuo and Zhu, Yue and Lei, Caiyan and Yuzuak, Seyit and Ekelöf, Måns and Pu, Gaobin and Zhao, Xiting and Muddiman, David C. and et al.}, year={2019}, month={May}, pages={704–714} }
 @article{fideler_johanningsmeier_ekelof_muddiman_2019, title={Discovery and quantification of bioactive peptides in fermented cucumber by direct analysis IR-MALDESI mass spectrometry and LC-QQQ-MS}, volume={271}, ISSN={["1873-7072"]}, DOI={10.1016/j.foodchem.2018.07.187}, abstractNote={Bioactive peptides have been identified in lactic acid bacteria fermented foods including cultured milk, sourdough, and cured meats; however, their presence has not been investigated in fermented vegetables. In this study, infrared, matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry (MS) was employed to identify bioactive peptides in fermented cucumber. Natural and starter culture fermented cucumbers were prepared in triplicate in sodium chloride brines and compared to acidified cucumbers. Putative matches of known food-derived bioactive peptides were identified by direct analysis using IR-MALDESI-MS. Peptides were confirmed by IR-MALDESI MS/MS and quantified by LC-MS/MS. Three angiotensin converting enzyme (ACE) inhibitory peptides, IPP (0.42–0.49 mg/kg), LPP (0.30–0.33 mg/kg), and VPP (0.32–0.35 mg/kg) were formed in fermented cucumbers. A fourth ACE inhibitory peptide, KP (0.93–1.5 mg/kg), was enhanced 3–5 fold in fermented cucumbers compared with acidified cucumbers. This work demonstrates that lactic acid bacteria fermentation can enhance bioactive peptide content in vegetables.}, journal={FOOD CHEMISTRY}, author={Fideler, Jennifer and Johanningsmeier, Suzanne D. and Ekelof, Mans and Muddiman, David C.}, year={2019}, month={Jan}, pages={715–723} }
 @article{lakeh_tu_muddiman_abdollahi_2019, title={Discriminating normal regions within cancerous hen ovarian tissue using multivariate hyperspectral image analysis}, volume={33}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.8362}, abstractNote={RationaleIdentification of subregions under different pathological conditions on cancerous tissue is of great significance for understanding cancer progression and metastasis. Infrared matrix‐assisted laser desorption electrospray ionization mass spectrometry (IR‐MALDESI‐MS) can be potentially used for diagnostic purposes since it can monitor spatial distribution and abundance of metabolites and lipids in biological tissues. However, the large size and high dimensionality of hyperspectral data make analysis and interpretation challenging. To overcome these barriers, multivariate methods were applied to IR‐MALDESI data for the first time, aiming at efficiently resolving mass spectral images, from which these results were then used to identify normal regions within cancerous tissue.MethodsMolecular profiles of healthy and cancerous hen ovary tissues were generated by IR‐MALDESI‐MS. Principal component analysis (PCA) combined with color‐coding built a single tissue image which summarizes the high‐dimensional data features. Pixels with similar color indicated similar composition. PCA results from healthy tissue were further used to test each pixel in cancerous tissue to determine if it is healthy. Multivariate curve resolution‐alternating least squares (MCR‐ALS) was used to obtain major spatial features existing in ovary tissues, and group molecules with the same distribution patterns simultaneously.ResultsPCA as the predominating dimensionality reduction approach captured over 90% spectral variances by the first three PCs. The PCA images show the cancerous tissue is more chemically heterogeneous than healthy tissue, where at least four regions with different m/z profiles can be differentiated. PCA modeling assigns top regions of cancerous tissue as healthy‐like. MCR‐ALS extracted three and four major compounds from healthy and cancerous tissue, respectively. Evaluating similarities of resolved spectra uncovered the chemical components that were distinct in some regions on cancerous tissue, serving as a supplementary way to differentiate healthy and cancerous regions.ConclusionsTwo unsupervised chemometric methods including PCA and MCR‐ALS were applied for resolving and visualizing IR‐MALDESI‐MS data acquired from hen ovary tissues, improving the interpretation of mass spectrometry imaging results. Then possible normal regions were differentiated from cancerous tissue sections. No prior knowledge is required using either chemometric method, so our approach is readily suitable for unstained tissue samples, which allows one to reveal the molecular events happening during disease progression.}, number={4}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Lakeh, Mahsa Akbari and Tu, Anqi and Muddiman, David C. and Abdollahi, Hamid}, year={2019}, month={Feb}, pages={381–391} }
 @article{thompson_rosen_prince_white_sykes_cruz_mathews_deleage_estes_charlins_et al._2019, title={Heterogeneous antiretroviral drug distribution and HIV/SHIV detection in the gut of three species}, volume={11}, ISSN={["1946-6242"]}, DOI={10.1126/scitranslmed.aap8758}, abstractNote={Imaging reveals that antiretroviral drugs are not distributed evenly in the mammalian gut, with potential implications for HIV replication.}, number={499}, journal={SCIENCE TRANSLATIONAL MEDICINE}, author={Thompson, Corbin G. and Rosen, Elias P. and Prince, Heather M. A. and White, Nicole and Sykes, Craig and Cruz, Gabriela and Mathews, Michelle and Deleage, Claire and Estes, Jacob D. and Charlins, Paige and et al.}, year={2019}, month={Jul} }
 @article{tu_muddiman_2019, title={Internal Energy Deposition in Infrared Matrix-Assisted Laser Desorption Electrospray Ionization With and Without the Use of Ice as a Matrix}, volume={30}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-019-02323-2}, abstractNote={The internal energy deposited into analytes during the ionization process largely influences the extent of fragmentation, thus the appearance of the resulting mass spectrum. The internal energy distributions of a series of para-substituted benzyl pyridinium cations in liquid and solid-state generated by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) were measured using the survival yield method, of which results were subsequently compared with conventional electrospray ionization (ESI). The comparable mean internal energy values (e.g., 1.8-1.9 eV at a collision energy of 15 eV) and peak widths obtained with IR-MALDESI and ESI support that IR-MALDESI are essentially a soft ionization technique where analytes do not gain considerable internal energy during the laser-induced desorption process and/or lose energy during uptake into charged electrospray droplets. An unusual fragment ion, protonated pyridine, was only found for solid IR-MALDESI at relatively high collision energies, which is presumably resulted from direct ionization of the pre-charged analytes in form of salts. Analysis of tissue with an ice layer consistently yielded ion populations with higher internal energy than its counterpart without an ice layer, likely due to a substantially enhanced number of IR absorbers with ice. Further measurements with holo-myoglobin show that IR-MALDESI-MS retains the noncovalently bound heme-protein complexes under both native-like and denaturing conditions, while complete loss of the heme group occurred in denaturing ESI-MS, showing that the softness of IR-MALDESI is equivalent or superior to ESI for biomolecules.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Tu, Anqi and Muddiman, David C.}, year={2019}, month={Nov}, pages={2380–2391} }
 @article{kalmar_oh_dean_muddiman_2020, title={Investigating host-pathogen meta-metabolic interactions of Magnaporthe oryzae infected barley using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry}, volume={412}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-019-02216-z}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging is a useful tool for identifying important meta-metabolomic features pertinent for enhancing our understanding of biological systems. Magnaporthe oryzae (M. oryzae) is a filamentous fungus that is the primary cause of rice blast disease. True to its name, M. oryzae primarily destroys rice crops and can also destroy other cereal crops as well. In a previous study, the F-box E3 ligase protein in M. oryzae was noted to be crucial for its growth and pathogenicity. In this study, we inoculated three separate sets of barley with wild-type M. oryzae, an F-box E3 ligase protein knock out of M. oryzae, and a control solution. Over the course of the infection (8 days), we imaged each treatment after development of an advanced polarity switching method, which allowed for the detection of low and high molecular weight compounds that ionize in positive or negative polarities. A set of features from initial experiments were chosen for another analysis using tandem mass spectrometry. Serotonin, a barley defense metabolite, was a compound identified in both positive and negative modes. Serotonin was putatively identified using MS1 data including carbon estimation and sulfur counting then confirmed based on tandem mass spectrometry fragmentation patterns. Metabolites in the melanin pathway, important for infection development of M. oryzae, were also identified using MS1 data but were unable to be confirmed with MS/MS due to their low abundances.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Kalmar, Jaclyn Gowen and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2020}, month={Jan}, pages={139–147} }
 @article{salvato_loziuk_kiyota_daneluzzi_araujo_muddiman_mazzafera_2019, title={Label-Free Quantitative Proteomics of Enriched Nuclei from Sugarcane (Saccharum ssp) Stems in Response to Drought Stress}, volume={19}, ISSN={["1615-9861"]}, DOI={10.1002/pmic.201900004}, abstractNote={AbstractDrought is considered the major abiotic stress limiting crop productivity. This study seeks to identify proteins involved in the drought response in sugarcane stems submitted to drought stress. The integration of nuclei enrichment sample preparation with the shotgun proteomic approach results in great coverage of the sugarcane stem proteome with 5381 protein groups identified. A total of 1204 differentially accumulated proteins are detected in response to drought, among which 586 and 618 are increased and reduced in abundance, respectively. A total of 115 exclusive proteins are detected, being 41 exclusives of drought‐stressed plants and 74 exclusives of control plants. In the control plants, most of these proteins are related to cell wall metabolism, indicating that drought affects negatively the cell wall metabolism. Also, 37 transcription factors (TFs) are identified, which are low abundant nuclear proteins and are differentially accumulated in response to drought stress. These TFs are associated to protein domains such as leucine‐rich (bZIP), C2H2, NAC, C3H, LIM, Myb‐related, heat shock factor (HSF) and auxin response factor (ARF). Increased abundance of chromatin remodeling and RNA processing proteins are also observed. It is suggested that these variations result from an imbalance of protein synthesis and degradation processes induced by drought.}, number={14}, journal={PROTEOMICS}, author={Salvato, Fernando and Loziuk, Philip and Kiyota, Eduardo and Daneluzzi, Gabriel Silva and Araujo, Pedro and Muddiman, David C. and Mazzafera, Paulo}, year={2019}, month={Jul} }
 @article{khodjaniyazova_hanne_cole_muddiman_2019, title={Mass spectrometry imaging (MSI) of fresh bones using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={11}, ISSN={["1759-9679"]}, url={https://doi.org/10.1039/C9AY01886G}, DOI={10.1039/c9ay01886g}, abstractNote={Direct analysis and IR-MALDESI mass spectrometry imaging of fresh mouse bones that underwent no chemical treatments other than flash-freezing.}, number={46}, journal={ANALYTICAL METHODS}, publisher={Royal Society of Chemistry (RSC)}, author={Khodjaniyazova, Sitora and Hanne, Nicholas J. and Cole, Jacqueline H. and Muddiman, David C.}, year={2019}, month={Dec}, pages={5929–5938} }
 @article{reis borges_salvato_loziuk_muddiman_azevedo_2019, title={Quantitative proteomic analysis of tomato genotypes with differential cadmium tolerance}, volume={26}, ISSN={["1614-7499"]}, DOI={10.1007/s11356-019-05766-y}, abstractNote={This is a report on comprehensive characterization of cadmium (Cd)-exposed root proteomes in tomato using label-free quantitative proteomic approach. Two genotypes differing in Cd tolerance, Pusa Ruby (Cd-tolerant) and Calabash Rouge (Cd-sensitive), were exposed during 4 days to assess the Cd-induced effects on root proteome. The overall changes in both genotypes in terms of differentially accumulated proteins (DAPs) were mainly associated to cell wall, redox, and stress responses. The proteome of the sensitive genotype was more responsive to Cd excess, once it presented higher number of DAPs. Contrasting protein accumulation in cellular component was observed: Cd-sensitive enhanced intracellular components, while the Cd-tolerant increased proteins of extracellular and envelope regions. Protective and regulatory mechanisms were different between genotypes, once the tolerant showed alterations of various protein groups that lead to a more efficient system to cope with Cd challenge. These findings could shed some light on the molecular basis underlying the Cd stress response in tomato, providing fundamental insights for the development of Cd-safe cultivars. Graphical abstract.}, number={25}, journal={ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH}, author={Reis Borges, Karina Lima and Salvato, Fernanda and Loziuk, Philip L. and Muddiman, David C. and Azevedo, Ricardo Antunes}, year={2019}, month={Sep}, pages={26039–26051} }
 @article{tu_muddiman_2019, title={Systematic evaluation of repeatability of IR-MALDESI-MS and normalization strategies for correcting the analytical variation and improving image quality}, volume={411}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-019-01953-5}, abstractNote={Mass spectrometry imaging is a powerful tool widely used in biological, clinical, and forensic research, but its often poor repeatability limits its application for quantitative and large-scale analysis. A systematic evaluation of infrared matrix-assisted laser desorption electrospray ionization mass spectrometry (IR-MALDESI-MS) repeatability in absolute ion abundances during short- and long-term experiments was carried out on liver slices from the same rat with minimal biological variability to be expected. Results of median %RSDs ranging from 14 to 45, pooled %RMADs ranging from 11 to 33, and Pearson correlation coefficients ranging from 0.83 to 1.00 demonstrated an acceptable repeatability of IR-MALDESI-MS. Normalization is commonly applied for the purpose of accounting for analytical variability of spectra generated from different runs so as to reveal real biological differences. Nine data normalization strategies were performed on the rat liver data sets to examine their effects on reducing analytical variation, and further on a hen ovary data set containing more morphological features for the investigation of their impact on ion images. Results demonstrated that the majority of normalization approaches benefit data quality to some extent, and local normalization methods significantly outperform their global counterparts, resulting in a reduction of median %RSD up to 22. Local median normalization was found to be promisingly robust for both homogeneous and heterogeneous samples.}, number={22}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Tu, Anqi and Muddiman, David C.}, year={2019}, month={Sep}, pages={5729–5743} }
 @article{bai_khodjaniyazova_garrard_muddiman_2020, title={Three-Dimensional Imaging with Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry}, volume={31}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.9b00066}, abstractNote={Mass spectrometry imaging as a field has pushed its frontiers to three dimensions. Most three-dimensional mass spectrometry imaging (3D MSI) approaches require serial sectioning that results in a loss of biological information between analyzed slices and difficulty in reconstruction of 3D images. In this contribution, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) was demonstrated to be applicable for 3D MSI that does not require sectioning because IR laser ablates material on a micrometer scale. A commercially available over-the-counter pharmaceutical was used as a model to demonstrate the feasibility of IR-MALDESI for 3D MSI. Depth resolution (i.e., z-resolution) as a function of laser energy levels and density of ablated material was investigated. The best achievable depth resolution from a pill was 2.3 μm at 0.3 mJ/pulse. 2D and 3D MSI were performed on the tablet to show the distribution of pill-specific molecules. A 3D MSI analysis on a region of interest of 15 × 15 voxels across 50 layers was performed. Our results demonstrate that IR-MALDESI is feasible with 3D MSI on a pill, and future work will be focused on analyses of biological tissues.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Bai, Hongxia and Khodjaniyazova, Sitora and Garrard, Kenneth P. and Muddiman, David}, year={2020}, month={Feb}, pages={292–297} }
 @article{beri_kirkwood_muddiman_bereman_2018, title={A novel integrated strategy for the detection and quantification of the neurotoxin beta-N-methylamino-l-alanine in environmental samples}, volume={410}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-018-0930-0}, abstractNote={We describe a set of new tools for the detection and quantification of β-N-methylamino-L-alanine (BMAA) which includes a novel stable isotope-labeled BMAA standard ( 13 C 3 , 15 N 2 ) and a chip-based capillary electrophoresis mass spectrometry platform for separation and detection. Baseline resolution of BMAA from its potentially confounding structural isomers N-2-aminoethylglycine (AEG) and 2,4-diaminobutyric acid (2,4-DAB) is achieved using the chip-based CE-MS system in less than 1 min. Detection and linearity of response are demonstrated across > 3.5 orders of dynamic range using parallel reaction monitoring (PRM). The lower limit of detection and quantification were calculated for BMAA detection at 40 nM (4.8 ng/mL) and 400 nM (48 ng/mL), respectively. Finally, the strategy was applied to detect BMAA in seafood samples purchased at a local market in Raleigh, NC where their harvest location was known. BMAA was detected in a sea scallop sample. Because the BMAA/stable isotope-labeled  13 C 3 , 15 N 2 -BMAA (SIL-BMAA) ratio in the scallop sample was below the limit of quantification, a semiquantitative analysis of BMAA content was carried out, and BMAA content was estimated to be approximately 820 ng BMAA/1 g of wet scallop tissue. Identification was verified by high mass measurement accuracy of precursor (< 5 ppm) and product ions (< 10 ppm), comigration with SIL-BMAA spike-in standard, and conservation of ion abundance ratios for product ions between BMAA and SIL-BMAA. Interestingly, BMAA was not identified in the free protein fraction but only detected after protein hydrolysis which suggests that BMAA is tightly bound by and/or incorporated into proteins. Graphical abstract Utilization of novel 13C3,15N2-BMAA and chip-based CE-MS/MS for detection and quantification of BMAA in environmental samples.}, number={10}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Beri, Joshua and Kirkwood, Kaylie I. and Muddiman, David C. and Bereman, Michael S.}, year={2018}, month={Apr}, pages={2597–2605} }
 @article{yan_liu_kim_liu_huang_yang_lin_chen_yang_wang_et al._2019, title={CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa}, volume={222}, ISSN={["1469-8137"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055556739&partnerID=MN8TOARS}, DOI={10.1111/nph.15505}, abstractNote={Summary


Lignin is the major phenolic polymer in plant secondary cell walls and is polymerized from monomeric subunits, the monolignols. Eleven enzyme families are implicated in monolignol biosynthesis. Here, we studied the functions of members of the cinnamyl alcohol dehydrogenase (CAD) and cinnamoyl‐CoA reductase (CCR) families in wood formation in Populus trichocarpa, including the regulatory effects of their transcripts and protein activities on monolignol biosynthesis.

Enzyme activity assays from stem‐differentiating xylem (SDX) proteins showed that RNAi suppression of PtrCAD1 in P. trichocarpa transgenics caused a reduction in SDX CCR activity. RNAi suppression of PtrCCR2, the only CCR member highly expressed in SDX, caused a reciprocal reduction in SDX protein CAD activities. The enzyme assays of mixed and coexpressed recombinant proteins supported physical interactions between PtrCAD1 and PtrCCR2.

Biomolecular fluorescence complementation and pull‐down/co‐immunoprecipitation experiments supported a hypothesis of PtrCAD1/PtrCCR2 heterodimer formation.

These results provide evidence for the formation of PtrCAD1/PtrCCR2 protein complexes in monolignol biosynthesis in planta.

}, number={1}, journal={NEW PHYTOLOGIST}, author={Yan, Xiaojing and Liu, Jie and Kim, Hoon and Liu, Baoguang and Huang, Xiong and Yang, Zhichang and Lin, Ying-Chung Jimmy and Chen, Hao and Yang, Chenmin and Wang, Jack P. and et al.}, year={2019}, month={Apr}, pages={244–260} }
 @article{ekelof_manni_nazari_bokhart_muddiman_2018, title={Characterization of a novel miniaturized burst-mode infrared laser system for IR-MALDESI mass spectrometry imaging}, volume={410}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-018-0918-9}, abstractNote={Laser systems are widely used in mass spectrometry as sample probes and ionization sources. Mid-infrared lasers are particularly suitable for analysis of high water content samples such as animal and plant tissues, using water as a resonantly excited sacrificial matrix. Commercially available mid-IR lasers have historically been bulky and expensive due to cooling requirements. This work presents a novel air-cooled miniature mid-IR laser with adjustable burst-mode output and details an evaluation of its performance for mass spectrometry imaging. The miniature laser was found capable of generating sufficient energy for complete ablation of animal tissue in the context of an IR-MALDESI experiment with exogenously added ice matrix, yielding several hundred confident metabolite identifications.}, number={9}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Ekelof, Mans and Manni, Jeffrey, Sr. and Nazari, Milad and Bokhart, Mark and Muddiman, David C.}, year={2018}, month={Mar}, pages={2395–2402} }
 @article{khodjaniyazova_nazari_garrard_matos_jackson_muddiman_2018, title={Characterization of the Spectral Accuracy of an Orbitrap Mass Analyzer Using Isotope Ratio Mass Spectrometry}, volume={90}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ACS.ANALCHEM.7B03983}, DOI={10.1021/ACS.ANALCHEM.7B03983}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source coupled to the Q Exactive Plus has been extensively used in untargeted mass spectrometry imaging (MSI) analyses of biological tissue sections. Although the Orbitrap is a high-resolution and accurate-mass (HRAM) mass analyzer, these attributes alone cannot be used for the reliable identification of unknown analytes observed in complex biological matrices. Spectral accuracy (SA) is the ability of the mass spectrometer to accurately measure the isotopic distributions which, when used with high mass measurement accuracy (MMA), can facilitate the elucidation of a single elemental composition. To investigate the effects of different ion populations on an Orbitrap's SA and MMA, a solution of caffeine, the tetrapeptide MRFA, and ultramark was analyzed using a Q Exactive Plus across eight distinct automatic gain control (AGC) targets. The same compounds from the same lot numbers were also individually analyzed using isotope ratio mass spectrometry (IRMS) to accurately determine the isotopic abundance of 13C, 15N, and 34S. We demonstrated that at optimum absolute ion abundances the Orbitrap can be used to accurately count carbons, nitrogens, and sulfurs in samples with varying masses. Additionally, absolute monoisotopic ion abundances required for high SA were empirically determined by using the expected (IRMS) and experimental (Orbitrap) isotopic distributions to calculate the Pearson chi-square test. These thresholds for absolute ion abundances can be used in untargeted MSI studies to shorten an identification list by rapidly screening for isotopic distributions whose absolute ion abundances are high enough to accurately estimate the number of atoms.}, number={3}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Khodjaniyazova, Sitora and Nazari, Milad and Garrard, Kenneth P. and Matos, Mayara P. V. and Jackson, Glen P. and Muddiman, David C.}, year={2018}, month={Jan}, pages={1897–1906} }
 @article{ekelöf_garrard_judd_rosen_xie_kashuba_muddiman_2018, title={Evaluation of Digital Image Recognition Methods for Mass Spectrometry Imaging Data Analysis}, volume={29}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1007/S13361-018-2073-0}, DOI={10.1007/s13361-018-2073-0}, abstractNote={Analyzing mass spectrometry imaging data can be laborious and time consuming, and as the size and complexity of datasets grow, so does the need for robust automated processing methods. We here present a method for comprehensive, semi-targeted discovery of molecular distributions of interest from mass spectrometry imaging data, using widely available image similarity scoring algorithms to rank images by spatial correlation. A fast and powerful batch search method using a MATLAB implementation of structural similarity (SSIM) index scoring with a pre-selected reference distribution is demonstrated for two sample imaging datasets, a plant metabolite study using Artemisia annua leaf, and a drug distribution study using maraviroc-dosed macaque tissue. Graphical Abstract ᅟ.}, number={12}, journal={Journal of The American Society for Mass Spectrometry}, publisher={Springer Science and Business Media LLC}, author={Ekelöf, Måns and Garrard, Kenneth P. and Judd, Rika and Rosen, Elias P. and Xie, De-Yu and Kashuba, Angela D. M. and Muddiman, David C.}, year={2018}, month={Oct}, pages={2467–2470} }
 @article{bagley_ekelof_rock_patisaul_muddiman_2018, title={IR-MALDESI mass spectrometry imaging of underivatized neurotransmitters in brain tissue of rats exposed to tetrabromobisphenol A}, volume={410}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-018-1420-0}, abstractNote={There is a pressing need to develop tools for assessing possible neurotoxicity, particularly for chemicals where the mode of action is poorly understood. Tetrabromobisphenol A (TBBPA), a highly abundant brominated flame retardant, has lately been targeted for neurotoxicity analysis by concerned public health entities in the EU and USA because it is a suspected thyroid disruptor and neurotoxicant. In this study, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) coupled to a Q Exactive Plus mass spectrometer was used for the analysis of neurotransmitters in the brains of rats exposed to TBBPA in gestation and lactation through their mothers. Three neurotransmitters of interest were studied in three selected regions of the brain: caudate putamen, substantia nigra (SN), and dorsal raphe. Stable isotope labeled (SIL) standards were used as internal standards and a means to achieve relative quantification. This study serves as a demonstration of a new application of IR-MALDESI, namely that neurotransmitter distributions can be confidently and rapidly imaged without derivatization.}, number={30}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Bagley, M. Caleb and Ekelof, Mans and Rock, Kylie and Patisaul, Heather and Muddiman, David C.}, year={2018}, month={Dec}, pages={7979–7986} }
 @article{wang_matthews_williams_shi_yang_tunlaya-anukit_chen_li_liu_lin_et al._2018, title={Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-03863-z}, DOI={10.1038/s41467-018-03863-z}, abstractNote={AbstractA multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Jack P. and Matthews, Megan L. and Williams, Cranos M. and Shi, Rui and Yang, Chenmin and Tunlaya-Anukit, Sermsawat and Chen, Hsi-Chuan and Li, Quanzi and Liu, Jie and Lin, Chien-Yuan and et al.}, year={2018}, month={Dec}, pages={1579} }
 @article{muddiman_2018, title={Jürgen H. Gross: Mass spectrometry: a textbook, 3rd ed.}, volume={410}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/S00216-018-0870-8}, DOI={10.1007/S00216-018-0870-8}, number={8}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Muddiman, David C.}, year={2018}, month={Feb}, pages={2051–2052} }
 @article{nazari_bokhart_loziuk_muddiman_2018, title={Quantitative mass spectrometry imaging of glutathione in healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={143}, ISSN={["1364-5528"]}, DOI={10.1039/c7an01828b}, abstractNote={IR-MALDESI quantitative mass spectrometry imaging of glutathione in healthy and cancerous hen ovarian tissues.}, number={3}, journal={ANALYST}, author={Nazari, Milad and Bokhart, Mark T. and Loziuk, Philip L. and Muddiman, David C.}, year={2018}, month={Feb}, pages={654–661} }
 @article{yao_xue_he_bao_xie_ge_2017, title={Climate projections of spatial variations in coastal storm surges along the Gulf of Mexico and U.S. east coast}, volume={16}, ISSN={1672-5182 1993-5021}, url={http://dx.doi.org/10.1007/S11802-017-3012-6}, DOI={10.1007/s11802-017-3012-6}, number={1}, journal={Journal of Ocean University of China}, publisher={Springer Nature}, author={Yao, Zhigang and Xue, Zuo and He, Ruoying and Bao, Xianwen and Xie, Jun and Ge, Qian}, year={2017}, month={Jan}, pages={1–7} }
 @article{oh_robertson_parker_muddiman_dean_2017, title={Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae}, volume={15}, ISSN={1477-5956}, url={http://dx.doi.org/10.1186/s12953-017-0128-y}, DOI={10.1186/s12953-017-0128-y}, abstractNote={Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed. M. oryzae strain 70–15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source. Proteins were isolated and subjected to unfractionated gel-free based liquid chromatography-tandem mass spectrometry (LC-MS/MS). The subcellular localization and function of the identified proteins were predicted using bioinformatics tools. A total of 5498 M. oryzae proteins were identified. Comparative analysis of protein expression showed 363 proteins and 266 proteins significantly induced or uniquely expressed under nitrogen starved or nitrogen supplemented conditions, respectively. A functional analysis of differentially expressed proteins revealed that during nitrogen starvation nitrogen catabolite repression, melanin biosynthesis, protein degradation and protein translation pathways underwent extensive alterations. In addition, nitrogen starvation induced accumulation of various extracellular proteins including small extracellular proteins consistent with observations of a link between nitrogen starvation and the development of pathogenicity in M. oryzae. The results from this study provide a comprehensive understanding of fungal responses to nitrogen availability.}, number={1}, journal={Proteome Science}, publisher={Springer Science and Business Media LLC}, author={Oh, Yeonyee and Robertson, Suzanne L. and Parker, Jennifer and Muddiman, David C. and Dean, Ralph A.}, year={2017}, month={Nov} }
 @article{nazari_ekelöf_khodjaniyazova_elsen_williams_muddiman_2017, title={Cover Image}, volume={31}, ISSN={0951-4198}, url={http://dx.doi.org/10.1002/RCM.8002}, DOI={10.1002/RCM.8002}, abstractNote={The cover image, by Milad Nazari et al., is based on the Research Article Direct Screening of Enzyme Activity using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI), DOI: 10.1002/rcm.7971.}, number={22}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Nazari, Milad and Ekelöf, Måns and Khodjaniyazova, Sitora and Elsen, Nathaniel L. and Williams, Jon D. and Muddiman, David C.}, year={2017}, month={Oct}, pages={i-i} }
 @article{kottke_lee_jonke_seneviratne_hecht_muddiman_torres_fedorov_2017, title={DRILL: An Electrospray Ionization-Mass Spectrometry Interface for Improved Sensitivity via Inertial Droplet Sorting and Electrohydrodynamic Focusing in a Swirling Flow}, volume={89}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.7b01555}, abstractNote={We describe the DRILL (dry ion localization and locomotion) device, which is an interface for electrospray ionization (ESI)-mass spectrometry (MS) that exploits a swirling flow to enable the use of inertial separation to prescribe different fates for electrosprayed droplets based on their size. This source adds a new approach to charged droplet trajectory manipulation which, when combined with hydrodynamic drag forces and electric field forces, provides a rich range of possible DRILL operational modes. Here, we experimentally demonstrate sensitivity improvement obtained via vortex-induced inertial sorting of electrosprayed droplets/ions: one possible mode of DRILL operation. In this mode, DRILL removes larger droplets while accelerating the remainder of the ESI plume, producing a high velocity stream of gas-enriched spray with small, highly charged droplets and ions and directing it toward the MS inlet. The improved signal-to-noise ratio (10-fold enhancement) in the detection of angiotensin I is demonstrated using the DRILL interface coupled to ESI-MS along with an improved limit of detection (10-fold enhancement, 100 picomole) in the detection of angiotensin II. The utility of DRILL has also been demonstrated by liquid chromatography (LC)-MS: a stable isotope labeled peptide cocktail was spiked into a complex native tissue extract and quantified by unscheduled multiple reaction monitoring on a TSQ Vantage. DRILL demonstrated improved signal strength (up to a 700-fold) for 8 out of 9 peptides and had no effects on the peak shape of the transitions.}, number={17}, journal={ANALYTICAL CHEMISTRY}, author={Kottke, Peter A. and Lee, Jurt Y. and Jonke, Alex P. and Seneviratne, Chinthaka A. and Hecht, Elizabeth S. and Muddiman, David C. and Torres, Matthew P. and Fedorov, Andrei G.}, year={2017}, month={Sep}, pages={8981–8987} }
 @article{king_hecht_muddiman_2018, title={Demonstration of hydrazide tagging for O-glycans and a central composite design of experiments optimization using the INLIGHT (TM) reagent}, volume={410}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-017-0828-2}, abstractNote={The INLIGHT™ strategy for N-linked glycan derivatization has been shown to overcome many of the challenges associated with glycan analysis. The hydrazide tag reacts efficiently with the glycans, increasing their non-polar surface area, allowing for reversed-phase separations and increased ionization efficiency. We have taken the INLIGHT™ strategy and adopted it for use with O-linked glycans. A central composite design was utilized to find optimized tagging conditions (45% acetic acid, 0.1 μg/μL tag concentration, 37 C, 1.75 h). Derivatization at optimized conditions was much quicker than any hydrazide derivatization strategy used previously. Human immunoglobulin A (IgA) and bovine submaxillary mucin (BSM) were then deglycosylated through hydrazinolysis and the removed glycans were tagged under optimum conditions. XIC of tagged glycans and MS2 data show successful hydrazide tagging of O-linked glycans for the first time. Graphical abstract The INLIGHT™ hydrazide tag was optimized using a central composite design for derivatization of O-linked glycans. Two glycoprotein standards were deglycosylated through hydrazinolysis and tagged at the optimized conditions. MS/MS data shows INLIGHT™ derivatization of glycans demonstrating successful hydrazide tagging of O-glycans for the first time.}, number={5}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={King, Samuel R. and Hecht, Elizabeth S. and Muddiman, David C.}, year={2018}, month={Feb}, pages={1409–1415} }
 @article{nazari_malico_ekelöf_lund_williams_muddiman_2017, title={Direct analysis of terpenes from biological buffer systems using SESI and IR-MALDESI}, volume={410}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/s00216-017-0570-9}, DOI={10.1007/s00216-017-0570-9}, abstractNote={Terpenes are the largest class of natural products with a wide range of applications including use as pharmaceuticals, fragrances, flavorings, and agricultural products. Terpenes are biosynthesized by the condensation of a variable number of isoprene units resulting in linear polyisoprene diphosphate units, which can then be cyclized by terpene synthases into a range of complex structures. While these cyclic structures have immense diversity and potential in different applications, their direct analysis in biological buffer systems requires intensive sample preparation steps such as salt cleanup, extraction with organic solvents, and chromatographic separations. Electrospray post-ionization can be used to circumvent many sample cleanup and desalting steps. SESI and IR-MALDESI are two examples of ionization methods that employ electrospray post-ionization at atmospheric pressure and temperature. By coupling the two techniques and doping the electrospray solvent with silver ions, olefinic terpenes of different classes and varying degrees of volatility were directly analyzed from a biological buffer system with no sample workup steps.}, number={3}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Nazari, Milad and Malico, Alexandra A. and Ekelöf, Måns and Lund, Sean and Williams, Gavin J. and Muddiman, David C.}, year={2017}, month={Aug}, pages={953–962} }
 @article{nazari_ekelof_khodjaniyazova_elsen_williams_muddiman_2017, title={Direct screening of enzyme activity using infrared matrix-assisted laser desorption electrospray ionization}, volume={31}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.7971}, abstractNote={RationaleHigh‐throughput screening (HTS) is a critical step in the drug discovery process. However, most mass spectrometry (MS)‐based HTS methods require sample cleanup steps prior to analysis. In this work we present the utility of infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) for monitoring an enzymatic reaction directly from a biological buffer system with no sample cleanup and at high throughput.MethodsIR‐MALDESI was used to directly analyze reaction mixtures from a well plate at different time points after reaction initiation. The percent conversion of precursors to products was used to screen the enzyme activity. The reaction was performed with two different concentrations of precursors and enzyme in order to assess the dynamic range of the assay. Eventually, a pseudo‐HTS study was designed to investigate the utility of IR‐MALDESI screening enzyme activity in a high‐throughput manner.ResultsIR‐MALDESI was able to readily monitor the activity of IDH1 over time at two different concentrations of precursors and enzyme. The calculated Z‐factors of 0.65 and 0.41 confirmed the suitability of the developed method for screening enzyme activity in HTS manner. Finally, in a single‐blind pseudo‐HTS analysis IR‐MALDESI was able to correctly predict the identity of all samples, where 8/10 samples were identified with high confidence and the other two samples with lower confidence.ConclusionsThe enzymatic activity of IDH1 was screened by directly analyzing the reaction content from the buffer in well plates with no sample cleanup steps. This proof‐of‐concept study demonstrates the robustness of IR‐MALDESI for direct analysis of enzymatic reactions from biological buffers with no sample cleanup and its immense potential for HTS applications.}, number={22}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Nazari, Milad and Ekelof, Mans and Khodjaniyazova, Sitora and Elsen, Nathaniel L. and Williams, Jon D. and Muddiman, David C.}, year={2017}, month={Nov}, pages={1868–1874} }
 @article{bokhart_manni_garrard_ekelöf_nazari_muddiman_2017, title={IR-MALDESI Mass Spectrometry Imaging at 50 Micron Spatial Resolution}, volume={28}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1007/S13361-017-1740-X}, DOI={10.1007/S13361-017-1740-X}, abstractNote={High spatial resolution in mass spectrometry imaging (MSI) is crucial to understanding the biology dictated by molecular distributions in complex tissue systems. Here, we present MSI using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) at 50 μm resolution. An adjustable iris, beam expander, and an aspherical focusing lens were used to reduce tissue ablation diameters for MSI at high resolution. The laser beam caustic was modeled using laser ablation paper to calculate relevant laser beam characteristics. The minimum laser spot diameter on the tissue was determined using tissue staining and microscopy. Finally, the newly constructed optical system was used to image hen ovarian tissue with and without oversampling, detailing tissue features at 50 μm resolution. Graphical Abstract ᅟ.}, number={10}, journal={Journal of The American Society for Mass Spectrometry}, publisher={Springer Nature}, author={Bokhart, Mark T. and Manni, Jeffrey and Garrard, Kenneth P. and Ekelöf, Måns and Nazari, Milad and Muddiman, David C.}, year={2017}, month={Jul}, pages={2099–2107} }
 @article{ekeloef_muddiman_2018, title={IR-MALDESI method optimization based on time-resolved measurement of ion yields}, volume={410}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-017-0585-2}, abstractNote={In the field of mass spectrometry imaging, typical experiments involve ionization directly from complex samples with no pre-ionization separation, relying on high resolving power mass analyzers to separate ions of interest. When an ion trapping step is involved in the analysis, the dynamic range of the analysis may be limited by the capacity of the ion trap, which is easily exceeded. To minimize collection of undesired ambient species while maximizing collection of analyte signal, accurate timing between ion generation and collection is a requirement. Here, a method for achieving synchronicity between infrared laser ablation and ion collection on a Q Exactive Plus mass spectrometer is described and demonstrated through measurement of ion accumulation at fixed time points following a laser ablation event with electrospray post-ionization of ablated material. In a model imaging experiment using infrared matrix-assisted laser desorption electrospray ionization, fixing the injection time at the minimum duration required to capture all ions generated by the last laser pulse in a sequence is shown to maximize target ion abundances. Using optimized timing is shown to yield a doubling or better of useful signal compared to previously used parameters. Graphical abstract Illustration of the effects of signal optimization on data quality for a single lipid species (cholesterol) measured from mouse liver tissue.}, number={3}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Ekeloef, Mans and Muddiman, David C.}, year={2018}, month={Jan}, pages={963–970} }
 @article{thompson_rosen_mathews_white_sykes_fedoriw_charlins_mulder_kovarova_adamson_et al._2017, title={Imaging antiretroviral distribution within gastrointestinal tissues across pre-clinical species: implications for hiv eradication}, volume={101}, number={S1}, journal={Clinical Pharmacology & Therapeutics}, author={Thompson, C. and Rosen, E. P. and Mathews, M. and White, N. and Sykes, C. and Fedoriw, Y. and Charlins, P. and Mulder, L. and Kovarova, M. and Adamson, L. and et al.}, year={2017}, pages={S17–17} }
 @article{bokhart_nazari_garrard_muddiman_2017, title={MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses}, volume={29}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1007/S13361-017-1809-6}, DOI={10.1007/S13361-017-1809-6}, abstractNote={A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.}, number={1}, journal={Journal of The American Society for Mass Spectrometry}, publisher={Springer Science and Business Media LLC}, author={Bokhart, Mark T. and Nazari, Milad and Garrard, Kenneth P. and Muddiman, David C.}, year={2017}, month={Sep}, pages={8–16} }
 @article{zhang_zhang_nazari_bagley_miller_williams_muddiman_lindsey_2017, title={Mass spectrometric detection of chlorophyll a and the tetrapyrrole secondary metabolite tolyporphin A in the filamentous cyanobacterium HT-58-2. Approaches to high-throughput screening of intact cyanobacteria}, volume={21}, ISSN={["1099-1409"]}, DOI={10.1142/s108842461750078x}, abstractNote={ Tolyporphins are unusual tetrapyrrole macrocycles produced by the filamentous cyanobacterium–microbial community HT-58-2, the only known source to date. Numerous cyanobacterial samples have been collected worldwide but most have not been screened for secondary metabolites. Identification of tolyporphins typically has entailed lipophilic extraction followed by chromatographic fractionation and spectroscopic and/or mass spectrometric analysis. For quantitation, lengthy lipophilic extraction, sample processing and HPLC separation are needed. Examination by MALDI-TOF-MS (with the matrix 1,5-diaminonaphthalene) of lipophilic crude extracts of small-scale HT-58-2 samples (2 mL) without chromatographic fractionation enabled semi-quantitation of tolyporphin A over a 41-day growth period. Screening for tolyporphin A in intact or slightly sheared and vortexed HT-58-2 samples (no lipophilic extraction), and confirmation of identity by tandem MS, were carried out by IR-MALDESI-FTMS. Tolyporphin A was identified by the molecular ion and four characteristic fragments. The molecular ion of chlorophyll [Formula: see text] also was observed. The sheared and vortexed sample contained substantial numbers of intact cells as demonstrated by regrowth of the filamentous cyanobacterium–microbial culture. The semi-quantitative and rapid qualitative methods developed herein should facilitate examination of other tolyporphin-producing organisms among the vast worldwide strains of cyanobacteria as well as investigation of the biosynthesis of tolyporphins. }, number={11}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Zhang, Yunlong and Zhang, Ran and Nazari, Milad and Bagley, Michael C. and Miller, Eric S. and Williams, Philip G. and Muddiman, David C. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={759–768} }
 @article{mccord_muddiman_khaledi_2017, title={Perfluorinated alcohol induced coacervates as extraction media for proteomic analysis}, volume={1523}, ISSN={["1873-3778"]}, DOI={10.1016/j.chroma.2017.06.025}, abstractNote={We describe a novel method for using hexafluoroisopropanol (HFIP) induced coacervates with a variety of surfactants to extract proteins from a yeast whole cell lysate and conduct a global proteomic investigation on the extracted proteins. Yeast whole cell lysates were prepared and proteins were extracted using two workflows: 1) Proteins were extracted into the coacervate generated from the mixture of HFIP, surfactant, and cell lysate. 2) Proteins were extracted from cell lysate using a surfactant solution, and HFIP was added to the supernatant to generate a coacervate phase with concentrated proteins. Both initial extractions were followed by a modified filter-aided sample preparation (FASP) cleanup. The methodology yields significant protein concentrations in the coacervate phase (2–3 orders of magnitude increase in concentration) and an increase in proteome sequence coverage (+5%), membrane proteins identifications (+50%), and identification of proteins from low abundance cellular subfractions (>10% of total IDs).}, journal={JOURNAL OF CHROMATOGRAPHY A}, author={McCord, James P. and Muddiman, David C. and Khaledi, Morteza G.}, year={2017}, month={Nov}, pages={293–299} }
 @article{mccord_sun_deutsch_moritz_muddiman_2017, title={The PeptideAtlas of the Domestic Laying Hen}, volume={16}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.6b00952}, abstractNote={Proteomics-based biological research is greatly expanded by high-quality mass spectrometry studies, which are themselves enabled by access to quality mass spectrometry resources, such as high-quality curated proteome data repositories. We present a PeptideAtlas for the domestic chicken, containing an extensive and robust collection of chicken tissue and plasma samples with substantial value for the chicken proteomics community for protein validation and design of downstream targeted proteome quantitation. The chicken PeptideAtlas contains 6646 canonical proteins at a protein FDR of 1.3%, derived from ∼100 000 peptides at a peptide level FDR of 0.1%. The rich collection of readily accessible data is easily mined for the purposes of data validation and experimental planning, particularly in the realm of developing proteome quantitation workflows. Herein we demonstrate the use of the atlas to mine information on common chicken acute-phase proteins and biomarkers for cancer detection research, as well as their localization and polymorphisms. This wealth of information will support future proteome-based research using this highly important agricultural organism in pursuit of both chicken and human health outcomes.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={McCord, James and Sun, Zhi and Deutsch, Eric W. and Moritz, Robert L. and Muddiman, David C.}, year={2017}, month={Mar}, pages={1352–1363} }
 @article{cui_garrigues_gauglitz_hilder_hopfgartner_muddiman_roda_sanz-medel_wise_woolley_et al._2017, title={The scope of Analytical and Bioanalytical Chemistry (ABC)}, volume={410}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/S00216-017-0743-6}, DOI={10.1007/S00216-017-0743-6}, number={3}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Nature}, author={Cui, H. and Garrigues, P. and Gauglitz, G. and Hilder, E. and Hopfgartner, G. and Muddiman, D. C. and Roda, A. and Sanz-Medel, A. and Wise, S. A. and Woolley, A. T. and et al.}, year={2017}, month={Nov}, pages={649–650} }
 @article{hecht_loziuk_muddiman_2017, title={Xylose Migration During Tandem Mass Spectrometry of N-Linked Glycans}, volume={28}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-016-1588-5}, abstractNote={Understanding the rearrangement of gas-phase ions via tandem mass spectrometry is critical to improving manual and automated interpretation of complex datasets. N-glycan analysis may be carried out under collision induced (CID) or higher energy collision dissociation (HCD), which favors cleavage at the glycosidic bond. However, fucose migration has been observed in tandem MS, leading to the formation of new bonds over four saccharide units away. In the following work, we report the second instance of saccharide migration ever to occur for N-glycans. Using horseradish peroxidase as a standard, the beta-1,2 xylose was observed to migrate from a hexose to a glucosamine residue on the (Xyl)Man3GlcNac2 glycan. This investigation was followed up in a complex N-linked glycan mixture derived from stem differentiating xylem tissue, and the rearranged product ion was observed for 75% of the glycans. Rearrangement was not favored in isomeric glycans with a core or antennae fucose and unobserved in glycans predicted to have a permanent core-fucose modification. As the first empirical observation of this rearrangement, this work warrants dissemination so it may be searched in de novo sequencing glycan workflows. Graphical Abstract ᅟ.}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Hecht, Elizabeth S. and Loziuk, Philip L. and Muddiman, David C.}, year={2017}, month={Apr}, pages={729–732} }
 @article{hecht_mccord_muddiman_2016, title={A Quantitative Glycomics and Proteomics Combined Purification Strategy}, volume={3}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/53735}, DOI={10.3791/53735}, abstractNote={There is a growing desire in the biological and clinical sciences to integrate and correlate multiple classes of biomolecules to unravel biology, define pathways, improve treatment, understand disease, and aid biomarker discovery. N-linked glycosylation is one of the most important and robust post-translational modifications on proteins and regulates critical cell functions such as signaling, adhesion, and enzymatic function. Analytical techniques to purify and analyze N-glycans have remained relatively static over the last decade. While accurate and effective, they commonly require significant expertise and resources. Though some high-throughput purification schemes have been developed, they have yet to find widespread adoption and often rely on the enrichment of glycopeptides. One promising method, developed by Thomas-Oates et al., filter aided N-glycan separation (FANGS), was qualitatively demonstrated on tissues. Herein, we adapted FANGS to plasma and coupled it to the individuality normalization when labeling with glycan hydrazide tags strategy in order to achieve accurate relative quantification by liquid chromatography mass spectrometry and enhanced electrospray ionization. Furthermore, we designed new functionality to the protocol by achieving tandem, shotgun proteomics and glycosylation site analysis on hen plasma. We showed that N-glycans purified on filter and derivatized by hydrophobic hydrazide tags were comparable in terms of abundance and class to those by solid phase extraction (SPE); the latter is considered a gold standard in the field. Importantly, the variability in the two protocols was not statistically different. Proteomic data that was collected in-line with glycomic data had the same depth compared to a standard trypsin digest. Peptide deamidation is minimized in the protocol, limiting non-specific deamidation detected at glycosylation motifs. This allowed for direct glycosylation site analysis, though the protocol can accommodate 18O site labeling as well. Overall, we demonstrated a new in-line high-throughput, unbiased, filter based protocol for quantitative glycomics and proteomics analysis.}, number={109}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Hecht, Elizabeth S. and McCord, James P. and Muddiman, David C.}, year={2016}, month={Mar} }
 @article{lin_li_tunlaya-anukit_shi_sun_wang_liu_loziuk_edmunds_miller_et al._2016, title={A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa}, volume={12}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-016-0978-Y}, DOI={10.1007/S11295-016-0978-Y}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Lin, Chien-Yuan and Li, Quanzi and Tunlaya-Anukit, Sermsawat and Shi, Rui and Sun, Ying-Hsuan and Wang, Jack P. and Liu, Jie and Loziuk, Philip and Edmunds, Charles W. and Miller, Zachary D. and et al.}, year={2016}, month={Mar} }
 @article{heaven_flint_randall_sosunov_wilson_barnes_goldman_muddiman_brenner_2016, title={Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease}, volume={15}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.6b00316}, abstractNote={Alexander disease (AxD) is a neurodegenerative disorder characterized by astrocytic protein aggregates called Rosenthal fibers (RFs). We used mouse models of AxD to determine the protein composition of RFs to obtain information about disease mechanisms including the hypothesis that sequestration of proteins in RFs contributes to disease. A method was developed for RF enrichment, and analysis of the resulting fraction using isobaric tags for relative and absolute quantitation mass spectrometry identified 77 proteins not previously associated with RFs. Three of five proteins selected for follow-up were confirmed enriched in the RF fraction by immunobloting of both the AxD mouse models and human patients: receptor for activated protein C kinase 1 (RACK1), G1/S-specific cyclin D2, and ATP-dependent RNA helicase DDX3X. Immunohistochemistry validated cyclin D2 as a new RF component, but results for RACK1 and DDX3X were equivocal. None of these was decreased in the non-RF fractions compared to controls. A similar result was obtained for the previously known RF component, alphaB-crystallin, which had been a candidate for sequestration. Thus, no support was obtained for the sequestration hypothesis for AxD. Providing possible insight into disease progression, the association of several of the RF proteins with stress granules suggests a role for stress granules in the origin of RFs.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Heaven, Michael R. and Flint, Daniel and Randall, Shan M. and Sosunov, Alexander A. and Wilson, Landon and Barnes, Stephen and Goldman, James E. and Muddiman, David C. and Brenner, Michael}, year={2016}, month={Jul}, pages={2265–2282} }
 @article{ekelöf_mcmurtrie_nazari_johanningsmeier_muddiman_2016, title={Direct Analysis of Triterpenes from High-Salt Fermented Cucumbers Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI)}, volume={28}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1007/S13361-016-1541-7}, DOI={10.1007/S13361-016-1541-7}, abstractNote={High-salt samples present a challenge to mass spectrometry (MS) analysis, particularly when electrospray ionization (ESI) is used, requiring extensive sample preparation steps such as desalting, extraction, and purification. In this study, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) coupled to a Q Exactive Plus mass spectrometer was used to directly analyze 50-μm thick slices of cucumber fermented and stored in 1 M sodium chloride brine. From the several hundred unique substances observed, three triterpenoid lipids produced by cucumbers, β-sitosterol, stigmasterol, and lupeol, were putatively identified based on exact mass and selected for structural analysis. The spatial distribution of the lipids were imaged, and the putative assignments were confirmed by tandem mass spectrometry performed directly on the same cucumber, demonstrating the capacity of the technique to deliver confident identifications from highly complex samples in molar concentrations of salt without the need for sample preparation.}, number={2}, journal={Journal of The American Society for Mass Spectrometry}, publisher={Springer Science and Business Media LLC}, author={Ekelöf, Måns and McMurtrie, Erin K. and Nazari, Milad and Johanningsmeier, Suzanne D. and Muddiman, David C.}, year={2016}, month={Nov}, pages={370–375} }
 @article{nazari_muddiman_2016, title={Enhanced Lipidome Coverage in Shotgun Analyses by using Gas-Phase Fractionation}, volume={27}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-016-1446-5}, abstractNote={A high resolving power shotgun lipidomics strategy using gas-phase fractionation and data-dependent acquisition (DDA) was applied toward comprehensive characterization of lipids in a hen ovarian tissue in an untargeted fashion. Using this approach, a total of 822 unique lipids across a diverse range of lipid categories and classes were identified based on their MS/MS fragmentation patterns. Classes of glycerophospholipids and glycerolipids, such as glycerophosphocholines (PC), glycerophosphoethanolamines (PE), and triglycerides (TG), are often the most abundant peaks observed in shotgun lipidomics analyses. These ions suppress the signal from low abundance ions and hinder the chances of characterizing low abundant lipids when DDA is used. These issues were circumvented by utilizing gas-phase fractionation, where DDA was performed on narrow m/z ranges instead of a broad m/z range. Employing gas-phase fractionation resulted in an increase in sensitivity by more than an order of magnitude in both positive- and negative-ion modes. Furthermore, the enhanced sensitivity increased the number of lipids identified by a factor of ≈4, and facilitated identification of low abundant lipids from classes such as cardiolipins that are often difficult to observe in untargeted shotgun analyses and require sample-specific preparation steps prior to analysis. This method serves as a resource for comprehensive profiling of lipids from many different categories and classes in an untargeted manner, as well as for targeted and quantitative analyses of individual lipids. Furthermore, this comprehensive analysis of the lipidome can serve as a species- and tissue-specific database for confident identification of other MS-based datasets, such as mass spectrometry imaging.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Nazari, Milad and Muddiman, David C.}, year={2016}, month={Nov}, pages={1735–1744} }
 @article{parker_oh_moazami_pierce_loziuk_dean_muddiman_2016, title={Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein}, volume={512}, ISSN={["1096-0309"]}, DOI={10.1016/j.ab.2016.08.017}, abstractNote={Ubiquitination is a dynamic process that is responsible for regulation of cellular responses to stimuli in a number of biological systems. Previous efforts to study this post-translational modification have focused on protein enrichment; however, recent research utilizes the presence of the di-glycine (Gly-Gly) remnants following trypsin digestion to immuno-enrich ubiquitinated peptides. Monoclonal antibodies developed to the cleaved ubiquitin modification epitope, (tert-butoxycarbonyl) glycylglycine (Boc-Gly-Gly-NHS)1, are used to identify the Gly-Gly signature. Here, we have successfully generated the Boc-Gly-Gly-NHS modification and showed that when conjugated to a lysine containing protein, such as lysozyme, it can be applied as a standard protein to examine ubiquitinated peptide enrichment within a complex background.}, journal={ANALYTICAL BIOCHEMISTRY}, author={Parker, J. and Oh, Y. and Moazami, Y. and Pierce, J. G. and Loziuk, P. L. and Dean, R. A. and Muddiman, D. C.}, year={2016}, month={Nov}, pages={114–119} }
 @article{sarkar_mischler_randall_collier_dorman_boggess_muddiman_rao_2016, title={Identification of Epigenetic Factor Proteins Expressed in Human Embryonic Stem Cell-Derived Trophoblasts and in Human Placental Trophoblasts}, volume={15}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.5b01118}, abstractNote={Human embryonic stem cells (hESCs) have been used to derive trophoblasts through differentiation in vitro. Intriguingly, mouse ESCs are prevented from differentiation to trophoblasts by certain epigenetic factor proteins such as Dnmt1, thus necessitating the study of epigenetic factor proteins during hESC differentiation to trophoblasts. We used stable isotope labeling by amino acids in cell culture and quantitative proteomics to study changes in the nuclear proteome during hESC differentiation to trophoblasts and identified changes in the expression of 30 epigenetic factor proteins. Importantly, the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B were downregulated. Additionally, we hypothesized that nuclear proteomics of hESC-derived trophoblasts may be used for screening epigenetic factor proteins expressed by primary trophoblasts in human placental tissue. Accordingly, we conducted immunohistochemistry analysis of six epigenetic factor proteins identified from hESC-derived trophoblasts-DNMT1, DNMT3B, BAF155, BAF60A, BAF57, and ING5-in 6-9 week human placentas. Indeed, expression of these proteins was largely, though not fully, consistent with that observed in 6-9 week placental trophoblasts. Our results support the use of hESC-derived trophoblasts as a model for placental trophoblasts, which will enable further investigation of epigenetic factors involved in human trophoblast development.}, number={8}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Sarkar, Prasenjit and Mischler, Adam and Randall, Shan M. and Collier, Timothy S. and Dorman, Karen F. and Boggess, Kim A. and Muddiman, David C. and Rao, Balaji M.}, year={2016}, month={Aug}, pages={2433–2444} }
 @misc{bokhart_muddiman_2016, title={Infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging analysis of biospecimens}, volume={141}, ISSN={["1364-5528"]}, DOI={10.1039/c6an01189f}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging (MSI) is a versatile imaging technique capable of in-depth analysis for a wide variety of biospecimens.}, number={18}, journal={ANALYST}, author={Bokhart, M. T. and Muddiman, D. C.}, year={2016}, pages={5236–5245} }
 @inbook{nazari_muddiman_2016, title={MALDESI: Fundamentals, Direct Analysis, and MS Imaging}, ISBN={9783319048185 9783319048192}, url={http://dx.doi.org/10.1007/978-3-319-04819-2_9}, DOI={10.1007/978-3-319-04819-2_9}, booktitle={Advances in MALDI and Laser-Induced Soft Ionization Mass Spectrometry}, publisher={Springer International Publishing}, author={Nazari, Milad and Muddiman, David C.}, year={2016}, pages={169–182} }
 @article{loziuk_hecht_muddiman_2017, title={N-linked glycosite profiling and use of Skyline as a platform for characterization and relative quantification of glycans in differentiating xylem of Populus trichocarpa}, volume={409}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-016-9776-5}, abstractNote={Our greater understanding of the importance of N-linked glycosylation in biological systems has spawned the field of glycomics and development of analytical tools to address the many challenges regarding our ability to characterize and quantify this complex and important modification as it relates to biological function. One of the unmet needs of the field remains a systematic method for characterization of glycans in new biological systems. This study presents a novel workflow for identification of glycans using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT™) strategy developed in our lab. This consists of monoisotopic mass extraction followed by peak pair identification of tagged glycans from a theoretical library using an in-house program. Identification and relative quantification could then be performed using the freely available bioinformatics tool Skyline. These studies were performed in the biological context of studying the N-linked glycome of differentiating xylem of the poplar tree, a widely studied model woody plant, particularly with respect to understanding lignin biosynthesis during wood formation. Through our workflow, we were able to identify 502 glycosylated proteins including 12 monolignol enzymes and 1 peroxidase (PO) through deamidation glycosite analysis. Finally, our novel semi-automated workflow allowed for rapid identification of 27 glycans by intact mass and by NAT/SIL peak pairing from a library containing 1573 potential glycans, eliminating the need for extensive manual analysis. Implementing Skyline for relative glycan quantification allowed for improved accuracy and precision of quantitative measurements over current processing tools which we attribute to superior algorithms correction for baseline variation and MS1 peak filtering.}, number={2}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Loziuk, Philip L. and Hecht, Elizabeth S. and Muddiman, David C.}, year={2017}, month={Jan}, pages={487–497} }
 @misc{hecht_oberg_muddiman_2016, title={Optimizing Mass Spectrometry Analyses: A Tailored Review on the Utility of Design of Experiments}, volume={27}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-016-1344-x}, abstractNote={Mass spectrometry (MS) has emerged as a tool that can analyze nearly all classes of molecules, with its scope rapidly expanding in the areas of post-translational modifications, MS instrumentation, and many others. Yet integration of novel analyte preparatory and purification methods with existing or novel mass spectrometers can introduce new challenges for MS sensitivity. The mechanisms that govern detection by MS are particularly complex and interdependent, including ionization efficiency, ion suppression, and transmission. Performance of both off-line and MS methods can be optimized separately or, when appropriate, simultaneously through statistical designs, broadly referred to as "design of experiments" (DOE). The following review provides a tutorial-like guide into the selection of DOE for MS experiments, the practices for modeling and optimization of response variables, and the available software tools that support DOE implementation in any laboratory. This review comes 3 years after the latest DOE review (Hibbert DB, 2012), which provided a comprehensive overview on the types of designs available and their statistical construction. Since that time, new classes of DOE, such as the definitive screening design, have emerged and new calls have been made for mass spectrometrists to adopt the practice. Rather than exhaustively cover all possible designs, we have highlighted the three most practical DOE classes available to mass spectrometrists. This review further differentiates itself by providing expert recommendations for experimental setup and defining DOE entirely in the context of three case-studies that highlight the utility of different designs to achieve different goals. A step-by-step tutorial is also provided.}, number={5}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Hecht, Elizabeth S. and Oberg, Ann L. and Muddiman, David C.}, year={2016}, month={May}, pages={767–785} }
 @article{nazari_muddiman_2016, title={Polarity switching mass spectrometry imaging of healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={141}, ISSN={["1364-5528"]}, DOI={10.1039/c5an01513h}, abstractNote={IR-MALDESI polarity switching mass spectrometry imaging reveals differences in lipid distribution in hen ovarian cancer tissue.}, number={2}, journal={ANALYST}, author={Nazari, Milad and Muddiman, David C.}, year={2016}, pages={595–605} }
 @article{mechref_muddiman_2017, title={Recent advances in glycomics, glycoproteomics and allied topics}, volume={409}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-016-0093-9}, abstractNote={Published in the topical collection Glycomics, Glycoproteomics and Allied Topics with guest editors Yehia Mechref and David Muddiman.}, number={2}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Mechref, Yehia and Muddiman, David C.}, year={2017}, month={Jan}, pages={355–357} }
 @article{loziuk_meier_johnson_ghashghaei_muddiman_2016, title={TransOmic analysis of forebrain sections in Sp2 conditional knockout embryonic mice using IR-MALDESI imaging of lipids and LC-MS/MS label-free proteomics}, volume={408}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/s00216-016-9421-3}, DOI={10.1007/s00216-016-9421-3}, abstractNote={Quantitative methods for detection of biological molecules are needed more than ever before in the emerging age of "omics" and "big data." Here, we provide an integrated approach for systematic analysis of the "lipidome" in tissue. To test our approach in a biological context, we utilized brain tissue selectively deficient for the transcription factor Specificity Protein 2 (Sp2). Conditional deletion of Sp2 in the mouse cerebral cortex results in developmental deficiencies including disruption of lipid metabolism. Silver (Ag) cationization was implemented for infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) to enhance the ion abundances for olefinic lipids, as these have been linked to regulation by Sp2. Combining Ag-doped and conventional IR-MALDESI imaging, this approach was extended to IR-MALDESI imaging of embryonic mouse brains. Further, our imaging technique was combined with bottom-up shotgun proteomic LC-MS/MS analysis and western blot for comparing Sp2 conditional knockout (Sp2-cKO) and wild-type (WT) cortices of tissue sections. This provided an integrated omics dataset which revealed many specific changes to fundamental cellular processes and biosynthetic pathways. In particular, step-specific altered abundances of nucleotides, lipids, and associated proteins were observed in the cerebral cortices of Sp2-cKO embryos.}, number={13}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Loziuk, Philip and Meier, Florian and Johnson, Caroline and Ghashghaei, H. Troy and Muddiman, David C.}, year={2016}, month={Mar}, pages={3453–3474} }
 @article{kazarian_rodriguez_deverell_mccord_muddiman_paull_2016, title={Wall modified photonic crystal fibre capillaries as porous layer open tubular columns for in-capillary micro-extraction and capillary chromatography}, volume={905}, ISSN={["1873-4324"]}, DOI={10.1016/j.aca.2015.10.005}, abstractNote={Wall modified photonic crystal fibre capillary columns for in-capillary micro-extraction and liquid chromatographic separations is presented. Columns contained 126 internal parallel 4 μm channels, each containing a wall bonded porous monolithic type polystyrene-divinylbenzene layer in open tubular column format (PLOT). Modification longitudinal homogeneity was monitored using scanning contactless conductivity detection and scanning electron microscopy. The multichannel open tubular capillary column showed channel diameter and polymer layer consistency of 4.2 ± 0.1 μm and 0.26 ± 0.02 μm respectively, and modification of 100% of the parallel channels with the monolithic polymer. The modified multi-channel capillaries were applied to the in-capillary micro-extraction of water samples. 500 μL of water samples containing single μg L−1 levels of polyaromatic hydrocarbons were extracted at a flow rate of 10 μL min−1, and eluted in 50 μL of acetonitrile for analysis using HPLC with fluorescence detection. HPLC LODs were 0.08, 0.02 and 0.05 μg L−1 for acenaphthene, anthracene and pyrene, respectively, with extraction recoveries of between 77 and 103%. The modified capillaries were also investigated briefly for direct application to liquid chromatographic separations, with the retention and elution of a standard protein (cytochrome c) under isocratic conditions demonstrated, proving chromatographic potential of the new column format, with run-to-run retention time reproducibility of below 1%.}, journal={ANALYTICA CHIMICA ACTA}, author={Kazarian, Artaches A. and Rodriguez, Estrella Sanz and Deverell, Jeremy A. and McCord, James and Muddiman, David C. and Paull, Brett}, year={2016}, month={Jan}, pages={1–7} }
 @article{nazari_bokhart_muddiman_2016, title={Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization (IR-MALDESI)}, volume={3}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/53942}, DOI={10.3791/53942}, abstractNote={Ambient ionization sources for mass spectrometry (MS) have been the subject of much interest in the past decade. Matrix-assisted laser desorption electrospray ionization (MALDESI) is an example of such methods, where features of matrix-assisted laser desorption/ionization (MALDI) (e.g., pulsed nature of desorption) and electrospray ionization (ESI) (e.g., soft-ionization) are combined. One of the major advantages of MALDESI is its inherent versatility. In MALDESI experiments, an ultraviolet (UV) or infrared (IR) laser can be used to resonantly excite an endogenous or exogenous matrix. The choice of matrix is not analyte dependent, and depends solely on the laser wavelength used for excitation. In IR-MALDESI experiments, a thin layer of ice is deposited on the sample surface as an energy-absorbing matrix. The IR-MALDESI source geometry has been optimized using statistical design of experiments (DOE) for analysis of liquid samples as well as biological tissue specimens. Furthermore, a robust IR-MALDESI imaging source has been developed, where a tunable mid-IR laser is synchronized with a computer controlled XY translational stage and a high resolving power mass spectrometer. A custom graphical user interface (GUI) allows user selection of the repetition rate of the laser, number of shots per voxel, step-size of the sample stage, and the delay between the desorption and scan events for the source. IR-MALDESI has been used in variety of applications such as forensic analysis of fibers and dyes and MSI of biological tissue sections. Distribution of different analytes ranging from endogenous metabolites to exogenous xenobiotics within tissue sections can be measured and quantified using this technique. The protocol presented in this manuscript describes major steps necessary for IR-MALDESI MSI of whole-body tissue sections.}, number={109}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Nazari, Milad and Bokhart, Mark T. and Muddiman, David C.}, year={2016}, month={Mar} }
 @article{lin_wang_li_chen_liu_loziuk_song_williams_muddiman_sederoff_et al._2015, title={4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa}, volume={8}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925201417&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2014.12.003}, abstractNote={Downregulation of 4-coumaric acid:coenzyme A ligase (4CL) can reduce lignin content in a number of plant species. In lignin precursor (monolignol) biosynthesis during stem wood formation in Populus trichocarpa, two enzymes, Ptr4CL3 and Ptr4CL5, catalyze the coenzyme A (CoA) ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. CoA ligation of 4-coumaric acid is essential for the 3-hydroxylation of 4-coumaroyl shikimic acid. This hydroxylation results from sequential reactions of 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) and 4-coumaric acid 3-hydroxylase 3 (PtrC3H3). Alternatively, 3-hydroxylation of 4-coumaric acid to caffeic acid may occur through an enzyme complex of cinnamic acid 4-hydroxylase 1 and 2 (PtrC4H1 and PtrC4H2) and PtrC3H3. We found that 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr4CL5. 4-Coumaroyl shikimic acid strongly inhibits the formation of 4-coumaroyl-CoA and caffeoyl-CoA. Caffeoyl shikimic acid inhibits only the formation of 4-coumaroyl-CoA. 4-Coumaroyl and caffeoyl shikimic acids both act as competitive and uncompetitive inhibitors. Metabolic flux in wild-type and PtrC3H3 downregulated P. trichocarpa transgenics has been estimated by absolute protein and metabolite quantification based on liquid chromatography–tandem mass spectrometry, mass action kinetics, and inhibition equations. Inhibition by 4-coumaroyl and caffeoyl shikimic acids may play significant regulatory roles when these inhibitors accumulate.}, number={1}, journal={MOLECULAR PLANT}, author={Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Chen, Hsi-Chuan and Liu, Jie and Loziuk, Philip and Song, Jina and Williams, Cranos and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2015}, month={Jan}, pages={176–187} }
 @article{sarkar_randall_collier_nero_russell_muddiman_rao_2015, title={Activin/Nodal Signaling Switches the Terminal Fate of Human Embryonic Stem Cell-derived Trophoblasts}, volume={290}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m114.620641}, abstractNote={Background: Specification of terminal fate in trophoblasts derived from human embryonic stem cells is not understood. Results: Inhibition of activin/nodal signaling triggers extravillous fate, but loss of inhibition causes syncytial fate. Conclusion: Activin/nodal signaling switches the terminal fate of trophoblasts. Significance: We provide a model system that allows for targeted derivation of extravillous trophoblasts and syncytiotrophoblasts. Human embryonic stem cells (hESCs) have been routinely treated with bone morphogenetic protein and/or inhibitors of activin/nodal signaling to obtain cells that express trophoblast markers. Trophoblasts can terminally differentiate to either extravillous trophoblasts or syncytiotrophoblasts. The signaling pathways that govern the terminal fate of these trophoblasts are not understood. We show that activin/nodal signaling switches the terminal fate of these hESC-derived trophoblasts. Inhibition of activin/nodal signaling leads to formation of extravillous trophoblast, whereas loss of activin/nodal inhibition leads to the formation of syncytiotrophoblasts. Also, the ability of hESCs to form bona fide trophoblasts has been intensely debated. We have examined hESC-derived trophoblasts in the light of stringent criteria that were proposed recently, such as hypomethylation of the ELF5-2b promoter region and down-regulation of HLA class I antigens. We report that trophoblasts that possess these properties can indeed be obtained from hESCs.}, number={14}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Sarkar, Prasenjit and Randall, Shan M. and Collier, Timothy S. and Nero, Anthony and Russell, Teal A. and Muddiman, David C. and Rao, Balaji M.}, year={2015}, month={Apr}, pages={8834–8848} }
 @article{rosen_thompson_bokhart_prince_sykes_muddiman_kashuba_2016, title={Analysis of Antiretrovirals in Single Hair Strands for Evaluation of Drug Adherence with Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry Imaging}, volume={88}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.5b03794}, abstractNote={Adherence to a drug regimen can be a strong predictor of health outcomes, and validated measures of adherence are necessary at all stages of therapy from drug development to prescription. Many of the existing metrics of drug adherence (e.g., self-report, pill counts, blood monitoring) have limitations, and analysis of hair strands has recently emerged as an objective alternative. Traditional methods of hair analysis based on LC-MS/MS (segmenting strands at ≥1 cm length) are not capable of preserving a temporal record of drug intake at higher resolution than approximately 1 month. Here, we evaluated the detectability of HIV antiretrovirals (ARVs) in hair from a range of drug classes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging (MSI) with 100 μm resolution. Infrared laser desorption of hair strands was shown to penetrate into the strand cortex, allowing direct measurement by MSI without analyte extraction. Using optimized desorption conditions, a linear correlation between IR-MALDESI ion abundance and LC-MS/MS response was observed for six common ARVs with estimated limits of detection less than or equal to 1.6 ng/mg hair. The distribution of efavirenz (EFV) was then monitored in a series of hair strands collected from HIV infected, virologically suppressed patients. Because of the role hair melanin plays in accumulation of basic drugs (like most ARVs), an MSI method to quantify the melanin biomarker pyrrole-2,3,5-tricarboxylic acid (PTCA) was evaluated as a means of normalizing drug response between patients to develop broadly applicable adherence criteria.}, number={2}, journal={ANALYTICAL CHEMISTRY}, author={Rosen, Elias P. and Thompson, Corbin G. and Bokhart, Mark T. and Prince, Heather M. A. and Sykes, Craig and Muddiman, David C. and Kashuba, Angela D. M.}, year={2016}, month={Jan}, pages={1336–1344} }
 @article{barry_groseclose_robichaud_castellino_muddiman_2015, title={Assessing drug and metabolite detection in liver tissue by UV-MALDI and IR-MALDESI mass spectrometry imaging coupled to FT-ICR MS}, volume={377}, ISSN={["1873-2798"]}, DOI={10.1016/j.ijms.2014.05.012}, abstractNote={Determining the distribution of a drug and its metabolites within tissue is a key facet of evaluating drug candidates. Drug distribution can have a significant implication in appraising drug efficacy and potential toxicity. The specificity and sensitivity of mass spectrometry imaging (MSI) make it a perfect complement to the analysis of drug distributions in tissue. The detection of lapatinib as well as several of its metabolites in liver tissue was determined by MSI using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) coupled to high resolving power Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. IR-MALDESI required minimal sample preparation while maintaining high sensitivity. The effect of the electrospray solvent composition on IR-MALDESI MSI signal from tissue analysis was investigated and an empirical comparison of IR-MALDESI and UV-MALDI for MSI analysis is also presented.}, journal={INTERNATIONAL JOURNAL OF MASS SPECTROMETRY}, author={Barry, Jeremy A. and Groseclose, M. Reid and Robichaud, Guillaume and Castellino, Stephen and Muddiman, David C.}, year={2015}, month={Feb}, pages={448–455} }
 @article{hecht_mccord_muddiman_2015, title={Definitive Screening Design Optimization of Mass Spectrometry Parameters for Sensitive Comparison of Filter and Solid Phase Extraction Purified, INLIGHT Plasma N-Glycans}, volume={87}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.5b01609}, abstractNote={High-throughput, quantitative processing of N-linked glycans would facilitate large-scale studies correlating the glycome with disease and open the field to basic and applied researchers. We sought to meet these goals by coupling filter-aided-N-glycan separation (FANGS) to the individuality normalization when labeling with glycan hydrazide tags (INLIGHT) for analysis of plasma. A quantitative comparison of this method was conducted against solid phase extraction (SPE), a ubiquitous and trusted method for glycan purification. We demonstrate that FANGS-INLIGHT purification was not significantly different from SPE in terms of glycan abundances, variability, functional classes, or molecular weight distributions. Furthermore, to increase the depth of glycome coverage, we executed a definitive screening design of experiments (DOE) to optimize the MS parameters for glycan analyses. We optimized MS parameters across five N-glycan responses using a standard glycan mixture, translated these to plasma and achieved up to a 3-fold increase in ion abundances.}, number={14}, journal={ANALYTICAL CHEMISTRY}, author={Hecht, Elizabeth S. and McCord, James P. and Muddiman, David C.}, year={2015}, month={Jul}, pages={7305–7312} }
 @article{loziuk_parker_li_lin_wang_li_sederoff_chiang_muddiman_2015, title={Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa}, volume={14}, ISSN={["1535-3907"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84942916917&partnerID=MN8TOARS}, DOI={10.1021/acs.jproteome.5b00233}, abstractNote={Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa.}, number={10}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Loziuk, Philip L. and Parker, Jennifer and Li, Wei and Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2015}, month={Oct}, pages={4158–4168} }
 @article{nepomuceno_muddiman_petitte_2015, title={Global Proteomic Analysis of Functional Compartments in Immature Avian Follicles Using Laser Microdissection Coupled to LC-MS/MS}, volume={14}, ISSN={["1535-3907"]}, url={http://europepmc.org/abstract/med/26211554}, DOI={10.1021/acs.jproteome.5b00346}, abstractNote={Laser microdissection (LMD) was utilized for the separation of the yolk, follicular wall (granulosa and theca), and surrounding stromal cells of small white follicles (SWF) obtained from reproductively active domestic fowl. Herein, we provide an in situ proteomics-based approach to studying follicular development through the use of LMD and mass spectrometry. This study resulted in a total of 2889 proteins identified from the three specific isolated compartments. White yolk from the smallest avian follicles resulted in the identification of 1984 proteins, while isolated follicular wall and ovarian stroma yielded 2470 and 2456 proteins, respectively. GO annotations highlighted the functional differences between the compartments. Among the three compartments examined, the relative abundance of vitellogenins, steroidogenic enzymes, anti-Mullerian hormone, transcription factors, and proteins involved in retinoic acid receptors/retinoic acid synthesis, transcription factors, and cell surface receptors such as EGFR and their associated signaling pathways reflected known cellular function of the ovary. This study has provided a global proteome for SWF, white yolk, and ovarian stroma of the avian ovary that can be used as a baseline for future studies and verifies that the coupling of LMD with proteomic analysis can be used to evaluate proteins from small, physiologically functional compartments of complex tissue.}, number={9}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Nepomuceno, Angelito I. and Muddiman, David C. and Petitte, James N.}, year={2015}, month={Sep}, pages={3912–3923} }
 @article{nepomuceno_shao_jing_ma_petitte_idowu_muddiman_fang_hawkridge_2015, title={In-depth LC-MS/MS analysis of the chicken ovarian cancer proteome reveals conserved and novel differentially regulated proteins in humans}, volume={407}, ISSN={["1618-2650"]}, url={http://europepmc.org/abstract/med/26159569}, DOI={10.1007/s00216-015-8862-4}, abstractNote={Ovarian cancer (OVC) remains the most lethal gynecological malignancy in the world due to the combined lack of early-stage diagnostics and effective therapeutic strategies. The development and application of advanced proteomics technology and new experimental models has created unique opportunities for translational studies. In this study, we investigated the ovarian cancer proteome of the chicken, an emerging experimental model of OVC that develops ovarian tumors spontaneously. Matched plasma, ovary, and oviduct tissue biospecimens derived from healthy, early-stage OVC, and late-stage OVC birds were quantitatively characterized by label-free proteomics. Over 2600 proteins were identified in this study, 348 of which were differentially expressed by more than twofold (p ≤ 0.05) in early- and late-stage ovarian tumor tissue specimens relative to healthy ovarian tissues. Several of the 348 proteins are known to be differentially regulated in human cancers including B2M, CLDN3, EPCAM, PIGR, S100A6, S100A9, S100A11, and TPD52. Of particular interest was ovostatin 2 (OVOS2), a novel 165-kDa protease inhibitor found to be strongly upregulated in chicken ovarian tumors (p = 0.0005) and matched plasma (p = 0.003). Indeed, RT-quantitative PCR and Western blot analysis demonstrated that OVOS2 mRNA and protein were also upregulated in multiple human OVC cell lines compared to normal ovarian epithelia (NOE) cells and immunohistochemical staining confirmed overexpression of OVOS2 in primary human ovarian cancers relative to non-cancerous tissues. Collectively, these data provide the first evidence for involvement of OVOS2 in the pathogenesis of both chicken and human ovarian cancer.}, number={22}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Nepomuceno, Angelito I. and Shao, Huanjie and Jing, Kai and Ma, Yibao and Petitte, James N. and Idowu, Michael O. and Muddiman, David C. and Fang, Xianjun and Hawkridge, Adam M.}, year={2015}, month={Sep}, pages={6851–6863} }
 @article{rosen_bokhart_nazari_muddiman_2015, title={Influence of C-Trap Ion Accumulation Time on the Detectability of Analytes in IR-MALDESI MSI}, volume={87}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.5b02641}, abstractNote={Laser desorption followed by post electrospray ionization requires synchronized timing of the key events (sample desorption/ionization, mass spectrometry analysis, and sample translation) necessary to conduct mass spectrometry imaging (MSI) with adequate analyte sensitivity. In infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI analyses, two laser pulses are used for analysis at each volumetric element, or voxel, of a biological sample and ion accumulation in the C-trap exceeding 100 ms is necessary to capture all sample-associated ions using an infrared laser with a 20 Hz repetition rate. When coupled to an Orbitrap-based mass spectrometer like the Q Exactive Plus, this time window for ion accumulation exceeds dynamically controlled trapping of samples with comparable ion flux by Automatic Gain Control (AGC), which cannot be used during MSI analysis. In this work, a next-generation IR-MALDESI source has been designed and constructed that incorporates a mid-infrared OPO laser capable of operating at 100 Hz and allows requisite C-trap inject time during MSI to be reduced to 30 ms. Analyte detectability of the next-generation IR-MALDESI integrated source has been evaluated as a function of laser repetition rate (100-20 Hz) with corresponding C-trap ion accumulation times (30-110 ms) in both untargeted and targeted analysis of biological samples. Reducing the C-trap ion accumulation time resulted in increased ion abundance by up to 3 orders of magnitude for analytes ranging from xenobiotics to endogenous lipids, and facilitated the reduction of voxel-to-voxel variability by more than 3-fold.}, number={20}, journal={ANALYTICAL CHEMISTRY}, author={Rosen, Elias P. and Bokhart, Mark T. and Nazari, Milad and Muddiman, David C.}, year={2015}, month={Oct}, pages={10483–10490} }
 @article{rosen_bokhart_ghashghaei_muddiman_2015, title={Influence of Desorption Conditions on Analyte Sensitivity and Internal Energy in Discrete Tissue or Whole Body Imaging by IR-MALDESI}, volume={26}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1007/s13361-015-1114-1}, DOI={10.1007/s13361-015-1114-1}, abstractNote={Analyte signal in a laser desorption/postionization scheme such as infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is strongly coupled to the degree of overlap between the desorbed plume of neutral material from a sample and an orthogonal electrospray. In this work, we systematically examine the effect of desorption conditions on IR-MALDESI response to pharmaceutical drugs and endogenous lipids in biological tissue using a design of experiments approach. Optimized desorption conditions have then been used to conduct an untargeted lipidomic analysis of whole body sagittal sections of neonate mouse. IR-MALDESI response to a wide range of lipid classes has been demonstrated, with enhanced lipid coverage received by varying the laser wavelength used for mass spectrometry imaging (MSI). Targeted MS(2) imaging (MS(2)I) of an analyte, cocaine, deposited beneath whole body sections allowed determination of tissue-specific ion response factors, and CID fragments of cocaine were monitored to comment on wavelength-dependent internal energy deposition based on the "survival yield" method.}, number={6}, journal={Journal of The American Society for Mass Spectrometry}, publisher={Springer Science and Business Media LLC}, author={Rosen, Elias P. and Bokhart, Mark T. and Ghashghaei, H. Troy and Muddiman, David C.}, year={2015}, month={Apr}, pages={899–910} }
 @article{schilling_nepomuceno_planchart_yoder_kelly_muddiman_daniels_hiramatsu_reading_2015, title={Machine learning reveals sex-specific 17β-estradiol-responsive expression patterns in white perch (Morone americana) plasma proteins}, volume={15}, ISSN={1615-9853}, url={http://dx.doi.org/10.1002/pmic.201400606}, DOI={10.1002/pmic.201400606}, abstractNote={With growing abundance and awareness of endocrine disrupting compounds (EDCs) in the environment, there is a need for accurate and reliable detection of EDC exposure. Our objective in the present study was to observe differences within and between the global plasma proteomes of sexually mature male and female white perch (Morone americana) before (Initial Control, IC) and after 17β‐estradiol (E2) induction. Semiquantitative nanoLC‐MS/MS data were analyzed by machine learning support vector machines (SVMs) and by two‐way ANOVA. By ANOVA, the expression levels of 44, 77, and 57 proteins varied significantly by gender, treatment, and the interaction of gender and treatment, respectively. SVMs perfectly classified male and female perch IC and E2‐induced plasma samples using the protein expression data. E2‐induced male and female perch plasma proteomes contained significantly higher levels of the yolk precursors vitellogenin Aa and Ab (VtgAa, VtgAb), as well as latrophilin and seven transmembrane domain‐containing protein 1 (Eltd1) and kininogen 1 (Kng1). This is the first report that Eltd1 and Kng1 may be E2‐responsive proteins in fishes and therefore may be useful indicators of estrogen induction.}, number={15}, journal={PROTEOMICS}, publisher={Wiley}, author={Schilling, Justin and Nepomuceno, Angelito I. and Planchart, Antonio and Yoder, Jeffrey A. and Kelly, Robert M. and Muddiman, David C. and Daniels, Harry V. and Hiramatsu, Naoshi and Reading, Benjamin J.}, year={2015}, month={Jun}, pages={2678–2690} }
 @article{thompson_bokhart_sykes_adamson_fedoriw_luciw_muddiman_kashuba_rosen_2015, title={Mass Spectrometry Imaging Reveals Heterogeneous Efavirenz Distribution within Putative HIV Reservoirs}, volume={59}, ISSN={["1098-6596"]}, DOI={10.1128/aac.04952-14}, abstractNote={ABSTRACT
          Persistent HIV replication within active viral reservoirs may be caused by inadequate antiretroviral penetration. Here, we used mass spectrometry imaging with infrared matrix-assisted laser desorption–electrospray ionization to quantify the distribution of efavirenz within tissues from a macaque dosed orally to a steady state. Intratissue efavirenz distribution was heterogeneous, with the drug concentrating in the lamina propria of the colon, the primary follicles of lymph nodes, and the brain gray matter. These are the first imaging data of an antiretroviral drug in active viral reservoirs.}, number={5}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Thompson, Corbin G. and Bokhart, Mark T. and Sykes, Craig and Adamson, Lourdes and Fedoriw, Yuri and Luciw, Paul A. and Muddiman, David C. and Kashuba, Angela D. M. and Rosen, Elias P.}, year={2015}, month={May}, pages={2944–2948} }
 @article{schilling_loziuk_muddiman_daniels_reading_2015, title={Mechanisms of Egg Yolk Formation and Implications on Early Life History of White Perch (Morone americana)}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0143225}, abstractNote={The three white perch (Morone americana) vitellogenins (VtgAa, VtgAb, VtgC) were quantified accurately and precisely in the liver, plasma, and ovary during pre-, early-, mid-, and post-vitellogenic oocyte growth using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Western blotting generally mirrored the PC-IDMS results. By PC-IDMS, VtgC was quantifiable in pre-vitellogenic ovary tissues and VtgAb was quantifiable in pre-vitellogenic liver tissues however, neither protein was detected by western blotting in these respective tissues at this time point. Immunohistochemistry indicated that VtgC was present within pre-vitellogenic oocytes and localized to lipid droplets within vitellogenic oocytes. Affinity purification coupled to tandem mass spectrometry using highly purified VtgC as a bait protein revealed a single specific interacting protein (Y-box binding protein 2a-like [Ybx2a-like]) that eluted with suramin buffer and confirmed that VtgC does not bind the ovary vitellogenin receptors (LR8 and Lrp13). Western blotting for LR8 and Lrp13 showed that both receptors were expressed during vitellogenesis with LR8 and Lrp13 expression highest in early- and mid-vitellogenesis, respectively. The VtgAa within the ovary peaked during post-vitellogenesis, while VtgAb peaked during early-vitellogenesis in both white perch and the closely related striped bass (M. saxatilis). The VtgC was steadily accumulated by oocytes beginning during pre-vitellogenesis and continued until post-vitellogenesis and its composition varies widely between striped bass and white perch. In striped bass, the VtgC accounted for 26% of the vitellogenin-derived egg yolk, however in the white perch it comprised only 4%. Striped bass larvae have an extended developmental window and these larvae have yolk stores that may enable them to survive in the absence of food for twice as long as white perch after hatch. Thus, the VtgC may play an integral role in providing nutrients to late stage fish larvae prior to the onset of exogenous feeding and its composition in the egg yolk may relate to different early life histories among this diverse group of animals.}, number={11}, journal={PLOS ONE}, author={Schilling, Justin and Loziuk, Philip L. and Muddiman, David C. and Daniels, Harry V. and Reading, Benjamin J.}, year={2015}, month={Nov} }
 @article{franck_gokce_randall_oh_eyre_muddiman_dean_2015, title={Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development}, volume={14}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/PR501064Q}, DOI={10.1021/PR501064Q}, abstractNote={The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development.}, number={6}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Franck, William L. and Gokce, Emine and Randall, Shan M. and Oh, Yeonyee and Eyre, Alex and Muddiman, David C. and Dean, Ralph A.}, year={2015}, month={May}, pages={2408–2424} }
 @article{wang_chuang_loziuk_chen_lin_shi_qu_muddiman_sederoff_chiang_2015, title={Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis}, volume={112}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1510473112}, DOI={10.1073/PNAS.1510473112}, abstractNote={Significance
          
            To meet environmental and developmental needs, the monolignol biosynthetic pathway for lignification in plant cell walls is regulated by complex mechanisms involving transcriptional, posttranscriptional, and metabolic controls. However, posttranslational modification by protein phosphorylation had not been demonstrated in the regulation of monolignol biosynthesis. Here, we show that reversible monophosphorylation at Ser
            123
            or Ser
            125
            acts as an on/off switch for the activity of 5-hydroxyconiferaldehyde
            O
            -methyltransferase 2 (PtrAldOMT2). Phosphorylation induces a loss of function of PtrAldOMT2, which directly affects metabolic flux for syringyl monolignol biosynthesis. The Ser
            123
            /Ser
            125
            phosphorylation sites are conserved across 98% of AldOMTs from 46 diverse plant species. Protein phosphorylation provides a rapid and energetically efficient mode of regulating PtrAldOMT2 activity for syringyl monolignol biosynthesis and represents an additional level of control for this important pathway.
          }, number={27}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Wang, Jack P. and Chuang, Ling and Loziuk, Philip L. and Chen, Hao and Lin, Ying-Chung and Shi, Rui and Qu, Guan-Zheng and Muddiman, David C. and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2015}, month={Jun}, pages={8481–8486} }
 @article{hecht_scholl_walker_taylor_cliby_motsinger-reif_muddiman_2015, title={Relative Quantification and Higher-Order Modeling of the Plasma Glycan Cancer Burden Ratio in Ovarian Cancer Case-Control Samples}, volume={14}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.5b00703}, abstractNote={An early-stage, population-wide biomarker for ovarian cancer (OVC) is essential to reverse its high mortality rate. Aberrant glycosylation by OVC has been reported, but studies have yet to identify an N-glycan with sufficiently high specificity. We curated a human biorepository of 82 case-control plasma samples, with 27%, 12%, 46%, and 15% falling across stages I-IV, respectively. For relative quantitation, glycans were analyzed by the individuality normalization when labeling with glycan hydrazide tags (INLIGHT) strategy for enhanced electrospray ionization, MS/MS analysis. Sixty-three glycan cancer burden ratios (GBRs), defined as the log10 ratio of the case-control extracted ion chromatogram abundances, were calculated above the limit of detection. The final GBR models, built using stepwise forward regression, included three significant terms: OVC stage, normalized mean GBR, and tag chemical purity; glycan class, fucosylation, or sialylation were not significant variables. After Bonferroni correction, seven N-glycans were identified as significant (p < 0.05), and after false discovery rate correction, an additional four glycans were determined to be significant (p < 0.05), with one borderline (p = 0.05). For all N-glycans, the vectors of the effects from stages II-IV were sequentially reversed, suggesting potential biological changes in OVC morphology or in host response.}, number={10}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Hecht, Elizabeth S. and Scholl, Elizabeth H. and Walker, S. Hunter and Taylor, Amber D. and Cliby, William A. and Motsinger-Reif, Alison A. and Muddiman, David C.}, year={2015}, month={Oct}, pages={4394–4401} }
 @article{muddiman_2016, title={What if you could only publish 50 papers your entire career?}, volume={408}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-015-9208-y}, abstractNote={Ethical questions in science are often centered on the veracity, accuracy, and expediency of results in published articles. A majority of the support for academic studies is sponsored by taxpayers, resulting in an obligation to disseminate the research, a notion supported by the proliferation of Library of Congress journals, eJournals, and publically available reports. Yet a majority of publications have little impact, resulting in few or no peer citations, or are not even read by other scientists in the same field, resulting in the duplication of funding for questions that have already been effectively addressed. This begs the question, if a mechanism were in place to reduce the pressure to publish, would these problems be marginalized? What if you could only publish 50 papers your entire career as corresponding author? This translates mathematically to 2 % of your scientific footprint per manuscript. Would you change the depth of your inquiry, rigor of experimental design and data interpretation, and the clarity in which you put your work into the context of the literature? Ultimately, would your conclusions propel your field forward in a significant way? Regardless of journal type or impact factor, each manuscript should detail a complete and significant study. The effort required to publish with a clear conceptual framework—from experimental design to evidence-based positive or negative conclusions—goes beyond that of many papers submitted to meet a minimal publishable unit (MPU). Though this shift to the highest publishable unit (HPU) will not mean every paper is a blockbuster, it would guarantee that each manuscript fulfills one or more of three goals:}, number={3}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Muddiman, David C.}, year={2016}, month={Jan}, pages={663–664} }
 @article{cochran_barry_robichaud_muddiman_2015, title={Analysis of trace fibers by IR-MALDESI imaging coupled with high resolving power MS}, volume={407}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-014-8042-y}, abstractNote={Trace evidence is a significant portion of forensic cases. Textile fibers are a common form of trace evidence that are gaining importance in criminal cases. Currently, qualitative techniques that do not yield structural information are primarily used for fiber analysis, but mass spectrometry is gaining an increasing role in this field. Mass spectrometry yields more quantitative structural information about the dye and polymer that can be used for more conclusive comparisons. Matrix-assisted laser desorption electrospray ionization (MALDESI) is a hybrid ambient ionization source being investigated for use in mass spectrometric fiber analysis. In this manuscript, IR-MALDESI was used as a source for mass spectrometry imaging (MSI) of a dyed nylon fiber cluster and single fiber. Information about the fiber polymer as well as the dye were obtained from a single fiber which was on the order of 10 μm in diameter. These experiments were performed directly from the surface of a tape lift of the fiber with a background of extraneous fibers.}, number={3}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Cochran, Kristin H. and Barry, Jeremy A. and Robichaud, Guillaume and Muddiman, David C.}, year={2015}, month={Jan}, pages={813–820} }
 @article{muddiman_weintraub_2014, title={Are Presentations at ASMS Conferences Publications?}, volume={25}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-013-0791-x}, abstractNote={ADVERTISEMENT RETURN TO ISSUEEditorialNEXTAre Presentations at ASMS Conferences Publications?David C. MuddimanDavid C. MuddimanW. M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, USAMore by David C. Muddiman and Susan T. WeintraubSusan T. WeintraubDepartment of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USAMore by Susan T. WeintraubCite this: J. Am. Soc. Mass Spectrom. 2014, 25, 3, 301–302Publication Date (Web):January 3, 2014Publication History Published online3 January 2014Published inissue 1 March 2014https://doi.org/10.1007/s13361-013-0791-xCopyright © 2014 © American Society for Mass Spectrometry 2014RIGHTS & PERMISSIONSArticle Views45Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (109 KB) Get e-Alerts}, number={3}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Muddiman, David C. and Weintraub, Susan T.}, year={2014}, month={Mar}, pages={301–302} }
 @inbook{barry_muddiman_robichaud_2014, place={New York}, title={Atmospheric Pressure Mass Spectrometry Imaging}, DOI={10.1002/9780470027318.a9399}, abstractNote={
            Mass spectrometry imaging
            (MSI) has afforded the ability to determine the spatial distribution of numerous molecular classes simultaneously directly from sample surfaces including biological tissue sections. The combination of label‐free multiplexed spatial information with the specificity and sensitivity of mass spectrometric detection make MSI an attractive alternative to existing imaging methodologies. Along with the continued growth of MSI, the recent decade has seen numerous developments in technologies that generate ions at
            atmospheric pressure
            (AP). A majority of these AP ionization techniques have also demonstrated the capabilities to perform MSI under AP conditions with minimal sample preparation and handling. This review aims to summarize the advancements in AP ionization in the context of their application to MSI.
          }, booktitle={Encyclopedia of Analytical Chemistry: Applications, Theory and Instrumentation}, publisher={Wiley}, author={Barry, J and Muddiman, D and Robichaud, G}, editor={Meyers, R.A.Editor}, year={2014}, month={Dec}, pages={1–44} }
 @article{hall_bereman_nepomuceno_thompson_muddiman_smart_2014, title={C/EBPα regulates CRL4Cdt2-mediated degradation of p21 in response to UVB-induced DNA damage to control the G1/S checkpoint}, volume={13}, ISSN={1538-4101 1551-4005}, url={http://dx.doi.org/10.4161/15384101.2014.962957}, DOI={10.4161/15384101.2014.962957}, abstractNote={The bZIP transcription factor, C/EBPα is highly inducible by UVB and other DNA damaging agents in keratinocytes. C/EBPα-deficient keratinocytes fail to undergo cell cycle arrest in G1 in response to UVB-induced DNA damage and mice lacking epidermal C/EBPα are highly susceptible to UVB-induced skin cancer. The mechanism through which C/EBPα regulates the cell cycle checkpoint in response to DNA damage is unknown. Here we report untreated C/EBPα-deficient keratinocytes have normal levels of the cyclin-dependent kinase inhibitor, p21, however, UVB-treated C/EBPα-deficient keratinocytes fail to up-regulate nuclear p21 protein levels despite normal up-regulation of Cdkn1a mRNA levels. UVB-treated C/EBPα-deficient keratinocytes displayed a 4-fold decrease in nuclear p21 protein half-life due to the increased proteasomal degradation of p21 via the E3 ubiquitin ligase CRL4Cdt2. Cdt2 is the substrate recognition subunit of CRL4Cdt2 and Cdt2 mRNA and protein levels were up-regulated in UVB-treated C/EBPα-deficient keratinocytes. Knockdown of Cdt2 restored p21 protein levels in UVB-treated C/EBPα-deficient keratinocytes. Lastly, the failure to accumulate p21 in response to UVB in C/EBPα-deficient keratinocytes resulted in decreased p21 interactions with critical cell cycle regulatory proteins, increased CDK2 activity, and inappropriate entry into S-phase. These findings reveal C/EBPα regulates G1/S cell cycle arrest in response to DNA damage via the control of CRL4Cdt2 mediated degradation of p21.}, number={22}, journal={Cell Cycle}, publisher={Informa UK Limited}, author={Hall, Jonathan R and Bereman, Michael S and Nepomuceno, Angelito I and Thompson, Elizabeth A and Muddiman, David C and Smart, Robert C}, year={2014}, month={Oct}, pages={3602–3610} }
 @article{nazari_muddiman_2015, title={Cellular-level mass spectrometry imaging using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) by oversampling}, volume={407}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-014-8376-5}, abstractNote={Mass spectrometry imaging (MSI) allows for the direct and simultaneous analysis of the spatial distribution of molecular species from sample surfaces such as tissue sections. One of the goals of MSI is monitoring the distribution of compounds at the cellular resolution in order to gain insights about the biology that occurs at this spatial level. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging of cervical tissue sections was performed using a spot-to-spot distance of 10 μm by utilizing the method of oversampling, where the target plate is moved by a distance that is less than the desorption radius of the laser. In addition to high spatial resolution, high mass accuracy (±1 ppm) and high mass resolving power (140,000 at m/z = 200) were achieved by coupling the IR-MALDESI imaging source to a hybrid quadrupole Orbitrap mass spectrometer. Ion maps of cholesterol in tissues were generated from voxels containing <1 cell, on average. Additionally, the challenges of imaging at the cellular level in terms of loss of sensitivity and longer analysis time are discussed.}, number={8}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Nazari, Milad and Muddiman, David C.}, year={2015}, month={Mar}, pages={2265–2271} }
 @article{schilling_nepomuceno_schaff_muddiman_daniels_reading_2014, title={Compartment Proteomics Analysis of White Perch (Morone americana) Ovary Using Support Vector Machines}, volume={13}, ISSN={["1535-3907"]}, DOI={10.1021/pr401067g}, abstractNote={Compartment proteomics enable broad characterization of target tissues. We employed a simple fractionation method and filter-aided sample preparation (FASP) to characterize the cytosolic and membrane fractions of white perch ovary tissues by semiquantitative tandem mass spectrometry using label-free quantitation based on normalized spectral counts. FASP depletes both low-molecular-weight and high-molecular-weight substances that could interfere with protein digestion and subsequent peptide separation and detection. Membrane proteins are notoriously difficult to characterize due to their amphipathic nature and association with lipids. The simple fractionation we employed effectively revealed an abundance of proteins from mitochondria and other membrane-bounded organelles. We further demonstrate that support vector machines (SVMs) offer categorical classification of proteomics data superior to that of parametric statistical methods such as analysis of variance (ANOVA). Specifically, SVMs were able to perfectly (100% correct) classify samples as either membrane or cytosolic fraction during cross-validation based on the expression of 242 proteins with the highest ANOVA p-values (i.e., those that were not significant for enrichment in either fraction). The white perch ovary cytosolic and membrane proteomes and transcriptome presented in this study can support future investigations into oogenesis and early embryogenesis of white perch and other members of the genus Morone.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schilling, Justin and Nepomuceno, Angelito and Schaff, Jennifer E. and Muddiman, David C. and Daniels, Harry V. and Reading, Benjamin J.}, year={2014}, month={Mar}, pages={1515–1526} }
 @article{wang_naik_chen_shi_lin_liu_shuford_li_sun_tunlaya-anukit_et al._2014, title={Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa}, volume={26}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.113.120881}, DOI={10.1105/tpc.113.120881}, abstractNote={A proteomic-based predictive kinetic metabolic-flux model was developed for monolignol biosynthesis in Populus trichocarpa. Absolute quantities of all monolignol pathway proteins and 189 kinetic parameters were generated to construct the model, which was experimentally validated in transgenic P. trichocarpa and provides a comprehensive description of the monolignol biosynthetic pathway. We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of the monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, a comprehensive study was performed to obtain the reaction and inhibition kinetic parameters of all 21 enzymes based on functional recombinant proteins. A total of 104 Michaelis-Menten kinetic parameters and 85 inhibition kinetic parameters were derived from these enzymes. Through mass spectrometry, we obtained the absolute quantities of all 21 pathway enzymes in the secondary differentiating xylem. This extensive experimental data set, generated from a single tissue specialized in wood formation, was used to construct the predictive kinetic metabolic-flux model to provide a comprehensive mathematical description of the monolignol biosynthetic pathway. The model was validated using experimental data from transgenic P. trichocarpa plants. The model predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis. This model provides an explanation of the effects of genetic and transgenic perturbations of the monolignol biosynthetic pathway in flowering plants.}, number={3}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Wang, Jack P. and Naik, Punith P. and Chen, Hsi-Chuan and Shi, Rui and Lin, Chien-Yuan and Liu, Jie and Shuford, Christopher M. and Li, Quanzi and Sun, Ying-Hsuan and Tunlaya-Anukit, Sermsawat and et al.}, year={2014}, month={Mar}, pages={894–914} }
 @article{loziuk_sederoff_chiang_muddiman_2014, title={Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry}, volume={139}, ISSN={["1364-5528"]}, DOI={10.1039/c4an00567h}, abstractNote={Relative abundance values and their associated variability are dynamic and dependent on absolute abundance.}, number={21}, journal={ANALYST}, author={Loziuk, Philip L. and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2014}, pages={5439–5450} }
 @article{randall_koryakina_williams_muddiman_2014, title={Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis}, volume={28}, ISSN={0951-4198}, url={http://dx.doi.org/10.1002/rcm.7051}, DOI={10.1002/rcm.7051}, abstractNote={RATIONALESite occupancy measurements using liquid chromatography/mass spectrometry (LC/MS) are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases.METHODSSite occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of NPSA.RESULTSA consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied.CONCLUSIONSNonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements. Copyright © 2014 John Wiley & Sons, Ltd.}, number={23}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Randall, Shan M. and Koryakina, Irina and Williams, Gavin J. and Muddiman, David C.}, year={2014}, month={Oct}, pages={2511–2522} }
 @article{baker_muddiman_loo_2014, title={Focus on Advancing High Performance Mass Spectrometry, Honoring Dr. Richard D. Smith, Recipient of the 2013 Award for a Distinguished Contribution in Mass Spectrometry}, volume={25}, ISSN={["1879-1123"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344809100001&KeyUID=WOS:000344809100001}, DOI={10.1007/s13361-014-1007-8}, abstractNote={ADVERTISEMENT RETURN TO ISSUEEditorialNEXTFocus on Advancing High Performance Mass Spectrometry, Honoring Dr. Richard D. Smith, Recipient of the 2013 Award for a Distinguished Contribution in Mass SpectrometryErin S. BakerErin S. BakerPacific Northwest National Laboratory, Richland, WA, USAMore by Erin S. Baker, David C. MuddimanDavid C. MuddimanDepartment of Chemistry, North Carolina State University, Raleigh, NC, USAMore by David C. Muddiman, and Joseph A. LooJoseph A. LooDepartment of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USAMore by Joseph A. LooCite this: J. Am. Soc. Mass Spectrom. 2014, 25, 12, 1997–1999Publication Date (Web):October 18, 2014Publication History Published online18 October 2014Published inissue 1 December 2014https://pubs.acs.org/doi/10.1007/s13361-014-1007-8https://doi.org/10.1007/s13361-014-1007-8editorialACS PublicationsCopyright © 2014 © American Society for Mass Spectrometry 2014. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views100Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (439 KB) Get e-Alerts}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Baker, Erin S. and Muddiman, David C. and Loo, Joseph A.}, year={2014}, month={Dec}, pages={1997–1999} }
 @article{zhang_marega_chen_wu_xu_muddiman_bonifazi_yang_2014, title={Hierarchical Self-Assembly of Supramolecular Hydrophobic Metallacycles into Ordered Nanostructures}, volume={9}, ISSN={["1861-471X"]}, DOI={10.1002/asia.201402410}, abstractNote={AbstractWe describe herein the hierarchical self‐assembly of discrete supramolecular metallacycles into ordered fibers or spherical particles through multiple noncovalent interactions. A new series of well‐defined metallacycles decorated with long alkyl chains were obtained through metal–ligand interactions, which were capable of aggregating into ordered fibroid or spherical nanostructures on the surface, mostly driven by hydrophobic interactions. In‐depth studies indicated that the morphology diversity was originated from the structural information encoded in the metallacycles, including the number of alkyl chains and their spatial orientation. Interestingly, the morphology of the metallacycle aggregates could be tuned by changing the solvent polarity. These findings are of special significance since they provide a simple yet highly controllable approach to prepare ordered and tunable nanostructures from small building blocks by means of hierarchical self‐assembly.}, number={10}, journal={CHEMISTRY-AN ASIAN JOURNAL}, author={Zhang, Jing and Marega, Riccardo and Chen, Li-Jun and Wu, Nai-Wei and Xu, Xing-Dong and Muddiman, David C. and Bonifazi, Davide and Yang, Hai-Bo}, year={2014}, month={Oct}, pages={2928–2936} }
 @article{robichaud_barry_muddiman_2014, title={IR-MALDESI Mass Spectrometry Imaging of Biological Tissue Sections Using Ice as a Matrix}, volume={25}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-013-0787-6}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging of biological tissue sections using a layer of deposited ice as an energy-absorbing matrix was investigated. Dynamics of plume ablation were first explored using a nanosecond exposure shadowgraphy system designed to simultaneously collect pictures of the plume with a camera and collect the Fourier transform ion cyclotron resonance FT-ICR mass spectrum corresponding to that same ablation event. Ablation of fresh tissue analyzed with and without using ice as a matrix were compared using this technique. Effect of spot-to-spot distance, number of laser shots per pixel, and tissue condition (matrix) on ion abundance were also investigated for 50 μm-thick tissue sections. Finally, the statistical method called design of experiments was used to compare source parameters and determine the optimal conditions for IR-MALDESI of tissue sections using deposited ice as a matrix. With a better understanding of the fundamentals of ablation dynamics and a systematic approach to explore the experimental space, it was possible to improve ion abundance by nearly one order of magnitude.}, number={3}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Robichaud, Guillaume and Barry, Jeremy A. and Muddiman, David C.}, year={2014}, month={Mar}, pages={319–328} }
 @article{barry_robichaud_bokhart_thompson_sykes_kashuba_muddiman_2014, title={Mapping Antiretroviral Drugs in Tissue by IR-MALDESI MSI Coupled to the Q Exactive and Comparison with LC-MS/MS SRM Assay}, volume={25}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-014-0884-1}, abstractNote={This work describes the coupling of the IR-MALDESI imaging source with the Q Exactive mass spectrometer. IR-MALDESI MSI was used to elucidate the spatial distribution of several HIV drugs in cervical tissues that had been incubated in either a low or high concentration. Serial sections of those analyzed by IR-MALDESI MSI were homogenized and analyzed by LC-MS/MS to quantify the amount of each drug present in the tissue. By comparing the two techniques, an agreement between the average intensities from the imaging experiment and the absolute quantities for each drug was observed. This correlation between these two techniques serves as a prerequisite to quantitative IR-MALDESI MSI. In addition, a targeted MS2 imaging experiment was also conducted to demonstrate the capabilities of the Q Exactive and to highlight the added selectivity that can be obtained with SRM or MRM imaging experiments.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Barry, Jeremy A. and Robichaud, Guillaume and Bokhart, Mark T. and Thompson, Corbin and Sykes, Craig and Kashuba, Angela D. M. and Muddiman, David C.}, year={2014}, month={Dec}, pages={2038–2047} }
 @misc{muddiman_2015, title={Michael Gross: 25 Years of Dedication and Leadership of JASMS (1990-2015)}, volume={26}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-014-1040-7}, abstractNote={ADVERTISEMENT RETURN TO ISSUELetter to EditorNEXTMichael Gross: 25 Years of Dedication and Leadership of JASMS (1990–2015)David C. MuddimanDavid C. MuddimanDepartment of Chemistry, North Carolina State University, 27695, Raleigh, NC, USAMore by David C. MuddimanCite this: J. Am. Soc. Mass Spectrom. 2015, 26, 1, 1–4Publication Date (Web):December 24, 2014Publication History Published online24 December 2014Published inissue 1 January 2015https://pubs.acs.org/doi/10.1007/s13361-014-1040-7https://doi.org/10.1007/s13361-014-1040-7editorialACS PublicationsCopyright © 2014 © American Society for Mass Spectrometry 2014. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views104Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (456 KB) Get e-Alerts}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Muddiman, David C.}, year={2015}, month={Jan}, pages={1–4} }
 @article{bokhart_rosen_thompson_sykes_kashuba_muddiman_2015, title={Quantitative mass spectrometry imaging of emtricitabine in cervical tissue model using infrared matrix-assisted laser desorption electrospray ionization}, volume={407}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-014-8220-y}, abstractNote={A quantitative mass spectrometry imaging (QMSI) technique using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is demonstrated for the antiretroviral (ARV) drug emtricitabine in incubated human cervical tissue. Method development of the QMSI technique leads to a gain in sensitivity and removal of interferences for several ARV drugs. Analyte response was significantly improved by a detailed evaluation of several cationization agents. Increased sensitivity and removal of an isobaric interference was demonstrated with sodium chloride in the electrospray solvent. Voxel-to-voxel variability was improved for the MSI experiments by normalizing analyte abundance to a uniformly applied compound with similar characteristics to the drug of interest. Finally, emtricitabine was quantified in tissue with a calibration curve generated from the stable isotope-labeled analog of emtricitabine followed by cross-validation using liquid chromatography tandem mass spectrometry (LC-MS/MS). The quantitative IR-MALDESI analysis proved to be reproducible with an emtricitabine concentration of 17.2 ± 1.8 μg/gtissue. This amount corresponds to the detection of 7 fmol/voxel in the IR-MALDESI QMSI experiment. Adjacent tissue slices were analyzed using LC-MS/MS which resulted in an emtricitabine concentration of 28.4 ± 2.8 μg/gtissue.}, number={8}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Bokhart, Mark T. and Rosen, Elias and Thompson, Corbin and Sykes, Craig and Kashuba, Angela D. M. and Muddiman, David C.}, year={2015}, month={Mar}, pages={2073–2084} }
 @article{meier_garrard_muddiman_2014, title={Silver dopants for targeted and untargeted direct analysis of unsaturated lipids via infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={28}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.7041}, abstractNote={RATIONALEUnsaturated lipids play a crucial role in cellular processes as signaling factors, membrane building blocks or energy storage molecules. However, adequate mass spectrometry imaging of this diverse group of molecules remains challenging. In this study we implemented silver cationization for direct analysis by infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) to enhance the ion abundances for olefinic lipids and facilitate peak assignment.METHODSTrace amounts of silver nitrate were doped into the electrospray solvent of an IR‐MALDESI imaging source coupled to an Orbitrap mass analyzer. Calcifediol was examined as a model compound to demonstrate the effect of silver dopants on sensitivity and assay robustness. Dried human serum spots were subsequently analyzed to compare Ag‐doped solvents with previously described solvent compositions. Mass differences as well as ion abundance ratio filters were employed to interpret results based on the characteristic isotopic pattern of silver.RESULTSOlefinic lipids were readily observed as silver adducts in IR‐MALDESI analyses. Silver cationization decreased the limit of detection for calcifediol by at least one order of magnitude and was not affected in complex biological matrices. The ion abundance ratio and mass difference of [M + 107Ag+]+ and [M + 109Ag+]+ were successfully applied to facilitate the spectral assignment of silver adducts. Overall, silver cationization increased the analyte coverage in human serum by 43% compared with a standard IR‐MALDESI approach.CONCLUSIONSSilver cationization has been shown to enhance IR‐MALDESI sensitivity and selectivity for unsaturated lipids, even when applied to complex samples. Increased compound coverage, enhanced robustness as well as the developed tools for peak assignment and mapping of isotopic patterns will clearly benefit future mass spectrometry imaging studies. Copyright © 2014 John Wiley & Sons, Ltd.}, number={22}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Meier, Florian and Garrard, Kenneth P. and Muddiman, David C.}, year={2014}, month={Nov}, pages={2461–2470} }
 @article{chen_song_wang_lin_ducoste_shuford_liu_li_shi_nepomuceno_et al._2014, title={Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling}, volume={26}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.113.119685}, DOI={10.1105/tpc.113.119685}, abstractNote={This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa. The activity of the heterotetramer can be described by a mathematical model that explains the effects of each isoform with mixtures of substrates and three types of inhibition, providing insights into the regulation of metabolic flux for this pathway. As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein–protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation.}, number={3}, journal={The Plant Cell}, publisher={Oxford University Press (OUP)}, author={Chen, Hsi-Chuan and Song, Jina and Wang, Jack P. and Lin, Ying-Chung and Ducoste, Joel and Shuford, Christopher M. and Liu, Jie and Li, Quanzi and Shi, Rui and Nepomuceno, Angelito and et al.}, year={2014}, month={Mar}, pages={876–893} }
 @article{nepomuceno_gibson_randall_muddiman_2014, title={Accurate Identification of Deamidated Peptides in Global Proteomics Using a Quadrupole Orbitrap Mass Spectrometer}, volume={13}, ISSN={["1535-3907"]}, DOI={10.1021/pr400848n}, abstractNote={Deamidation of asparagine and glutamine residues is a common post-translational modification. Researchers often rely on mass spectrometric based proteomic techniques for the identification of these post-translational sites. Mass spectral analysis of deamidated peptides is complicated and often misassigned due to overlapping (13)C peak of the amidated form with the deamidated monoisotopic peak; these two peaks are only separated by 19.34 mDa. For proper assignment, it is inherently important to use a mass spectrometer with high mass measurement accuracy and high resolving power. Herein, mouse brain tissue lysate was prepared using filter-aided sample preparation (FASP) method and Stage Tip fractionation followed by analysis on a nanoLC coupled with a quadrupole orbitrap (Q-Exactive) mass spectrometer to accurately identify more than 5400 proteins. Mass spectral data was processed using MASCOT and ProteoIQ for accurate identification of peptides and proteins. MASCOT search values for precursor and MS/MS mass tolerances were investigated, and it was determined that data searched with greater than 5 ppm precursor mass tolerance resulted in the misassignment of deamidated peptides. Peptides that were identified with a mass measurement accuracy of ±5 ppm were correctly assigned.}, number={2}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Nepomuceno, Angelito I. and Gibson, Radiance J. and Randall, Shan M. and Muddiman, David C.}, year={2014}, month={Feb}, pages={777–785} }
 @article{white_goekce_nepomuceno_muddiman_sanders_davis_2013, title={Comparative Proteomic Analysis and IgE Binding Properties of Peanut Seed and Testa (Skin)}, volume={61}, ISSN={["1520-5118"]}, DOI={10.1021/jf400184y}, abstractNote={To investigate the protein composition and potential allergenicity of peanut testae or skins, proteome analysis was conducted using nanoLC-MS/MS sequencing. Initial amino acid analysis suggested differences in protein compositions between the blanched seed (skins removed) and skin. Phenolic compounds hindered analysis of proteins in skins when the conventional extraction method was used; therefore, phenol extraction of proteins was necessary. A total of 123 proteins were identified in blanched seed and skins, and 83 of the proteins were common between the two structures. The skins contained all of the known peanut allergens in addition to 38 proteins not identified in the seed. Multiple defense proteins with antifungal activity were identified in the skins. Western blotting using sera from peanut-allergic patients revealed that proteins extracted from both the blanched seed and skin bound significant levels of IgE. However, when phenolic compounds were present in the skin protein extract, no IgE binding was observed. These findings indicate that peanut skins contain potentially allergenic proteins; however, the presence of phenolic compounds may attenuate this effect.}, number={16}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, author={White, Brittany L. and Goekce, Emine and Nepomuceno, Angelito I. and Muddiman, David C. and Sanders, Timothy H. and Davis, Jack P.}, year={2013}, month={Apr}, pages={3957–3968} }
 @article{randall_cardasis_muddiman_2013, title={Factorial Experimental Designs Elucidate Significant Variables Affecting Data Acquisition on a Quadrupole Orbitrap Mass Spectrometer}, volume={24}, ISSN={["1044-0305"]}, DOI={10.1007/s13361-013-0693-y}, abstractNote={Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P < 0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation.}, number={10}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Randall, Shan M. and Cardasis, Helene L. and Muddiman, David C.}, year={2013}, month={Oct}, pages={1501–1512} }
 @article{walker_taylor_muddiman_2013, title={Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): A Novel Glycan-Relative Quantification Strategy}, volume={24}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-013-0681-2}, abstractNote={The Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT) strategy for the sample preparation, data analysis, and relative quantification of N-linked glycans is presented. Glycans are derivatized with either natural (L) or stable-isotope labeled (H) hydrazide reagents and analyzed using reversed phase liquid chromatography coupled online to a Q Exactive mass spectrometer. A simple glycan ladder, maltodextrin, is first used to demonstrate the relative quantification strategy in samples with negligible analytical and biological variability. It is shown that after a molecular weight correction attributable to isotopic overlap and a post-acquisition normalization of the data to account for any systematic bias, a plot of the experimental H:L ratio versus the calculated H:L ratio exhibits a correlation of unity for maltodextrin samples mixed in different ratios. We also demonstrate that the INLIGHT approach can quantify species over four orders of magnitude in ion abundance. The INLIGHT strategy is further demonstrated in pooled human plasma, where it is shown that the post-acquisition normalization is more effective than using a single spiked-in internal standard. Finally, changes in glycosylation are able to be detected in complex biological matrices, when spiked with a glycoprotein. The ability to spike in a glycoprotein and detect change at the glycan level validates both the sample preparation and data analysis strategy, making INLIGHT an invaluable relative quantification strategy for the field of glycomics.}, number={9}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Walker, S. Hunter and Taylor, Amber D. and Muddiman, David C.}, year={2013}, month={Sep}, pages={1376–1384} }
 @article{robichaud_garrard_barry_muddiman_2013, title={MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform}, volume={24}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-013-0607-z}, abstractNote={During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.}, number={5}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Robichaud, Guillaume and Garrard, Kenneth P. and Barry, Jeremy A. and Muddiman, David C.}, year={2013}, month={May}, pages={718–721} }
 @article{barry_robichaud_muddiman_2013, title={Mass Recalibration of FT-ICR Mass Spectrometry Imaging Data Using the Average Frequency Shift of Ambient Ions}, volume={24}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-013-0659-0}, abstractNote={Achieving and maintaining high mass measurement accuracy (MMA) throughout a mass spectrometry imaging (MSI) experiment is vital to the identification of the observed ions. However, when using FTMS instruments, fluctuations in the total ion abundance at each pixel due to inherent biological variation in the tissue section can introduce space charge effects that systematically shift the observed mass. Herein we apply a recalibration based on the observed cyclotron frequency shift of ions found in the ambient laboratory environment, polydimethylcyclosiloxanes (PDMS). This calibration method is capable of achieving part per billion (ppb) mass accuracy with relatively high precision for an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI dataset. Comparisons with previously published mass calibration approaches are also presented.}, number={7}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Barry, Jeremy A. and Robichaud, Guillaume and Muddiman, David C.}, year={2013}, month={Jul}, pages={1137–1145} }
 @article{chen_song_williams_shuford_liu_wang_li_shi_gokce_ducoste_et al._2013, title={Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes}, volume={161}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84874626790&partnerID=MN8TOARS}, DOI={10.1104/pp.112.210971}, abstractNote={Abstract
               4-Coumaric acid:coenzyme A ligase (4CL) is involved in monolignol biosynthesis for lignification in plant cell walls. It ligates coenzyme A (CoA) with hydroxycinnamic acids, such as 4-coumaric and caffeic acids, into hydroxycinnamoyl-CoA thioesters. The ligation ensures the activated state of the acid for reduction into monolignols. In Populus spp., it has long been thought that one monolignol-specific 4CL is involved. Here, we present evidence of two monolignol 4CLs, Ptr4CL3 and Ptr4CL5, in Populus trichocarpa. Ptr4CL3 is the ortholog of the monolignol 4CL reported for many other species. Ptr4CL5 is novel. The two Ptr4CLs exhibited distinct Michaelis-Menten kinetic properties. Inhibition kinetics demonstrated that hydroxycinnamic acid substrates are also inhibitors of 4CL and suggested that Ptr4CL5 is an allosteric enzyme. Experimentally validated flux simulation, incorporating reaction/inhibition kinetics, suggested two CoA ligation paths in vivo: one through 4-coumaric acid and the other through caffeic acid. We previously showed that a membrane protein complex mediated the 3-hydroxylation of 4-coumaric acid to caffeic acid. The demonstration here of two ligation paths requiring these acids supports this 3-hydroxylation function. Ptr4CL3 regulates both CoA ligation paths with similar efficiencies, whereas Ptr4CL5 regulates primarily the caffeic acid path. Both paths can be inhibited by caffeic acid. The Ptr4CL5-catalyzed caffeic acid metabolism, therefore, may also act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux. A high level of caffeic acid was detected in stem-differentiating xylem of P. trichocarpa. Our results suggest that Ptr4CL5 and caffeic acid coordinately modulate the CoA ligation flux for monolignol biosynthesis.}, number={3}, journal={PLANT PHYSIOLOGY}, author={Chen, Hsi-Chuan and Song, Jina and Williams, Cranos M. and Shuford, Christopher M. and Liu, Jie and Wang, Jack P. and Li, Quanzi and Shi, Rui and Gokce, Emine and Ducoste, Joel and et al.}, year={2013}, month={Mar}, pages={1501–1516} }
 @article{andrews kingon_petitte_muddiman_hawkridge_2013, title={Multi-peptide nLC-PC-IDMS-SRM-based Assay for the quantification of biomarkers in the chicken ovarian cancer model}, volume={61}, ISSN={1046-2023}, url={http://dx.doi.org/10.1016/J.YMETH.2013.04.004}, DOI={10.1016/j.ymeth.2013.04.004}, abstractNote={A novel form of ovomacroglobulin/ovostatin (OVOS2) predicted from EST data was previously identified in the chicken ovarian cancer model using a mass spectrometry-based shotgun label-free proteomics strategy. The quantitative label-free data from plasma showed a significant increase over time with the spontaneous onset and progression of ovarian cancer making it a potential protein biomarker for further study. Two other proteins of interest identified from this initial study included vitellogenin-1 (Vit-1), a lipid-transport protein tied to egg production, and transthyretin (TTR), a retinol binding transport protein currently used in the clinical management of ovarian cancer. A multiplexed protein cleavage isotope dilution mass spectrometry (PC-IDMS) assay was developed to quantify OVOS2, Vit-1, and TTR by selected reaction monitoring (SRM). A total of 6 stable isotope labeled (SIL) peptide standards were used in the assay with three tryptic peptides from OVOS2, one for Vit-1, and two for TTR. The assay was developed for use with un-depleted raw plasma combined with the filter assisted sample preparation (FASP) method and its use was also demonstrated for matched ovary tissue samples. The PC-IDMS data for the two TTR peptides did not correlate with each other with more than a 10-fold difference in concentration for all 5 time points measured. The PC-IDMS data from the longitudinal plasma samples correlated well for OVOS2 and Vit-1 whereas TTR was inconclusive. Interestingly, the absolute amount for one of the OVOS2 SIL peptides was 2-fold less compared with the other two SIL peptides. These data illustrate the successes and challenges of qualifying quantitative levels of proteins from an in-gel digestion sample preparation followed by LC-MS/MS (GeLC) label-free discovery-based approach to a targeted SRM-based quantitative assay in plasma and tissues.}, number={3}, journal={Methods}, publisher={Elsevier BV}, author={Andrews Kingon, Genna L. and Petitte, James N. and Muddiman, David C. and Hawkridge, Adam M.}, year={2013}, month={Jun}, pages={323–330} }
 @article{shi_shuford_wang_sun_yang_chen_tunlaya-anukit_li_liu_muddiman_et al._2013, title={Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa}, volume={238}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882877816&partnerID=MN8TOARS}, DOI={10.1007/s00425-013-1905-1}, abstractNote={Phenylalanine ammonia-lyase (PAL) catalyzes the initial step of phenylpropanoid biosynthesis in plants. Five PAL genes (PtrPAL1 to 5) have been identified in Populus trichocarpa. These genes are classified into two subgroups according to their transcript sequence similarity and tissue specificity. However, the regulation of these genes and their protein functions are not well understood. In this study, enzymatic properties of each PtrPALs were characterized based on their recombinant proteins expressed in E.coli. Subcellular localizations of each PtrPALs in stem wood forming tissue were investigated and individual PtrPAL protein abundances in cytosol and membrane protein fractions were measured using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Protein/mRNA ratios of PtrPALs were further verified using RNA-Seq and gel-enhanced liquid chromatography mass spectrometry (GeLC-MS). All PtrPALs have similar catalytic properties for the deamination of L-phenylalanine, their major substrate. All PtrPALs have similar subcellular locations in stem wood forming tissue, with major amount in the cytosol (93-96 %) and less in the membrane (4-7 %). However, the protein/mRNA ratios of subgroup A (PtrPAL2, 4 and 5) are about five times that of subgroup B (PtrPAL1 and 3) in stem wood forming tissue, while all PtrPALs have similar transcript abundances. These results indicate a greater functional significance of subgroup A PtrPALs for stem wood formation, and highlight the role of gene post-transcriptional regulation.}, number={3}, journal={Planta}, author={Shi, R. and Shuford, C. M. and Wang, Jack P. and Sun, Y. H. and Yang, Z. C. and Chen, H. C. and Tunlaya-Anukit, S. and Li, Q. Z. and Liu, J. and Muddiman, David and et al.}, year={2013}, pages={487–497} }
 @article{muddiman_2014, title={Reply to the Comment on: "Utilizing Artificial Neural Networks in MATLAB to Achieve Parts-Per-Billion Mass Measurement Accuracy with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer" by D. Keith Williams Jr., Alexander L. Kovach, David C. Muddiman, and Kenneth W. Hanck. J-Am. Soc. Mass Spectrom. 20, 1303-1310 (2009)}, volume={25}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-013-0806-7}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVResearch ArticleNEXTReply to the Comment on: "Utilizing Artificial Neural Networks in MATLAB to Achieve Parts-Per-Billion Mass Measurement Accuracy with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer" by D. Keith Williams Jr., Alexander L. Kovach, David C. Muddiman, and Kenneth W. Hanck. J. Am. Soc. Mass Spectrom.20, 1303–1310 (2009)David C. MuddimanDavid C. MuddimanNorth Carolina State University, Raleigh, NC, USAMore by David C. MuddimanCite this: J. Am. Soc. Mass Spectrom. 2014, 25, 4, 697Publication Date (Web):December 21, 2013Publication History Published online21 December 2013Published inissue 1 April 2014https://pubs.acs.org/doi/10.1007/s13361-013-0806-7https://doi.org/10.1007/s13361-013-0806-7research-articleACS PublicationsCopyright © 2013 © American Society for Mass Spectrometry 2013Request reuse permissionsArticle Views16Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Muddiman, David C.}, year={2014}, month={Apr}, pages={697–697} }
 @article{franck_gokce_oh_muddiman_dean_2013, title={Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation}, volume={12}, ISSN={1535-9476 1535-9484}, url={http://dx.doi.org/10.1074/MCP.M112.025874}, DOI={10.1074/MCP.M112.025874}, abstractNote={Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.}, number={8}, journal={Molecular & Cellular Proteomics}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Franck, William L. and Gokce, Emine and Oh, Yeonyee and Muddiman, David C. and Dean, Ralph A.}, year={2013}, month={May}, pages={2249–2265} }
 @article{walker_taylor_muddiman_2013, title={The use of a xylosylated plant glycoprotein as an internal standard accounting for N-linked glycan cleavage and sample preparation variability}, volume={27}, DOI={10.1002/rcm.6579}, abstractNote={RATIONALETraditionally, free oligosaccharide internal standards are used to account for variability in glycan relative quantification experiments by mass spectrometry. However, a more suitable internal standard would be a glycoprotein, which could also control for enzymatic cleavage efficiency, allowing for more accurate quantitative experiments.METHODSHydrophobic, hydrazide N‐linked glycan reagents (both native and stable‐isotope labeled) are used to derivatize and differentially label N‐linked glycan samples for relative quantification, and the samples are analyzed by a reversed‐phase liquid chromatography chip system coupled online to a Q‐Exactive mass spectrometer. The inclusion of two internal standards, maltoheptaose (previously used) and horseradish peroxidase (HRP) (novel), is studied to demonstrate the effectiveness of using a glycoprotein as an internal standard in glycan relative quantification experiments.RESULTSHRP is a glycoprotein containing a xylosylated N‐linked glycan, which is unique from mammalian N‐linked glycans. Thus, the internal standard xylosylated glycan could be detected without interference to the sample. Additionally, it was shown that differences in cleavage efficiency can be detected by monitoring the HRP glycan. In a sample where cleavage efficiency variation is minimal, the HRP glycan performs as well as maltoheptaose.CONCLUSIONSBecause the HRP glycan performs as well as maltoheptaose but is also capable of correcting and accounting for cleavage variability, it is a more versatile internal standard and will be used in all subsequent biological studies. Because of the possible lot‐to‐lot variation of an enzyme, differences in biological matrix, and variable enzyme activity over time, it is a necessity to account for glycan cleavage variability in glycan relative quantification experiments. Copyright © 2013 John Wiley & Sons, Ltd.}, number={12}, journal={Rapid Communications in Mass Spectrometry}, author={Walker, S. H. and Taylor, A. D. and Muddiman, David}, year={2013}, pages={1354–1358} }
 @article{loziuk_wang_li_sederoff_chiang_muddiman_2013, title={Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments}, volume={12}, ISSN={["1535-3907"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84890109136&partnerID=MN8TOARS}, DOI={10.1021/pr4008442}, abstractNote={Workflows in bottom-up proteomics have traditionally implemented the use of proteolysis during sample preparation; enzymatic digestion is most commonly performed using trypsin. This results in the hydrolysis of peptide bonds forming tryptic peptides, which can then be subjected to LC-MS/MS analysis. While the structure, specificity, and kinetics of trypsin are well characterized, a lack of consensus and understanding has remained regarding fundamental parameters critical to obtaining optimal data from a proteomics experiment. These include the type of trypsin used, pH during digestion, incubation temperature as well as enzyme-to-substrate ratio. Through the use of design of experiments (DOE), we optimized these parameters, resulting in deeper proteome coverage and a greater dynamic range of measurement. The knowledge gained from optimization of a discovery-based proteomics experiment was applied to targeted LC-MS/MS experiments using protein cleavage-isotope dilution mass spectrometry for absolute quantification. We demonstrated the importance of these digest parameters with respect to our limit of detection as well as our ability to acquire more accurate quantitative measurements. Additionally, we were able to quantitatively account for peptide decay observed in previous studies, caused by nonspecific activity of trypsin. The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Loziuk, Philip L. and Wang, Jack and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2013}, month={Dec}, pages={5820–5829} }
 @article{muddiman_2012, title={Alexander R. Ivanov, Alexander V. Lazarev (Eds): Sample preparation in biological mass spectrometry}, volume={404}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/S00216-012-6260-8}, DOI={10.1007/S00216-012-6260-8}, number={5}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Muddiman, David C.}, year={2012}, month={Jul}, pages={1331–1332} }
 @misc{collier_muddiman_2012, title={Analytical strategies for the global quantification of intact proteins}, volume={43}, ISSN={["1438-2199"]}, DOI={10.1007/s00726-012-1285-z}, abstractNote={The quantification of intact proteins is a relatively recent development in proteomics. In eukaryotic organisms, proteins are present as multiple isoforms as the result of variations in genetic code, alternative splicing, post-translational modification and other processing events. Understanding the identities and biological functions of these isoforms and how their concentrations vary across different states is the central goal of proteomics. To date, the bulk of proteomics research utilizes a "bottom-up" approach, digesting proteins into their more manageable constitutive peptides, but sacrificing information about the specific isoform and combinations of post-translational modifications present on the protein. Very specific strategies for protein quantification such as the enzyme-linked immunosorbent assay and Western blot are commonplace in laboratories and clinics, but impractical for the study of global biological changes. Herein, we describe strategies for the quantification of intact proteins, their distinct advantages, and challenges to their employment. Techniques contained in this review include the more traditional and widely employed methodology of differential gel electrophoresis and more recently developed mass spectrometry-based techniques including metabolic labeling, chemical labeling, and label-free methodologies.}, number={3}, journal={AMINO ACIDS}, author={Collier, Timothy S. and Muddiman, David Charles}, year={2012}, month={Sep}, pages={1109–1117} }
 @article{shuford_li_sun_chen_wang_shi_sederoff_chiang_muddiman_2012, title={Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry}, volume={11}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr300205a}, DOI={10.1021/pr300205a}, abstractNote={The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level.}, number={6}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Shuford, Christopher M. and Li, Quanzi and Sun, Ying-Hsuan and Chen, Hsi-Chuan and Wang, Jack and Shi, Rui and Sederoff, Ronald. R. and Chiang, Vincent L. and Muddiman, David C.}, year={2012}, month={May}, pages={3390–3404} }
 @article{li_zhao_chen_tan_wang_wang_lehman_muddiman_yang_2012, title={Coordination-Driven Self-Assembly of Charged and Neutral Dendritic Tetrakis(ferrocenyl) Rhomboids}, volume={31}, ISSN={["1520-6041"]}, DOI={10.1021/om3007932}, abstractNote={By combining 60° bis(ferrocenyl) di-Pt(II) acceptors and the complementary 120° dipyridyl or dicarboxylate donors substituted with [G-1]–[G-3] Frechet-type dendrons, self-assembly of a new series of charged or neutral dendritic tetrakis(ferrocenyl) rhomboids was realized under mild conditions in high yields, respectively. The structures of all difunctionalized rhomboids were characterized by multinuclear NMR (1H and 31P), ESI-TOF-MS, CSI-TOF-MS, and elemental analysis. Moreover, their electrochemical behavior was studied through cyclic voltammetry investigations. Further insight into the structural characterization of all rhomboidal metallacycles, such as the shape and size, was obtained via molecular simulation by PM6 semiempirical molecular orbital methods.}, number={20}, journal={ORGANOMETALLICS}, author={Li, Quan-Jie and Zhao, Guanz-Zhen and Chen, Li-Jun and Tan, Hongwei and Wang, Cui-Hong and Wang, De-Xian and Lehman, Danielle A. and Muddiman, David C. and Yang, Hai-Bo}, year={2012}, month={Oct}, pages={7241–7247} }
 @article{cochran_barry_muddiman_hinks_2013, title={Direct Analysis of Textile Fabrics and Dyes Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry}, volume={85}, ISSN={["0003-2700"]}, DOI={10.1021/ac302519n}, abstractNote={The forensic analysis of textile fibers uses a variety of techniques from microscopy to spectroscopy. One such technique that is often used to identify the dye(s) within the fiber is mass spectrometry (MS). In the traditional MS method, the dye must be extracted from the fabric and the dye components are separated by chromatography prior to mass spectrometric analysis. Direct analysis of the dye from the fabric allows the omission of the lengthy sample preparation involved in extraction, thereby significantly reducing the overall analysis time. Herein, a direct analysis of dyed textile fabric was performed using the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source for MS. In MALDESI, an IR laser with wavelength tuned to 2.94 μm is used to desorb the dye from the fabric sample with the aid of water as the matrix. The desorbed dye molecules are then postionized by electrospray ionization (ESI). A variety of dye classes were analyzed from various fabrics with little to no sample preparation allowing for the identification of the dye mass and in some cases the fiber polymer. Those dyes that were not detected using MALDESI were also not observed by direct infusion ESI of the dye standard.}, number={2}, journal={ANALYTICAL CHEMISTRY}, author={Cochran, Kristin H. and Barry, Jeremy A. and Muddiman, David C. and Hinks, David}, year={2013}, month={Jan}, pages={831–836} }
 @article{harton_pingali_nunnery_baker_walker_muddiman_koga_rials_urban_langan_2012, title={Evidence for Complex Molecular Architectures for Solvent-Extracted Lignins}, volume={1}, ISSN={["2161-1653"]}, DOI={10.1021/mz300045e}, abstractNote={Lignin, an abundant, naturally occurring biopolymer, is often considered "waste" and used as a simple fuel source in the paper-making process. However, lignin has emerged as a promising renewable resource for engineering materials, such as carbon fibers. Unfortunately, the molecular architecture of lignin (in vivo and extracted) is still elusive, with numerous conflicting reports in the literature, and knowledge of this structure is extremely important, not only for materials technologies, but also for production of biofuels such as cellulosic ethanol due to biomass recalcitrance. As such, the molecular structures of solvent-extracted (sulfur-free) lignins, which have been modified using various acyl chlorides, have been probed using small-angle X-ray (SAXS) and neutron (SANS) scattering in tetrahydrofuran (THF) solution along with hydrodynamic characterization using dilute solution viscometry and gel permeation chromatography (GPC) in THF. Mass spectrometry shows an absolute molecular weight ≈18-30 kDa (≈80-140 monomers), while GPC shows a relative molecular weight ∼3 kDa. A linear styrene oligomer (2.5 kDa) was also analyzed in THF using SANS. Results clearly show that lignin molecular architectures are somewhat rigid and complex, ranging from nanogels to hyperbranched macromolecules, not linear oligomers or physical assemblies of oligomers, which is consistent with previously proposed delignification (extraction) mechanisms. Future characterization using the methods discussed here can be used to guide extraction processes as well as genetic engineering technologies to convert lignin into value added materials with the potential for high positive impact on global sustainability.}, number={5}, journal={ACS MACRO LETTERS}, author={Harton, Shane E. and Pingali, Sai Venkatesh and Nunnery, Grady A. and Baker, Darren A. and Walker, S. Hunter and Muddiman, David C. and Koga, Tadanori and Rials, Timothy G. and Urban, Volker S. and Langan, Paul}, year={2012}, month={May}, pages={568–573} }
 @article{wang_shuford_li_song_lin_sun_chen_williams_muddiman_sederoff_et al._2012, title={Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis}, volume={236}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84865584315&partnerID=MN8TOARS}, DOI={10.1007/s00425-012-1663-5}, abstractNote={Flowering plants have syringyl and guaiacyl subunits in lignin in contrast to the guaiacyl lignin in gymnosperms. The biosynthesis of syringyl subunits is initiated by coniferaldehyde 5-hydroxylase (CAld5H). In Populus trichocarpa there are two closely related CAld5H enzymes (PtrCAld5H1 and PtrCAld5H2) associated with lignin biosynthesis during wood formation. We used yeast recombinant PtrCAld5H1 and PtrCAld5H2 proteins to carry out Michaelis-Menten and inhibition kinetics with LC-MS/MS based absolute protein quantification. CAld5H, a monooxygenase, requires a cytochrome P450 reductase (CPR) as an electron donor. We cloned and expressed three P. trichocarpa CPRs in yeast and show that all are active with both CAld5Hs. The kinetic analysis shows both CAld5Hs have essentially the same biochemical functions. When both CAld5Hs are coexpressed in the same yeast membranes, the resulting enzyme activities are additive, suggesting functional redundancy and independence of these two enzymes. Simulated reaction flux based on Michaelis-Menten kinetics and inhibition kinetics confirmed the redundancy and independence. Subcellular localization of both CAld5Hs as sGFP fusion proteins expressed in P. trichocarpa differentiating xylem protoplasts indicate that they are endoplasmic reticulum resident proteins. These results imply that during wood formation, 5-hydroxylation in monolignol biosynthesis of P. trichocarpa requires the combined metabolic flux of these two CAld5Hs to maintain adequate biosynthesis of syringyl lignin. The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis.}, number={3}, journal={PLANTA}, publisher={Springer Science + Business Media}, author={Wang, Jack P. and Shuford, Christopher M. and Li, Quanzi and Song, Jina and Lin, Ying-Chung and Sun, Ying-Hsuan and Chen, Hsi-Chuan and Williams, Cranos M. and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2012}, month={Sep}, pages={795–808} }
 @article{maurer_muddiman_2012, title={High-resolution mass spectrometry}, volume={403}, ISSN={["1618-2642"]}, DOI={10.1007/s00216-012-5959-x}, abstractNote={High-resolution mass spectrometry (HRMS) using doublefocusing mass analyzers was established in chemistry laboratories in the 1960s. Coupled to a direct insertion probe or to gas chromatography, it revolutionized the elemental analysis of organic compounds. It also became a powerful tool in bioanalytical research providing high selectivity and specificity. However, modern benchtop GC–MS instruments cost significantly less and have been coupled to the faster scanning quadrupole or ion-trap mass analyzers, largely displacing GC–HRMS in most fields. Modern LC–MS instruments using electrospray ionization have many applications in bioanalytical laboratories and in “omics” research. Manufacturers, for arguably the first time, recognized a sizeable market for HRMS. In the past few years, robust GC–MS and, particularly, LC–MS equipment, mainly using time-of-flight or Fourier-transform mass-analyzer technology, are becoming increasingly affordable by many laboratories. This is also apparent from the remarkable increase in the number of publications. Therefore, the objective of this special volume is to give an overview of the current use of HRMS in the life sciences. Four review articles critically assess the use of HRMS in clinical and forensic toxicology, doping control, drug metabolism studies, food analysis, and the environmental sciences. This overview is followed by four original papers with new results from application of HRMS to drug screening, doping control, glycomics, and proteomics. We hope you find this special issue an invaluable source of information; it is intended for all readers with an interest in application of HRMS in clinical and forensic toxicology, doping control, drug metabolism, food analysis, environmental sciences, and proteomics and related fields. We thank all authors for submitting their interesting contributions for this special issue, the referees for their critical but constructive comments, and the editorial office and the editors for their friendly cooperation.}, number={5}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Maurer, Hans H. and Muddiman, David C.}, year={2012}, month={May}, pages={1201–1202} }
 @article{gokce_franck_oh_dean_muddiman_2012, title={In-Depth Analysis of the Magnaporthe oryzae Conidial Proteome}, volume={11}, ISSN={["1535-3907"]}, DOI={10.1021/pr300604s}, abstractNote={The filamentous fungus Magnaporthe oryzae (M. oryzae) is the causative agent of rice blast disease and presents a significant threat to worldwide rice production. To establish the groundwork for future research on the pathogenic development of M. oryzae, a global proteomic study of conidia was performed. The filter aided sample preparation method (FASP) and anion StageTip fractionation combined with long, optimized shallow 210 min nanoLC gradients prior to mass spectrometry analysis on an Orbitrap XL was applied, which resulted in a doubling of protein identifications in comparison to our previous GeLC analysis. Herein, we report the identification of 2912 conidial proteins at a 1% protein false discovery rate (FDR) and we present the most extensive study performed on M. oryzae conidia to date. A similar distribution between identified proteins and the predicted proteome was observed when subcellular localization analysis was performed, suggesting the detected proteins build a representative portion of the predicted proteome. A higher percentage of cytoplasmic proteins (associated with translation, energy, and metabolism) were observed in the conidial proteome relative to the whole predicted proteome. Conversely, nuclear and extracellular proteins were less well represented in the conidial proteome. Further analysis by gene ontology revealed biological insights into identified proteins important for central metabolic processes and the physiology of conidia.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Gokce, Emine and Franck, William L. and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2012}, month={Dec}, pages={5827–5835} }
 @article{robichaud_barry_garrard_muddiman_2013, title={Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) Imaging Source Coupled to a FT-ICR Mass Spectrometer}, volume={24}, ISSN={["1044-0305"]}, DOI={10.1007/s13361-012-0505-9}, abstractNote={Mass spectrometry imaging (MSI) allows for the direct monitoring of the abundance and spatial distribution of chemical compounds over the surface of a tissue sample. This technology has opened the field of mass spectrometry to numerous innovative applications over the past 15 years. First used with SIMS and MALDI MS that operate under vacuum, interest has grown for mass spectrometry ionization sources that allow for effective imaging but where the analysis can be performed at ambient pressure with minimal or no sample preparation. We introduce here a versatile source for MALDESI imaging analysis coupled to a hybrid LTQ-FT-ICR mass spectrometer. The imaging source offers single shot or multi-shot capability per pixel with full control over the laser repetition rate and mass spectrometer scanning cycle. Scanning rates can be as fast as 1 pixel/second and a spatial resolution of 45 μm was achieved with oversampling. Design and integration of a versatile IR-MALDESI imaging source offering multi-shot capability with a commercial FT-ICR mass spectrometer.}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Robichaud, Guillaume and Barry, Jeremy A. and Garrard, Kenneth P. and Muddiman, David C.}, year={2013}, month={Jan}, pages={92–100} }
 @article{shuford_sederoff_chiang_muddiman_2012, title={Peptide Production and Decay Rates Affect the Quantitative Accuracy of Protein Cleavage Isotope Dilution Mass Spectrometry (PC-IDMS)}, volume={11}, ISSN={1535-9476 1535-9484}, url={http://dx.doi.org/10.1074/mcp.O112.017145}, DOI={10.1074/mcp.o112.017145}, abstractNote={No consensus has been reached on the proper time to add stable-isotope labeled (SIL) peptides in protein cleavage isotope dilution mass spectrometry workflows. While quantifying 24 monolignol pathway enzymes in the xylem tissue of Populus trichocarpa, we compared the protein concentrations obtained when adding the SIL standard peptides concurrently with the enzyme or after quenching of the digestion (i.e. postdigestion) and observed discrepancies for nearly all tryptic peptides investigated. In some cases, greater than 30-fold differences were observed. To explain these differences and potentially correct for them, we developed a mathematical model based on pseudo-first-order kinetics to account for the dynamic production and decay (e.g. degradation and precipitation) of the native peptide targets in conjunction with the decay of the SIL peptide standards. A time course study of the digests confirmed the results predicted by the proposed model and revealed that the discrepancy between concurrent and postdigestion introduction of the SIL standards was related to differential decay experienced by the SIL peptide and the native peptide in each method. Given these results, we propose concurrent introduction of the SIL peptide is most appropriate, though not free from bias. Mathematical modeling of this method reveals that overestimation of protein quantities would still result when rapid peptide decay occurs and that this bias would be further exaggerated by slow proteolysis. We derive a simple equation to estimate the bias for each peptide based on the relative rates of production and decay. According to this equation, nearly half of the peptides evaluated here were estimated to have quantitative errors greater than 10% and in a few cases over 100%. We conclude that the instability of peptides can often significantly bias the protein quantities measured in protein cleavage isotope dilution mass spectrometry-based assays and suggest peptide stability be made a priority when selecting peptides to use for quantification.}, number={9}, journal={Molecular & Cellular Proteomics}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Shuford, Christopher M. and Sederoff, Ronald R. and Chiang, Vincent L. and Muddiman, David C.}, year={2012}, month={May}, pages={814–823} }
 @article{koryakina_mcarthur_randall_draelos_musiol_muddiman_weber_williams_2012, title={Poly Specific trans-Acyltransferase Machinery Revealed via Engineered Acyl-CoA Synthetases}, volume={8}, ISSN={1554-8929 1554-8937}, url={http://dx.doi.org/10.1021/cb3003489}, DOI={10.1021/cb3003489}, abstractNote={Polyketide synthases construct polyketides with diverse structures and biological activities via the condensation of extender units and acyl thioesters. Although a growing body of evidence suggests that polyketide synthases might be tolerant to non-natural extender units, in vitro and in vivo studies aimed at probing and utilizing polyketide synthase specificity are severely limited to only a small number of extender units, owing to the lack of synthetic routes to a broad variety of acyl-CoA extender units. Here, we report the construction of promiscuous malonyl-CoA synthetase variants that can be used to synthesize a broad range of malonyl-CoA extender units substituted at the C2-position, several of which contain handles for chemoselective ligation and are not found in natural biosynthetic systems. We highlighted utility of these enzymes by probing the acyl-CoA specificity of several trans-acyltransferases, leading to the unprecedented discovery of poly specificity toward non-natural extender units, several of which are not found in naturally occurring biosynthetic pathways. These results reveal that polyketide biosynthetic machinery might be more tolerant to non-natural substrates than previously established, and that mutant synthetases are valuable tools for probing the specificity of biosynthetic machinery. Our data suggest new synthetic biology strategies for harnessing this promiscuity and enabling the regioselective modification of polyketides.}, number={1}, journal={ACS Chemical Biology}, publisher={American Chemical Society (ACS)}, author={Koryakina, Irina and McArthur, John and Randall, Shan and Draelos, Matthew M. and Musiol, Ewa M. and Muddiman, David C. and Weber, Tilmann and Williams, Gavin J.}, year={2012}, month={Oct}, pages={200–208} }
 @article{oh_franck_han_shows_gokce_muddiman_dean_2012, title={Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae}, volume={7}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0042868}, DOI={10.1371/journal.pone.0042868}, abstractNote={Protein ubiquitination, which is highly selective, regulates many important biological processes including cellular differentiation and pathogenesis in eukaryotic cells. Here, we integrated pharmacological, molecular and proteomic approaches to explore the role of ubiquitination in Magnaporthe oryzae, the leading fungal disease of rice world-wide. Inhibition of ubiquitin-mediated proteolysis using the 26S proteasome inhibitor, Bortezomib, significantly attenuated conidia germination, appressorium formation and pathogenicity in M. oryzae. Gene expression analysis revealed that many genes associated with protein ubiquitination were developmentally regulated during conidia germination. Only a few, including a polyubiquitin encoding gene, MGG_01282, were more abundantly expressed during appressorium formation and under nitrogen starvation. Targeted gene deletion of MGG_01282, in addition to a significant reduction in protein ubiquitination as determined by immuno blot assays, resulted in pleiotropic effects on M. oryzae including reduced growth and sporulation, abnormal conidia morphology, reduced germination and appressorium formation, and the inability to cause disease. Mutants were also defective in sexual development and were female sterile. Using mass spectrometry, we identified 63 candidate polyubiquitinated proteins under nitrogen starvation, which included overrepresentation of proteins involved in translation, transport and protein modification. Our study suggests that ubiquitination of target proteins plays an important role in nutrient assimilation, development and pathogenicity of M. oryzae.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Oh, Yeonyee and Franck, William L. and Han, Sang-Oh and Shows, Angela and Gokce, Emine and Muddiman, David C. and Dean, Ralph A.}, editor={Nielsen, KirstenEditor}, year={2012}, month={Aug}, pages={e42868} }
 @article{walker_carlisle_muddiman_2012, title={Systematic Comparison of Reverse Phase and Hydrophilic Interaction Liquid Chromatography Platforms for the Analysis of N-Linked Glycans}, volume={84}, ISSN={["1520-6882"]}, DOI={10.1021/ac3012494}, abstractNote={Due to the hydrophilic nature of glycans, reverse phase chromatography has not been widely used as a glycomic separation technique coupled to mass spectrometry. Other approaches such as hydrophilic interaction chromatography and porous graphitized carbon chromatography are often employed, though these strategies frequently suffer from decreased chromatographic resolution, long equilibration times, indefinite retention, and column bleed. Herein, it is shown that, through an efficient hydrazone formation derivatization of N-linked glycans (~4 h of additional sample preparation time which is carried out in parallel), numerous experimental and practical advantages are gained when analyzing the glycans by online reverse phase chromatography. These benefits include an increased number of glycans detected, increased peak capacity of the separation, and the ability to analyze glycans on the identical liquid chromatography-mass spectrometry platform commonly used for proteomic analyses. The data presented show that separation of derivatized N-linked glycans by reverse phase chromatography significantly out-performs traditional separation of native or derivatized glycans by hydrophilic interaction chromatography. Furthermore, the movement to a more ubiquitous separation technique will afford numerous research groups the opportunity to analyze both proteomic and glycomic samples on the same platform with minimal time and physical change between experiments, increasing the efficiency of "multiomic" biological approaches.}, number={19}, journal={ANALYTICAL CHEMISTRY}, author={Walker, S. Hunter and Carlisle, Brandon C. and Muddiman, David C.}, year={2012}, month={Oct}, pages={8198–8206} }
 @article{sarkar_randall_muddiman_rao_2012, title={Targeted Proteomics of the Secretory Pathway Reveals the Secretome of Mouse Embryonic Fibroblasts and Human Embryonic Stem Cells}, volume={11}, ISSN={["1535-9484"]}, DOI={10.1074/mcp.m112.020503}, abstractNote={Proteins endogenously secreted by human embryonic stem cells (hESCs) and those present in hESC culture medium are critical regulators of hESC self-renewal and differentiation. Current MS-based approaches for identifying secreted proteins rely predominantly on MS analysis of cell culture supernatants. Here we show that targeted proteomics of secretory pathway organelles is a powerful alternate approach for interrogating the cellular secretome. We have developed procedures to obtain subcellular fractions from mouse embryonic fibroblasts (MEFs) and hESCs that are enriched in secretory pathway organelles while ensuring retention of the secretory cargo. MS analysis of these fractions from hESCs cultured in MEF conditioned medium (MEF-CM) or MEFs exposed to hESC medium revealed 99 and 129 proteins putatively secreted by hESCs and MEFs, respectively. Of these, 53 and 62 proteins have been previously identified in cell culture supernatants of MEFs and hESCs, respectively, thus establishing the validity of our approach. Furthermore, 76 and 37 putatively secreted proteins identified in this study in MEFs and hESCs, respectively, have not been reported in previous MS analyses. The identification of low abundance secreted proteins via MS analysis of cell culture supernatants typically necessitates the use of altered culture conditions such as serum-free medium. However, an altered medium formulation might directly influence the cellular secretome. Indeed, we observed significant differences between the abundances of several secreted proteins in subcellular fractions isolated from hESCs cultured in MEF-CM and those exposed to unconditioned hESC medium for 24 h. In contrast, targeted proteomics of secretory pathway organelles does not require the use of customized media. We expect that our approach will be particularly valuable in two contexts highly relevant to hESC biology: obtaining a temporal snapshot of proteins secreted in response to a differentiation trigger, and identifying proteins secreted by cells that are isolated from a heterogeneous population.}, number={12}, journal={MOLECULAR & CELLULAR PROTEOMICS}, author={Sarkar, Prasenjit and Randall, Shan M. and Muddiman, David C. and Rao, Balaji M.}, year={2012}, month={Dec}, pages={1829–1839} }
 @article{sarkar_collier_randall_muddiman_rao_2012, title={The subcellular proteome of undifferentiated human embryonic stem cells}, volume={12}, ISSN={["1615-9853"]}, DOI={10.1002/pmic.201100507}, abstractNote={AbstractWe have characterized the subcellular proteome of human embryonic stem cells (hESCs) through MS analysis of the membrane, cytosolic, and nuclear fractions, isolated from the same sample of undifferentiated hESCs. Strikingly, 74% of all proteins identified were detected in a single subcellular fraction; we also carried out immunofluorescence studies to validate the subcellular localization suggested by proteomic analysis, for a subset of proteins. Our approach resulted in deeper proteome coverage – peptides mapping to 893, 2475, and 1185 proteins were identified in the nuclear, cytosolic, and membrane fractions, respectively. Additionally, we used spectral counting to estimate the relative abundance of all cytosolic proteins. A large number of proteins relevant to hESC biology, including growth factor receptors, cell junction proteins, transcription factors, chromatin remodeling proteins, and histone modifying enzymes were identified. Our analysis shows that components of a large number of interacting signaling pathways are expressed in hESCs. Finally, we show that proteomic analysis of the endoplasmic reticulum (ER) and Golgi compartments is a powerful alternative approach to identify secreted proteins since these are synthesized in the ER and transit through the Golgi. Taken together, our results show that systematic subcellular proteomic analysis is a valuable tool for studying hESC biology.}, number={3}, journal={PROTEOMICS}, author={Sarkar, Prasenjit and Collier, Timothy S. and Randall, Shan M. and Muddiman, David C. and Rao, Balaji M.}, year={2012}, month={Feb}, pages={421–430} }
 @article{shuford_poteat_buchwalter_muddiman_2011, title={Absolute quantification of free glutathione and cysteine in aquatic insects using isotope dilution and selected reaction monitoring}, volume={402}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/S00216-011-5416-2}, DOI={10.1007/s00216-011-5416-2}, abstractNote={A simple and robust isotope dilution mass spectrometry-based assay was developed for the determination of free cysteine and glutathione (GSH) in aquatic insects. Several experimental parameters were evaluated and optimized to provide specific and sensitive detection of both compounds by in situ derivatization with N-ethylmaleimide followed by acid alkylation quenching and reverse-phased liquid chromatography coupled with selected reaction monitoring. For both targets, the assay was evaluated over a concentration range of 0.313 to 320 μM and was demonstrated to have a quantitative dynamic range spanning nearly three orders of magnitude, with lower limits of quantification being 0.330 μM for GSH and 0.370 μM for cysteine. Additionally, measurements were observed to be highly reproducible over the course of several days. When applied to the analysis of four different species of insects, large biological variation between and within species was observed. Different feeding regimens were also tested within two species of insects but statistical comparisons revealed no significant difference in the levels of either compound.}, number={1}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Shuford, Christopher M. and Poteat, Monica D. and Buchwalter, David B. and Muddiman, David C.}, year={2011}, month={Sep}, pages={357–366} }
 @misc{shuford_muddiman_2011, title={Capitalizing on the hydrophobic bias of electrospray ionization through chemical modification in mass spectrometry-based proteomics}, volume={8}, ISSN={["1744-8387"]}, DOI={10.1586/epr.11.24}, abstractNote={Protein chemical derivatization has emerged as an invaluable bioanalytical approach in mass spectrometry-based proteomics with nearly unlimited potential. To date, derivatization strategies in proteomics have primarily focused on improving mass spectral identification and relative quantification of proteins, as well as increasing enrichment yield from complex mixtures. However, there is a great opportunity to develop and exploit front-end chemical processes to enhance the ability to detect low-abundant peptides and proteins for a large number of applications. The content of this article focuses on improvements in targeted, mass spectrometry-based proteomic strategies, achieved by taking advantage of the mechanism of ESI through the use of hydrophobic chemical derivatization.}, number={3}, journal={EXPERT REVIEW OF PROTEOMICS}, author={Shuford, Christopher M. and Muddiman, David C.}, year={2011}, month={Jun}, pages={317–323} }
 @article{collier_randall_sarkar_rao_dean_muddiman_2011, title={Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression}, volume={25}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.5151}, abstractNote={Protein quantification is one of the principal goals of mass spectrometry (MS)‐based proteomics, and many strategies exist to achieve it. Several approaches involve the incorporation of a stable‐isotope label using either chemical derivatization, enzymatically catalyzed incorporation of 18O, or metabolic labeling in a cell or tissue culture. These techniques can be cost or time prohibitive or not amenable to the biological system of interest. Label‐free techniques including those utilizing integrated ion abundance and spectral counting offer an alternative to stable‐isotope‐based methodologies. Herein, we present the comparison of stable‐isotope labeling of amino acids in cell culture (SILAC) with spectral counting for the quantification of human embryonic stem cells as they differentiate toward the trophectoderm at three time points. Our spectral counting experimental strategy resulted in the identification of 2641 protein groups across three time points with an average sequence coverage of 30.3%, of which 1837 could be quantified with more than five spectral counts. SILAC quantification was able to identify 1369 protein groups with an average coverage of 24.7%, of which 1027 could be quantified across all time points. Within this context we further explore the capacity of each strategy for proteome coverage, variation in quantification, and the relative sensitivity of each technique to the detection of change in relative protein expression. Copyright © 2011 John Wiley & Sons, Ltd.}, number={17}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Collier, Timothy S. and Randall, Shan M. and Sarkar, Prasenjit and Rao, Balaji M. and Dean, Ralph A. and Muddiman, David C.}, year={2011}, month={Sep}, pages={2524–2532} }
 @article{robichaud_dixon_potturi_cassidy_edwards_sohn_dow_muddiman_2011, title={Design, modeling, fabrication, and evaluation of the air amplifier for improved detection of biomolecules by electrospray ionization mass spectrometry}, volume={300}, ISSN={["1873-2798"]}, DOI={10.1016/j.ijms.2010.04.006}, abstractNote={Through a multi-disciplinary approach, the air amplifier is being evolved as a highly engineered device to improve detection limits of biomolecules when using electrospray ionization. Several key aspects have driven the modifications to the device through experimentation and simulations. We have developed a computer simulation that accurately portrays actual conditions and the results from these simulations are corroborated by the experimental data. These computer simulations can be used to predict outcomes from future designs resulting in a design process that is efficient in terms of financial cost and time. We have fabricated a new device with annular gap control over a range of 50 to 70 μm using piezoelectric actuators. This has enabled us to obtain better aerodynamic performance when compared to the previous design (2× more vacuum) and also more reproducible results. This is allowing us to study a broader experimental space than the previous design which is critical in guiding future directions. This work also presents and explains the principles behind a fractional factorial design of experiments methodology for testing a large number of experimental parameters in an orderly and efficient manner to understand and optimize the critical parameters that lead to obtain improved detection limits while minimizing the number of experiments performed. Preliminary results showed that several folds of improvements could be obtained for certain condition of operations (up to 34 folds).}, number={2-3}, journal={INTERNATIONAL JOURNAL OF MASS SPECTROMETRY}, author={Robichaud, Guillaume and Dixon, R. Brent and Potturi, Amarnatha S. and Cassidy, Dan and Edwards, Jack R. and Sohn, Alex and Dow, Thomas A. and Muddiman, David C.}, year={2011}, month={Mar}, pages={99–107} }
 @article{gokce_shuford_franck_dean_muddiman_2011, title={Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows}, volume={22}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-011-0237-2}, abstractNote={Normalization of spectral counts (SpCs) in label-free shotgun proteomic approaches is important to achieve reliable relative quantification. Three different SpC normalization methods, total spectral count (TSpC) normalization, normalized spectral abundance factor (NSAF) normalization, and normalization to selected proteins (NSP) were evaluated based on their ability to correct for day-to-day variation between gel-based sample preparation and chromatographic performance. Three spectral counting data sets obtained from the same biological conidia sample of the rice blast fungus Magnaporthe oryzae were analyzed by 1D gel and liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). Equine myoglobin and chicken ovalbumin were spiked into the protein extracts prior to 1D-SDS- PAGE as internal protein standards for NSP. The correlation between SpCs of the same proteins across the different data sets was investigated. We report that TSpC normalization and NSAF normalization yielded almost ideal slopes of unity for normalized SpC versus average normalized SpC plots, while NSP did not afford effective corrections of the unnormalized data. Furthermore, when utilizing TSpC normalization prior to relative protein quantification, t-testing and fold-change revealed the cutoff limits for determining real biological change to be a function of the absolute number of SpCs. For instance, we observed the variance decreased as the number of SpCs increased, which resulted in a higher propensity for detecting statistically significant, yet artificial, change for highly abundant proteins. Thus, we suggest applying higher confidence level and lower fold-change cutoffs for proteins with higher SpCs, rather than using a single criterion for the entire data set. By choosing appropriate cutoff values to maintain a constant false positive rate across different protein levels (i.e., SpC levels), it is expected this will reduce the overall false negative rate, particularly for proteins with higher SpCs.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Gokce, Emine and Shuford, Christopher M. and Franck, William L. and Dean, Ralph A. and Muddiman, David C.}, year={2011}, month={Dec}, pages={2199–2208} }
 @article{zhao_li_chen_tan_wang_lehman_muddiman_yang_2011, title={Facile Self-Assembly of Supramolecular Hexakisferrocenyl Triangles via Coordination-Driven Self-Assembly and Their Electrochemical Behavior}, volume={30}, ISSN={["1520-6041"]}, DOI={10.1021/om2003305}, abstractNote={A novel family of hexakis(ferrocenyl) triangles has been successfully constructed from newly designed 60° ferrocenyl building blocks via coordination-driven self-assembly. The structures of all triangles were characterized by multinuclear NMR (1H and 31P), ESI-TOF-MS, and elemental analysis, and their electrochemical behavior has been investigated.}, number={13}, journal={ORGANOMETALLICS}, author={Zhao, Guang-Zhen and Li, Quan-Jie and Chen, Li-Jun and Tan, Hongwei and Wang, Cui-Hong and Lehman, Danielle A. and Muddiman, David C. and Yang, Hai-Bo}, year={2011}, month={Jul}, pages={3637–3642} }
 @article{samy el-shall_muddiman_2011, title={Foreword}, volume={300}, ISSN={1387-3806}, url={http://dx.doi.org/10.1016/j.ijms.2010.11.015}, DOI={10.1016/j.ijms.2010.11.015}, number={2-3}, journal={International Journal of Mass Spectrometry}, publisher={Elsevier BV}, author={Samy El-Shall, M. and Muddiman, David C.}, year={2011}, month={Mar}, pages={72–73} }
 @article{barry_muddiman_2011, title={Global optimization of the infrared matrix-assisted laser desorption electrospray ionization (IR MALDESI) source for mass spectrometry using statistical design of experiments}, volume={25}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.5262}, abstractNote={Design of experiments (DOE) is a systematic and cost‐effective approach to system optimization by which the effects of multiple parameters and parameter interactions on a given response can be measured in few experiments. Herein, we describe the use of statistical DOE to improve a few of the analytical figures of merit of the infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) source for mass spectrometry. In a typical experiment, bovine cytochrome c was ionized via electrospray, and equine cytochrome c was desorbed and ionized by IR‐MALDESI such that the ratio of equine:bovine was used as a measure of the ionization efficiency of IR‐MALDESI. This response was used to rank the importance of seven source parameters including flow rate, laser fluence, laser repetition rate, ESI emitter to mass spectrometer inlet distance, sample stage height, sample plate voltage, and the sample to mass spectrometer inlet distance. A screening fractional factorial DOE was conducted to designate which of the seven parameters induced the greatest amount of change in the response. These important parameters (flow rate, stage height, sample to mass spectrometer inlet distance, and laser fluence) were then studied at higher resolution using a full factorial DOE to obtain the globally optimized combination of parameter settings. The optimum combination of settings was then compared with our previously determined settings to quantify the degree of improvement in detection limit. The limit of detection for the optimized conditions was approximately 10 attomoles compared with 100 femtomoles for the previous settings, which corresponds to a four orders of magnitude improvement in the detection limit of equine cytochrome c. Copyright © 2011 John Wiley & Sons, Ltd.}, number={23}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Barry, Jeremy A. and Muddiman, David C.}, year={2011}, month={Dec}, pages={3527–3536} }
 @article{walker_lilley_enamorado_comins_muddiman_2011, title={Hydrophobic Derivatization of N-linked Glycans for Increased Ion Abundance in Electrospray Ionization Mass Spectrometry}, volume={22}, ISSN={["1044-0305"]}, DOI={10.1007/s13361-011-0140-x}, abstractNote={A library of neutral, hydrophobic reagents was synthesized for use as derivatizing agents in order to increase the ion abundance of N-linked glycans in electrospray ionization mass spectrometry (ESI MS). The glycans are derivatized via hydrazone formation and are shown to increase the ion abundance of a glycan standard more than 4-fold. Additionally, the data show that the systematic addition of hydrophobic surface area to the reagent increases the glycan ion abundance, a property that can be further exploited in the analysis of glycans. The results of this study will direct the future synthesis of hydrophobic reagents for glycan analysis using the correlation between hydrophobicity and theoretical non-polar surface area calculation to facilitate the development of an optimum tag for glycan derivatization. The compatibility and advantages of this method are demonstrated by cleaving and derivatizing N-linked glycans from human plasma proteins. The ESI-MS signal for the tagged glycans are shown to be significantly more abundant, and the detection of negatively charged sialylated glycans is enhanced.}, number={8}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Walker, S. Hunter and Lilley, Laura M. and Enamorado, Monica F. and Comins, Daniel L. and Muddiman, David C.}, year={2011}, month={Aug}, pages={1309–1317} }
 @article{chang_muddiman_2011, title={Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms}, volume={12}, journal={BMC Genomics}, author={Chang, K. Y. and Muddiman, D. C.}, year={2011} }
 @article{andrews_dean_hawkridge_muddiman_2011, title={Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments}, volume={22}, ISSN={["1879-1123"]}, DOI={10.1007/s13361-011-0075-2}, abstractNote={Design of experiments (DOE) was used to determine improved settings for a LTQ-Orbitrap XL to maximize proteome coverage of Saccharomyces cerevisiae. A total of nine instrument parameters were evaluated with the best values affording an increase of approximately 60% in proteome coverage. Utilizing JMP software, 2 DOE screening design tables were generated and used to specify parameter values for instrument methods. DOE 1, a fractional factorial design, required 32 methods fully resolving the investigation of six instrument parameters involving only half the time necessary for a full factorial design of the same resolution. It was advantageous to complete a full factorial design for the analysis of three additional instrument parameters. Measured with a maximum of 1% false discovery rate, protein groups, unique peptides, and spectral counts gauged instrument performance. Randomized triplicate nanoLC-LTQ-Orbitrap XL MS/MS analysis of the S. cerevisiae digest demonstrated that the following five parameters significantly influenced proteome coverage of the sample: (1) maximum ion trap ionization time; (2) monoisotopic precursor selection; (3) number of MS/MS events; (4) capillary temperature; and (5) tube lens voltage. Minimal influence on the proteome coverage was observed for the remaining four parameters (dynamic exclusion duration, resolving power, minimum count threshold to trigger a MS/MS event, and normalized collision energy). The DOE approach represents a time- and cost-effective method for empirically optimizing MS-based proteomics workflows including sample preparation, LC conditions, and multiple instrument platforms.}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Andrews, Genna L. and Dean, Ralph A. and Hawkridge, Adam M. and Muddiman, David C.}, year={2011}, month={Apr}, pages={773–783} }
 @article{gokce_andrews_dean_muddiman_2011, title={Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS}, volume={879}, ISSN={["1873-376X"]}, DOI={10.1016/j.jchromb.2011.01.032}, abstractNote={Fractionation prior to mass spectrometry is an indispensable step in proteomics. In this paper we report the success of performing offline reversed phase high pressure liquid chromatography (HPLC) fractionation on a C18 2.0 mm×150 mm column at the peptide level with microliter per minute flow rates prior to online nano-flow reversed phase liquid chromatography mass spectrometry (nanoLC-MS) using the well-studied fungus Saccharomyces cerevisiae. A C18 75 μm×150 mm column was used online and the online elution gradients for each fraction were adjusted in order to obtain well resolved separation. Comparing this method directly to only performing nanoLC-MS we observed a 61.6% increase in the number of identified proteins. At a 1% false discovery rate 1028 proteins were identified using two dimensions of RPLC versus 636 proteins identified in a single nano-flow separation. The majority of proteins identified by one dimension of nano-LC were present in the proteins identified in our two dimensional strategy. Although increasing analysis time, this non-orthogonal and facile pre-fractionation method affords a more comprehensive examination of the proteome.}, number={9-10}, journal={JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES}, author={Gokce, Emine and Andrews, Genna L. and Dean, Ralph A. and Muddiman, David C.}, year={2011}, month={Mar}, pages={610–614} }
 @article{el-shall_muddiman_2011, title={John B. Fenn special issue recognizing the science of Professor John B. Fenn foreword}, volume={300}, number={2-3}, journal={International Journal of Mass Spectrometry}, author={El-Shall, M. S. and Muddiman, D. C.}, year={2011}, pages={72–73} }
 @article{muddiman_2011, title={John Bennett Fenn (1917-2010)}, volume={331}, ISSN={["0036-8075"]}, DOI={10.1126/science.1201766}, abstractNote={The hallmark of a southern gentleman's serpentine path to the Nobel Prize was his admiration for truth and the stimulation of a curious, prepared, and creative mind.}, number={6014}, journal={SCIENCE}, author={Muddiman, David C.}, year={2011}, month={Jan}, pages={160–160} }
 @article{chen_li_shuford_liu_muddiman_sederoff_chiang_2011, title={Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis}, volume={108}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1116416109}, abstractNote={
            The hydroxylation of 4- and 3-ring carbons of cinnamic acid derivatives during monolignol biosynthesis are key steps that determine the structure and properties of lignin. Individual enzymes have been thought to catalyze these reactions. In stem differentiating xylem (SDX) of
            Populus trichocarpa
            , two cinnamic acid 4-hydroxylases (PtrC4H1 and PtrC4H2) and a
            p
            -coumaroyl ester 3-hydroxylase (PtrC3H3) are the enzymes involved in these reactions. Here we present evidence that these hydroxylases interact, forming heterodimeric (PtrC4H1/C4H2, PtrC4H1/C3H3, and PtrC4H2/C3H3) and heterotrimeric (PtrC4H1/C4H2/C3H3) membrane protein complexes. Enzyme kinetics using yeast recombinant proteins demonstrated that the enzymatic efficiency (
            V
            max
            /
            k
            m
            ) for any of the complexes is 70–6,500 times greater than that of the individual proteins. The highest increase in efficiency was found for the PtrC4H1/C4H2/C3H3-mediated
            p
            -coumaroyl ester 3-hydroxylation. Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for these multiprotein complexes. The activities of the recombinant and SDX plant proteins demonstrate two protein-complex–mediated 3-hydroxylation paths in monolignol biosynthesis in
            P
            .
            trichocarpa
            SDX; one converts
            p
            -coumaric acid to caffeic acid and the other converts
            p
            -coumaroyl shikimic acid to caffeoyl shikimic acid. Cinnamic acid 4-hydroxylation is also mediated by the same protein complexes. These results provide direct evidence for functional involvement of membrane protein complexes in monolignol biosynthesis.
          }, number={52}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Chen, Hsi-Chuan and Li, Quanzi and Shuford, Christopher M. and Liu, Jie and Muddiman, David C. and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2011}, month={Dec}, pages={21253–21258} }
 @inbook{bereman_muddiman_2011, title={N-Linked Global Glycan Profiling by NanoLC Mass Spectrometry}, ISBN={9781617793189 9781617793196}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-61779-319-6_7}, DOI={10.1007/978-1-61779-319-6_7}, abstractNote={A method is detailed for the global profiling of underivatized N-linked glycans that are derived from complex protein mixtures. The method consists of five main steps that include the following: (1) protein denaturation; (2) enzymatic digestion; (3) solid phase extraction; (4) nanoLC MS analysis; and (5) data interpretation. Materials, methods, and algorithms for the identification of both glycan composition and structure are summarized. In addition, potential problems and their resolutions are addressed.}, booktitle={Methods in Molecular Biology}, publisher={Humana Press}, author={Bereman, Michael S. and Muddiman, David C.}, year={2011}, pages={87–97} }
 @article{dixon_bereman_petitte_hawkridge_muddiman_2011, title={One-year plasma N-linked glycome intra-individual and inter-individual variability in the chicken model of spontaneous ovarian adenocarcinoma}, volume={305}, ISSN={["1387-3806"]}, url={http://europepmc.org/abstract/med/21845070}, DOI={10.1016/j.ijms.2010.05.023}, abstractNote={Spontaneous epithelial ovarian cancer (EOC) in the chicken presents a similar pathogenesis compared with humans including CA-125 expression and genetic mutational frequencies (e.g., p53). The high prevalence of spontaneous EOC chickens also provides a unique experimental model for biomarker discovery at the genomic, proteomic, glycomic, and metabolomic level. In an effort to exploit this unique model for biomarker discovery, longitudinal plasma samples were collected from chickens at three month intervals for one year. The study described herein involved cleaving the N-glycans from these longitudinal chicken plasma samples and analyzing them via nanoLC-FTMS/MS. Glycans identified in this study were previously found in human plasma and this work provides a promising methodology to enable longitudinal studies of the N-linked plasma glycome profile during EOC progression. The structure, abundance, and intra-variability and inter-variability for 35 N-linked glycans identified in this study are reported. The full potential of the chicken model for biomarker discovery has yet to be realized, but the initial interrogation of longitudinally-procured samples provides evidence that supports the value of this strategy in the search for glycomic biomarkers.}, number={2-3}, journal={INTERNATIONAL JOURNAL OF MASS SPECTROMETRY}, author={Dixon, R. Brent and Bereman, Michael S. and Petitte, James N. and Hawkridge, Adam M. and Muddiman, David C.}, year={2011}, month={Aug}, pages={79–86} }
 @article{andrews_simons_young_hawkridge_muddiman_2011, title={Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)}, volume={83}, ISSN={["0003-2700"]}, DOI={10.1021/ac200812d}, abstractNote={The TripleTOF 5600 System, a hybrid quadrupole time-of-flight mass spectrometer, was evaluated to explore the key figures of merit in generating peptide and protein identifications that included spectral acquisition rates, data quality, proteome coverage, and biological depth. Employing a Saccharomyces cerevisiae tryptic digest, careful consideration of several performance features demonstrated that the speed of the TripleTOF contributed most to the resultant data. The TripleTOF system was operated with 8, 20, and 50 MS/MS events in an effort to compare with other MS technologies and to demonstrate the abilities of the instrument platform.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Andrews, Genna L. and Simons, Brigitte L. and Young, J. Bryce and Hawkridge, Adam M. and Muddiman, David C.}, year={2011}, month={Jul}, pages={5442–5446} }
 @article{blake_walker_muddiman_hinks_beck_2011, title={Spectral Accuracy and Sulfur Counting Capabilities of the LTQ-FT-ICR and the LTQ-Orbitrap XL for Small Molecule Analysis}, volume={22}, ISSN={["1044-0305"]}, DOI={10.1007/s13361-011-0244-3}, abstractNote={Color Index Disperse Yellow 42 (DY42), a high-volume disperse dye for polyester, was used to compare the capabilities of the LTQ-Orbitrap XL and the LTQ-FT-ICR with respect to mass measurement accuracy (MMA), spectral accuracy, and sulfur counting. The results of this research will be used in the construction of a dye database for forensic purposes; the additional spectral information will increase the confidence in the identification of unknown dyes found in fibers at crime scenes. Initial LTQ-Orbitrap XL data showed MMAs greater than 3 ppm and poor spectral accuracy. Modification of several Orbitrap installation parameters (e.g., deflector voltage) resulted in a significant improvement of the data. The LTQ-FT-ICR and LTQ-Orbitrap XL (after installation parameters were modified) exhibited MMA ≤ 3 ppm, good spectral accuracy (χ2 values for the isotopic distribution ≤ 2), and were correctly able to ascertain the number of sulfur atoms in the compound at all resolving powers investigated for AGC targets of 5.00 × 105 and 1.00 × 106.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Blake, Samantha L. and Walker, S. Hunter and Muddiman, David C. and Hinks, David and Beck, Keith R.}, year={2011}, month={Dec}, pages={2269–2275} }
 @article{walker_budhathoki-uprety_novak_muddiman_2011, title={Stable-Isotope Labeled Hydrophobic Hydrazide Reagents for the Relative Quantification of N-Linked Glycans by Electrospray Ionization Mass Spectrometry}, volume={83}, ISSN={["1520-6882"]}, url={http://dx.doi.org/10.1021/ac201376q}, DOI={10.1021/ac201376q}, abstractNote={This study presents the development of stable-isotope labeled hydrophobic, hydrazide reagents for the relative quantification of N-linked glycans. The P2GPN "light" ((12)C) and "heavy" ((13)C(6)) pair are used to differentially label two N-linked glycan samples. The samples are combined 1:1, separated using HILIC, and then mass differentiated and quantified using mass spectrometry. These reagents have several benefits: (1) impart hydrophobic character to the glycans affording an increase in electrospray ionization efficiency and MS detection; (2) indistinguishable chromatographic, MS, and MS/MS performance of the "light" and "heavy" reagents affording relative quantification; and (3) analytical variability is significantly reduced due to the two samples being mixed together after sample preparation. Obtaining these analytical benefits only requires ~4 h of sample preparation time. It is shown that these reagents are capable of quantifying changes in glycosylation in simple mixtures, and the analytical variability of the reagents in pooled plasma samples is shown to be less than ±30%. Additionally, the incorporation of an internal standard allows one to account for the difference in systematic error between the two samples due to the samples being processed in parallel and not mixed until after derivatization.}, number={17}, journal={ANALYTICAL CHEMISTRY}, author={Walker, S. Hunter and Budhathoki-Uprety, Januka and Novak, Bruce M. and Muddiman, David C.}, year={2011}, month={Sep}, pages={6738–6745} }
 @article{yang_gurgel_williams_bobay_cavanagh_muddiman_carbonell_2009, title={Binding site on human immunoglobulin G for the affinity ligand HWRGWV}, ISSN={0952-3499 1099-1352}, url={http://dx.doi.org/10.1002/jmr.967}, DOI={10.1002/jmr.967}, abstractNote={AbstractAffinity ligand HWRGWV has demonstrated the ability to isolate human immunoglobulin G (hIgG) from mammalian cell culture media. The ligand specifically binds hIgG through its Fc portion. This work shows that deglycosylation of hIgG has no influence on its binding to the HWRGWV ligand and the ligand does not compete with Protein A or Protein G in binding hIgG. It is suggested by the mass spectrometry (MS) data and docking simulation that HWRGWV binds to the pFc portion of hIgG and interacts with the amino acids in the loop Ser383–Asn389 (SNGQPEN) located in the CH3 domain. Subsequent modeling has suggested a possible three‐dimensional minimized solution structure for the interaction of hIgG and the HWRGWV ligand. The results support the fact that a peptide as small as a hexamer can have specific interactions with large proteins such as hIgG. Copyright © 2009 John Wiley & Sons, Ltd.}, journal={Journal of Molecular Recognition}, publisher={Wiley}, author={Yang, Haiou and Gurgel, Patrick V. and Williams, D. Keith, Jr and Bobay, Benjamin G. and Cavanagh, John and Muddiman, David C. and Carbonell, Ruben G.}, year={2009}, pages={n/a-n/a} }
 @article{yang_gurgel_williams_bobay_cavanagh_muddiman_carbonell_2010, title={Binding site on human immunoglobulin G for the affinity ligand HWRGWV}, volume={23}, number={3}, journal={Journal of Molecular Recognition}, author={Yang, H. O. and Gurgel, P. V. and Williams, D. K. and Bobay, B. G. and Cavanagh, J. and Muddiman, D. C. and Carbonell, R. G.}, year={2010}, pages={271–282} }
 @article{chang_georgianna_heber_payne_muddiman_2010, title={Detection of Alternative Splice Variants at the Proteome Level inAspergillus flavus}, volume={9}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr900602d}, DOI={10.1021/pr900602d}, abstractNote={Identification of proteins from proteolytic peptides or intact proteins plays an essential role in proteomics. Researchers use search engines to match the acquired peptide sequences to the target proteins. However, search engines depend on protein databases to provide candidates for consideration. Alternative splicing (AS), the mechanism where the exon of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore protein variants, enable higher eukaryotic organisms, with only a limited number of genes, to have the requisite complexity and diversity at the proteome level. Multiple alternative isoforms from one gene often share common segments of sequences. However, many protein databases only include a limited number of isoforms to keep minimal redundancy. As a result, the database search might not identify a target protein even with high quality tandem MS data and accurate intact precursor ion mass. We computationally predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from 20 371 expressed sequence tags to investigate whether an alternative splicing protein database can assign a greater proportion of mass spectrometry data. The newly constructed AS database provided 9807 new alternatively spliced variants in addition to 12 832 previously annotated proteins. The searches of the existing tandem MS spectra data set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal genes appeared to have multiple protein isoforms. In addition to the discovery of splice variants, AS database also showed potential to improve genome annotation. In summary, the introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome.}, number={3}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Chang, Kung-Yen and Georgianna, D. Ryan and Heber, Steffen and Payne, Gary A. and Muddiman, David C.}, year={2010}, month={Mar}, pages={1209–1217} }
 @article{collier_sarkar_franck_rao_dean_muddiman_2010, title={Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics}, volume={82}, ISSN={["1520-6882"]}, DOI={10.1021/ac101978b}, abstractNote={Numerous experimental strategies exist for relative protein quantification, one of the primary objectives of mass spectrometry based proteomics analysis. These strategies mostly involve the incorporation of a stable isotope label via either metabolic incorporation in cell or tissue culture (¹⁵N/¹⁴N metabolic labeling, stable isotope labeling by amino acids in cell culture (SILAC)), chemical derivatization (ICAT, iTRAQ, TMT), or enzymatically catalyzed incorporation (¹⁸O labeling). Also, these techniques can be cost or time prohibitive or not amenable to the biological system of interest (i.e., metabolic labeling of clinical samples, most animals, or fungi). This is the case with the quantification of fungal proteomes, which often require auxotroph mutants to fully metabolically label. Alternatively, label-free strategies for protein quantification such as using integrated ion abundance and spectral counting have been demonstrated for quantification affording over 2 orders of magnitude of dynamic range which is comparable to metabolic labeling strategies. Direct comparisons of these quantitative techniques are largely lacking in the literature but are highly warranted in order to evaluate the capabilities, limitations, and analytical variability of available quantitative strategies. Here, we present the direct comparison of SILAC to label-free quantification by spectral counting of an identical set of data from the bottom-up proteomic analysis of human embryonic stem cells, which are readily able to be quantified using both strategies, finding that both strategies result in a similar number of protein identifications. We also discuss necessary constraints for accurate quantification using spectral counting and assess the potential of this label-free strategy as a viable alternative for quantitative proteomics.}, number={20}, journal={ANALYTICAL CHEMISTRY}, author={Collier, Timothy S. and Sarkar, Prasenjit and Franck, William L. and Rao, Balaji M. and Dean, Ralph A. and Muddiman, David C.}, year={2010}, month={Oct}, pages={8696–8702} }
 @article{zhao_chen_wang_yang_ghosh_zheng_lyndon_muddiman_stang_2010, title={Facile Self-Assembly of Dendritic Multiferrocenyl Hexagons and Their Electrochemistry}, volume={29}, ISSN={["1520-6041"]}, DOI={10.1021/om1008605}, abstractNote={The design and synthesis of a new class of dendritic multiferrocenyl hexagons have been achieved via [3+3] coordination-driven self-assembly. The relative distribution of dendritic and ferrocenyl subunits on the periphery of supramolecular metallocycles can be precisely controlled. The structures of all compounds are confirmed by multinuclear NMR, ESI-MS/ESI-TOF-MS, and elemental analysis. The electrochemical properties of the newly designed dendritic multiferrocenyl complexes have been studied through cyclic voltammetry investigation.}, number={22}, journal={ORGANOMETALLICS}, author={Zhao, Guang-Zhen and Chen, Li-Jun and Wang, Cui-Hong and Yang, Hai-Bo and Ghosh, Koushik and Zheng, Yao-Rong and Lyndon, Matthew M. and Muddiman, David C. and Stang, Peter J.}, year={2010}, month={Nov}, pages={6137–6140} }
 @article{shuford_comins_whitten_burnett_muddiman_2010, title={Improving limits of detection for B-type natriuretic peptide using PC-IDMS: An application of the ALiPHAT strategy}, volume={135}, ISSN={["1364-5528"]}, DOI={10.1039/b919484c}, abstractNote={Hydrophobic tagging of biomolecules has been reported by our group and others to increase their ionization efficiency during electrospray ionization and facilitate their detection by mass spectrometry. As such, hydrophobic tagging should provide a viable method for augmenting MS-based quantification of low abundance proteins by decreasing their detection limits. Herein we have evaluated two commercial alkylation reagents and several newly synthesized hydrophobic alkylation reagents for their utility in quantifying B-type Natriuretic Peptide, a low abundance cardiac biomarker, by protein cleavage isotope dilution mass spectrometry. For the cysteine containing tryptic peptide evaluated, a approximately 3.5-fold decrease in the detection limit was observed for the best performing hydrophobic reagent, 2-iodo-N-octylacetamide, relative to the commonly used alkylation reagent, iodoacetamide. Additionally, we have evaluated the use of nonpolar surface areas as a metric for assessing the effectiveness of the alkylation reagents in improving ESI response.}, number={1}, journal={ANALYST}, author={Shuford, Christopher M. and Comins, Daniel L. and Whitten, Jerry L. and Burnett, John C., Jr. and Muddiman, David C.}, year={2010}, pages={36–41} }
 @article{bereman_comins_muddiman_2010, title={Increasing the hydrophobicity and electrospray response of glycans through derivatization with novel cationic hydrazides}, volume={46}, ISSN={["1364-548X"]}, DOI={10.1039/b915589a}, abstractNote={Novel tags are used to increase the hydrophobicity of glycans and impart a permanent charge yielding as great as a approximately 5-fold increase in electrospray response from both a standard and complex mixture.}, number={2}, journal={CHEMICAL COMMUNICATIONS}, author={Bereman, Michael S. and Comins, Daniel L. and Muddiman, David C.}, year={2010}, pages={237–239} }
 @article{walker_papas_comins_muddiman_2010, title={Interplay of Permanent Charge and Hydrophobicity in the Electrospray Ionization of Glycans}, volume={82}, ISSN={["1520-6882"]}, DOI={10.1021/ac101227a}, abstractNote={The analysis of N-linked glycans by mass spectrometry (MS) has been characterized by low signal-to-noise ratios and high limits of detection due to their hydrophilicity and lack of basic sites able to be protonated. As a result, every step in glycan sample preparation must be thoroughly optimized in order to minimize sample loss, contamination, and analytical variability. Importantly, properties of glycans and their derivatized counterparts must be thoroughly studied in order to exploit certain characteristics for enhancing MS analysis. Herein, the effectiveness of the incorporation of a permanent charge is studied and determined to hamper glycan analysis. Also, a procedure for glycan hydrazone formation is optimized and outlined where a large number of variables were simultaneously analyzed using a fractional factorial design (FFD) in order to determine which conditions affected the reaction efficiency of the hydrazone formation reaction. Finally, the hydrophobic tagging of glycans is shown to be a viable opportunity to further increase the ion abundance of glycans in MS.}, number={15}, journal={ANALYTICAL CHEMISTRY}, author={Walker, S. Hunter and Papas, Brian N. and Comins, Daniel L. and Muddiman, David C.}, year={2010}, month={Aug}, pages={6636–6642} }
 @article{hawkridge_wysocky_petitte_anderson_mozdziak_fletcher_horowitz_muddiman_2010, title={Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma}, volume={398}, ISSN={["1618-2650"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957867631&partnerID=MN8TOARS}, DOI={10.1007/s00216-010-3979-y}, abstractNote={The domestic chicken (Gallus domesticus) has emerged as a powerful experimental model for studying the onset and progression of spontaneous epithelial ovarian cancer (EOC) with a disease prevalence that can exceed 35% between 2 and 7 years of age. An experimental strategy for biomarker discovery is reported herein that combines the chicken model of EOC, longitudinal plasma sample collection with matched tissues, advanced mass spectrometry-based proteomics, and concepts derived from the index of individuality (Harris, Clin Chem 20: 1535–1542, 1974). Blood was drawn from 148 age-matched chickens starting at 2.5 years of age every 3 months for 1 year. At the conclusion of the 1 year sample collection period, the 73 birds that remained alive were euthanized, necropsied, and tissues were collected. Pathological assessment of resected tissues from these 73 birds confirmed that five birds (6.8%) developed EOC. A proteomics workflow including in-gel digestion, nanoLC coupled to high-performance mass spectrometry, and label-free (spectral counting) quantification was used to measure the biological intra-individual variability (CVW) of the chicken plasma proteome. Longitudinal plasma sample sets from two birds within the 73-bird biorepository were selected for this study; one bird was considered "healthy" and the second bird developed late-stage EOC. A total of 116 proteins from un-depleted plasma were identified with 80 proteins shared among all sample sets. Analytical variability (CVA) of the label-free proteomics workflow was measured using a single plasma sample analyzed five times and was found to be ≥CVW in both birds for 16 proteins (20%) and in either bird for 25 proteins (31%). Ovomacroglobulin (ovostatin) was found to increase (p < 0.001) over a 6 month period in the late-stage EOC bird providing an initial candidate protein for further investigation.}, number={2}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Hawkridge, Adam M. and Wysocky, Rebecca B. and Petitte, James N. and Anderson, Kenneth E. and Mozdziak, Paul E. and Fletcher, Oscar J. and Horowitz, Jonathan M. and Muddiman, David C.}, year={2010}, month={Sep}, pages={737–749} }
 @article{hawkridge_wysocky_petitte_anderson_mozdziak_fletcher_horowitz_muddiman_2010, title={Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma (vol 398, pg 737, 2010)}, volume={398}, ISSN={["1618-2642"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957848897&partnerID=MN8TOARS}, DOI={10.1007/s00216-010-4107-8}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Hawkridge, Adam M. and Wysocky, Rebecca B. and Petitte, James N. and Anderson, Kenneth E. and Mozdziak, Paul E. and Fletcher, Oscar J. and Horowitz, Jonathan M. and Muddiman, David C.}, year={2010}, month={Oct}, pages={1835–1835} }
 @article{muddiman_andrews_lewis_notey_kelly_2010, title={Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2}, volume={398}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-010-3955-6}, abstractNote={The proteome of extremely thermophilic microorganisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. The secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other thermostable biomolecules that, to date, have been characterized only to a limited extent. In the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negative impact on all downstream experiments. Following efficient secretome purification, GeLC-MS2 analysis and prediction servers suggested probable protein secretion to complement experimental data. In an effort to define the extracellular proteome of the extreme thermophilic bacterium Caldicellulosiruptor saccharolyticus, several techniques were considered regarding sample processing to achieve the most in-depth analysis of secreted proteins. Order of operation experiments, all including the C18 bead technique, demonstrated that two levels of sample purification were necessary to effectively desalt the sample and provide sufficient protein identifications. Five sample preparation combinations yielded 71 proteins and the majority described, as enzymatic and putative uncharacterized proteins, anticipate consolidated bioprocessing applications. Nineteen proteins were predicted by Phobius, SignalP, SecretomeP, or TatP for extracellular secretion, and 11 contained transmembrane domain stretches suggested by Phobius and transmembrane hidden Markov model. The sample preparation technique demonstrating the most effective outcome for C. saccharolyticus secreted proteins in this study, involved acetone precipitation followed by the C18 bead method in which 2.4% (63 proteins) of the predicted proteome was identified, including proteins suggested to have secretion and transmembrane moieties.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Muddiman, David and Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert}, year={2010}, month={Sep}, pages={377–389} }
 @article{andrews_lewis_notey_kelly_muddiman_2010, title={Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2 (vol 398, pg 377, 2010)}, volume={398}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-010-4102-0}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert and Muddiman, David}, year={2010}, month={Oct}, pages={1837–1837} }
 @article{muddiman_andrews_lewis_notey_kelly_2010, title={Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting}, volume={398}, ISSN={["1618-2642"]}, DOI={10.1007/s00216-010-3929-8}, abstractNote={Probing the intracellular proteome of Thermotoga maritima and Caldicellulosiruptor saccharolyticus in pure and co-culture affords a global investigation into the machinery and mechanisms enduring inside the bacterial thermophilic cell at the time of harvest. The second of a two part study, employing GeLC-MS2 a variety of proteins were confidently identified with <1% false discovery rate, and spectral counts for label-free relative quantification afforded indication of the dynamic proteome as a function of environmental stimuli. Almost 25% of the T. maritima proteome and 10% of the C. saccharolyticus proteome were identified. Through comparison of growth temperatures for T. maritima, a protein associated with chemotaxis was uniquely present in the sample cultivated at the non-optimal growth temperature. It is suspected that movement was induced due to the non-optimal condition as the organism may need to migrate in the culture to locate more nutrients. The inventory of C. saccharolyticus proteins identified in these studies and attributed to spectral counting, demonstrated that two CRISPR-associated proteins had increased expression in the pure culture versus the co-culture. Further focusing on this relationship, a C. saccharolyticus phage-shock protein was identified in the co-culture expanding a scenario that the co-culture had decreased antiviral resistance and accordingly an infection-related protein was present. Alterations in growth conditions of these bacterial thermophilic microorganisms offer a glimpse into the intricacy of microbial behavior and interaction.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Muddiman, David and Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert}, year={2010}, month={Sep}, pages={391–404} }
 @article{andrews_lewis_notey_kelly_muddiman_2010, title={Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting (vol 398, pg 391, 2010)}, volume={398}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-010-4050-8}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Andrews, Genna and Lewis, Derrick and Notey, Jaspreet and Kelly, Robert and Muddiman, David}, year={2010}, month={Oct}, pages={1839–1839} }
 @article{collier_sarkar_rao_muddiman_2010, title={Quantitative top-down proteomics of SILAC labeled human embryonic stem cells}, volume={21}, DOI={10.1016/j.jasms.2010.01.031}, abstractNote={Human embryonic stem cells (hESCs) are self-renewing pluripotent cells with relevance to treatment of numerous medical conditions. However, a global understanding of the role of the hESC proteome in maintaining pluripotency or triggering differentiation is still largely lacking. The emergence of top-down proteomics has facilitated the identification and characterization of intact protein forms that are not readily apparent in bottom-up studies. Combined with metabolic labeling techniques such as stable isotope labeling by amino acids in cell culture (SILAC), quantitative comparison of intact protein expression under differing experimental conditions is possible. Herein, quantitative top-down proteomics of hESCs is demonstrated using the SILAC method and nano-flow reverse phase chromatography directly coupled to a linear-ion-trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FT-ICR-MS). In this study, which to the best of our knowledge represents the first top-down analysis of hESCs, we have confidently identified 11 proteins by accurate intact mass, MS/MS, and amino acid counting facilitated by SILAC labeling. Although quantification is challenging due to the incorporation of multiple labeled amino acids (i.e., lysine and arginine) and arginine to proline conversion, we are able to quantitatively account for these phenomena using a mathematical model.}, number={6}, journal={Journal of the American Society for Mass Spectrometry}, author={Collier, T. S. and Sarkar, P. and Rao, B. and Muddiman, David}, year={2010}, pages={879–889} }
 @article{xu_yang_zheng_ghosh_lyndon_muddiman_stang_2010, title={Self-Assembly of Dendritic Tris(crown ether) Hexagons and Their Complexation with Dibenzylammonium Cations}, volume={75}, ISSN={["1520-6904"]}, DOI={10.1021/jo101648p}, abstractNote={The construction of a new series of dendritic tris(crown ether) hexagons via coordination-driven self-assembly is described. Combining 120° crown ether-containing diplatinum(II) acceptors with 120° dendritic dipyridyl donors in a 1:1 ratio allows for the formation of a new family of dendritic triple crown ether derivatives with a hexagonal cavity in quantitative yields. The number and the position of these pendant groups can be precisely controlled on the hexagonal metallacycle. The structures of all dendritic multiple crown ether hexgaons are confirmed by multinuclear NMR ((1)H and (31)P), ESI-MS and ESI-TOF-MS, and elemental analysis. The complexation of these dendritic trivalent receptors with dibenzylammonium cations was investigated by (1)H NMR titration experiments. The thermodynamic binding constants between the receptors and guests were established by using the nonlinear least-squares fit method based on (1)H NMR titration experiments. It was found that the association constants of each assembly decrease correspondingly upon the increase of the generation of the dendrons from [G0] to [G3], which might be caused by the steric effect of the dendrons on host-guest complexation.}, number={21}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Xu, Xing-Dong and Yang, Hai-Bo and Zheng, Yao-Rong and Ghosh, Koushik and Lyndon, Matthew M. and Muddiman, David C. and Stang, Peter J.}, year={2010}, month={Nov}, pages={7373–7380} }
 @article{dixon_muddiman_2010, title={Study of the ionization mechanism in hybrid laser based desorption techniques}, volume={135}, ISSN={["0003-2654"]}, DOI={10.1039/b926422a}, abstractNote={In order to study the ionization mechanism in MALDESI, the RASTIR source was implemented to separate in space the laser desorption event from the intersecting electrospray ionization beam. Deuterated solvents were electrosprayed from the RASTIR source which resulted in a near complete shift from [M + H(+)](1+) to [M + D(+)](1+) of the monoisotopic peak for reserpine. The purpose of these experiments is to test the hypothesis that the primary ionization pathway in MALDESI is through interaction of the laser-desorbed neutral species with the intersecting electrospray ionization beam. The combination of RASTIR coupled to MALDESI can be utilized to study small organic molecules as well as peptides and proteins. Moreover, the use of RASTIR combined with MALDESI lends itself to improve the overall efficiency of ionization.}, number={5}, journal={ANALYST}, author={Dixon, R. Brent and Muddiman, David C.}, year={2010}, pages={880–882} }
 @article{bereman_muddiman_2010, title={The effects of abundant plasma protein depletion on global glycan profiling using NanoLC FT-ICR mass spectrometry}, volume={396}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-009-3368-6}, abstractNote={We report the results of abundant plasma protein depletion on the analysis of underivatized N-linked glycans derived from plasma proteins by nanoLC Fourier-transform ion cyclotron resonance mass spectrometry. N-linked glycan profiles were compared between plasma samples where the six most abundant plasma proteins were depleted (n = 3) through a solid-phase immunoaffinity column and undepleted plasma samples (n = 3). Three exogenous glycan standards were spiked into all samples which allowed for normalization of the N-glycan abundances. The abundances of 20 glycans varying in type, structure, composition, and molecular weight (1,200–3,700 Da) were compared between the two sets of samples. Small fucosylated non-sialylated complex glycans were found to decrease in abundance in the depleted samples (greater than or equal to tenfold) relative to the undepleted samples. Protein depletion was found to marginally effect (less than threefold) the abundance of high mannose, hybrid, and large highly sialylated complex species. The significance of these findings in terms of future biomarker discovery experiments via global glycan profiling is discussed.}, number={4}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Bereman, Michael S. and Muddiman, David C.}, year={2010}, month={Feb}, pages={1473–1479} }
 @article{shuford_hawkridge_burnett_muddiman_2010, title={Utilizing Spectral Counting To Quantitatively Characterize Tandem Removal of Abundant Proteins (TRAP) in Human Plasma}, volume={82}, ISSN={["0003-2700"]}, DOI={10.1021/ac102248d}, abstractNote={Biomarker discovery efforts in serum and plasma are greatly hindered by the presence of high abundance proteins that prevent the detection and quantification of less abundant, yet biologically significant, proteins. The most common method for addressing this problem is to specifically remove the few abundant proteins through immunoaffinity depletion/subtraction. Herein, we improved upon this method by utilizing multiple depletion columns in series, so as to increase the efficiency of the abundant protein removal and augment the detection/identification of less abundant plasma proteins. Spectral counting was utilized to make quantitative comparisons between undepleted plasma, plasma depleted with a single depletion column, and plasma depleted using two or three depletion columns in tandem. In the undepleted plasma only 29 lower abundance protein groups were identified with the top-scoring protein from each group having a median spectral count of 3, while in the plasma processed using a single HSA depletion column 61 such protein groups were identified with a median spectral count of 8. In comparison, 76 lesser abundant protein groups were identified with a median spectral count of 11.5 in the two column setup (i.e., HSA followed by MARS Hu14). However, in the ultimate depleted plasma sample, which was created using three depletion columns in tandem, the number of less abundant protein groups identified increase to 81 and the median spectral count for the top-scoring proteins from each group increased to 15 counts per protein. Moreover, exogenous B-type natriuretic peptide-32, which was added to the plasma as a detection benchmark at 12 μg/mL, was only detected in the plasma sample depleted using three depletion columns in tandem. Collectively, these data demonstrate that this method, tandem removal of abundant proteins or TRAP, provides superior removal efficiency compared to traditional applications and improves the depth of proteome coverage in plasma.}, number={24}, journal={ANALYTICAL CHEMISTRY}, author={Shuford, Christopher M. and Hawkridge, Adam M. and Burnett, John C., Jr. and Muddiman, David C.}, year={2010}, month={Dec}, pages={10179–10185} }
 @article{williams_muddiman_2009, title={Absolute Quantification of C-Reactive Protein in Human Plasma Derived from Patients with Epithelial Ovarian Cancer Utilizing Protein Cleavage Isotope Dilution Mass Spectrometry}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr800922p}, abstractNote={A method employing protein cleavage isotope dilution mass spectrometry (PC-IDMS) was developed for quantification of C-reactive protein (CRP) in human plasma. This method was completed without the use of immunoaffinity chromatography or size exclusion chromatography, as previous mass spectrometric methods for the quantification of CRP have employed. A total of 110 human plasma samples were analyzed with PC-IDMS via 1-D nanoLC-MS/MS using a 30 min gradient with a triple quadrupole mass spectrometer operated in selective reaction monitoring (SRM) mode. The results from this newly developed method were compared to results generated from an enzyme-linked immunosorbent assay (ELISA) performed by an independent CLIA certified laboratory. The comparison of these results generated an R(2) = 0.9708 which indicates successful quantification of CRP from human plasma utilizing the methodology described herein. Interestingly, the PC-IDMS method provided concentration values that were approximately 10x the concentration reported by the ELISA method, which demonstrated that the method of detection is an important consideration when determining reference ranges of a particular analyte. In addition, data is shown that illustrates that, as epithelial ovarian cancer (EOC) progresses from stage I to stage IV, mean levels of CRP increase.}, number={2}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Williams, D. Keith, Jr. and Muddiman, David C.}, year={2009}, month={Feb}, pages={1085–1090} }
 @article{sampson_muddiman_2009, title={Atmospheric pressure infrared (10.6 mu m) laser desorption electrospray ionization (IR-LDESI) coupled to a LTQ Fourier transform ion cyclotron resonance mass spectrometer}, volume={23}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.4113}, abstractNote={AbstractWe present the implementation of a CO2 laser emitting infrared laser irradiation at 10.6 µm onto the versatile atmospheric pressure ionization platform. Infrared laser desorption electrospray ionization (IR‐LDESI) is demonstrated from liquid‐state samples at atmospheric pressure with and without ESI postionization. Multiply charged proteins ranging in molecular mass from 8.6 to 17 kDa were detected from liquid‐state samples without the addition of matrix. Copyright © 2009 John Wiley & Sons, Ltd.}, number={13}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Sampson, Jason S. and Muddiman, David C.}, year={2009}, month={Jul}, pages={1989–1992} }
 @article{forbes_dixon_muddiman_degertekin_fedorov_2009, title={Characterization of Charge Separation in the Array of Micromachined UltraSonic Electrospray (AMUSE) Ion Source for Mass Spectrometry}, volume={20}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2009.05.006}, abstractNote={An initial investigation into the effects of charge separation in the Array of Micromachined UltraSonic Electrospray (AMUSE) ion source is reported to gain understanding of ionization mechanisms and to improve analyte ionization efficiency and operation stability. In RF-only mode, AMUSE ejects, on average, an equal number of slightly positive and slightly negative charged droplets due to random charge fluctuations, providing inefficient analyte ionization. Charge separation at the nozzle orifice is achieved by the application of an external electric field. By bringing the counter electrode close to the nozzle array, strong electric fields can be applied at relatively low DC potentials. It has been demonstrated, through a number of electrode/electrical potential configurations, that increasing charge separation leads to improvement in signal abundance, signal-to-noise ratio, and signal stability.}, number={9}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Forbes, Thomas P. and Dixon, R. Brent and Muddiman, David C. and Degertekin, F. Levent and Fedorov, Andrei G.}, year={2009}, month={Sep}, pages={1684–1687} }
 @article{andrews_shuford_burnett_hawkridge_muddiman_2009, title={Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides}, volume={877}, ISSN={1570-0232}, url={http://dx.doi.org/10.1016/j.jchromb.2009.02.040}, DOI={10.1016/j.jchromb.2009.02.040}, abstractNote={The circulating concentration of a biomarker for congestive heart failure, Brain (B-type) Natriuretic Peptide (BNP-32), is measured using ELISA based assays in order to rapidly diagnose and monitor disease progression. The lack of molecular specificity afforded by these assays has recently come into question as emerging studies indicate there are potentially multiple heterogeneous forms of BNP in circulation with immunoreactive capabilities. In order to better understand the molecular biology of BNP-32 as it relates to congestive heart failure, it would thus be advantageous to use a detection platform such as Fourier transform ion cyclotron resonance mass spectrometry. This high resolving power mass spectrometer can provide unparalleled molecular specificity and can facilitate identification and characterization of the various molecular forms across all disease states. Unfortunately, BNP circulates at low concentrations (as low as 3fmol/mL). Thus, it will require a collaborative effort from a number of orthogonal front-end technologies to overcome the disconnect between the practical detection limits of this instrument platform and the physiological levels of BNP-32 and its alternative molecular forms. Herein, we begin optimization of these front-end techniques by first enhancing the conditions for online nanoLC-ESI-MS separations of BNP-32 and its proteolytic fragments. Through extensive analysis of various chromatographic parameters we determined that Michrom Magic C8 stationary phase used in conjunction with a continuous, vented column configuration provided advanced chromatographic performance for the nano-flow separations involving intact BNP-32 and its associated tryptic peptides. Furthermore, conditions for the tryptic digestion of BNP-32 were also studied. We demonstrate that the use of free cysteine as an alkylation quenching agent and a secondary digestion within the digestion scheme can provide targeted tryptic peptides with increased abundances. Combined, these data will serve to further augment the detection of BNP-32 by LC-MS.}, number={10}, journal={Journal of Chromatography B}, publisher={Elsevier BV}, author={Andrews, Genna L. and Shuford, Christopher M. and Burnett, John C., Jr. and Hawkridge, Adam M. and Muddiman, David C.}, year={2009}, month={Apr}, pages={948–954} }
 @article{bereman_young_deiters_muddiman_2009, title={Development of a Robust and High Throughput Method for Profiling N-Linked Glycans Derived from Plasma Glycoproteins by NanoLC-FTICR Mass Spectrometry}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr9002323}, abstractNote={Recent investigations continue to emphasize the importance of glycosylation in various diseases including cancer. In this work, we present a step-by-step protocol describing a method for N-linked glycan profiling of plasma glycoproteins by nanoflow liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). A large experimental space was initially explored and is described herein. Three internal standards were spiked into the sample and provided normalization of plasma glycan abundance across different experimental conditions. Incubation methods and times and the effect of NP40 detergent on glycan abundance were explored. It was found that an 18-h incubation with no detergent led to the greatest ion abundance; however, data could be obtained in less than one day from raw plasma samples utilizing microwave irradiation or shorter incubation periods. The intersample precision of three different glycans was less than 5.5% (RSD) when the internal standards were added prior to the initial processing step. The high mass measurement accuracy (<3 ppm) afforded by the FTICR mass spectrometer provided confident identifications of several glycan species.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Bereman, Michael S. and Young, Douglas D. and Deiters, Alexander and Muddiman, David C.}, year={2009}, month={Jul}, pages={3764–3770} }
 @article{williams_comins_whitten_muddiman_2009, title={Evaluation of the ALiPHAT Method for PC-IDMS and Correlation of Limits-of-Detection with Nonpolar Surface Area}, volume={20}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2009.07.019}, abstractNote={PC-IDMS experiments for two peptides, laminin nonapeptide and the N-terminal tryptic peptide of prostate specific antigen, were performed utilizing a variety of alkylating reagents. These experiments were conducted to investigate how hydrophobicity influences the limits-of-detection (LOD) by altering their electrospray ionization response. Nonpolar surface areas were calculated for both peptides and all alkylating reagents to provide an estimate of the hydrophobicity of the differently alkylated peptides. Decreases in LOD by 2-fold were observed for both peptides between the best and worst performing combination of alkylating reagent. However, while an increase in hydrophobicity was found to aid in decreasing LOD to an extent, beyond a certain hydrophobicity, we observed a decrease.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Williams, D. Keith, Jr. and Comins, Daniel L. and Whitten, Jerry L. and Muddiman, David C.}, year={2009}, month={Nov}, pages={2006–2012} }
 @article{hawkridge_muddiman_2009, title={Mass Spectrometry-Based Biomarker Discovery: Toward a Global Proteome Index of Individuality}, volume={2}, ISSN={["1936-1327"]}, DOI={10.1146/annurev.anchem.1.031207.112942}, abstractNote={Biomarker discovery and proteomics have become synonymous with mass spectrometry in recent years. Although this conflation is an injustice to the many essential biomolecular techniques widely used in biomarker-discovery platforms, it underscores the power and potential of contemporary mass spectrometry. Numerous novel and powerful technologies have been developed around mass spectrometry, proteomics, and biomarker discovery over the past 20 years to globally study complex proteomes (e.g., plasma). However, very few large-scale longitudinal studies have been carried out using these platforms to establish the analytical variability relative to true biological variability. The purpose of this review is not to cover exhaustively the applications of mass spectrometry to biomarker discovery, but rather to discuss the analytical methods and strategies that have been developed for mass spectrometry–based biomarker-discovery platforms and to place them in the context of the many challenges and opportunities yet to be addressed.}, journal={ANNUAL REVIEW OF ANALYTICAL CHEMISTRY}, author={Hawkridge, Adam M. and Muddiman, David C.}, year={2009}, pages={265–277} }
 @article{alcazar_hawkridge_collier_cousins_bhattacharya_muddiman_marin-castano_2009, title={Proteomics Characterization of Cell Membrane Blebs in Human Retinal Pigment Epithelium Cells}, volume={8}, ISSN={["1535-9484"]}, DOI={10.1074/mcp.M900203-MCP200}, abstractNote={Age-related macular degeneration (AMD) is the leading cause of legal blindness among the elderly population in the industrialized world, affecting about 14 million people in the United States alone. Smoking is a major environmental risk factor for AMD, and hydroquinone is a major component in cigarette smoke. Hydroquinone induces the formation of cell membrane blebs in human retinal pigment epithelium (RPE). Blebs may accumulate and eventually contribute first to sub-RPE deposits and then drusen formation, which is a prominent histopathologic feature in eyes with AMD. As an attempt to better understand the mechanisms involved in early AMD, we sought to investigate the proteomic profile of RPE blebs. Isolated blebs were subjected to SDS-PAGE fractionation, and in-gel trypsin-digested peptides were analyzed by LC-MS/MS that lead to the identification of a total of 314 proteins. Identified proteins were predominantly involved in oxidative phosphorylation, cell junction, focal adhesion, cytoskeleton regulation, and immunogenic processes. Importantly basigin and matrix metalloproteinase-14, key proteins involved in extracellular matrix remodeling, were identified in RPE blebs and shown to be more prevalent in AMD patients. Altogether our findings suggest, for the first time, the potential involvement of RPE blebs in eye disease and shed light on the implication of cell-derived microvesicles in human pathology.}, number={10}, journal={MOLECULAR & CELLULAR PROTEOMICS}, author={Alcazar, Oscar and Hawkridge, Adam M. and Collier, Timothy S. and Cousins, Scott W. and Bhattacharya, Sanjoy K. and Muddiman, David C. and Marin-Castano, Maria E.}, year={2009}, month={Oct}, pages={2201–2211} }
 @article{tata_subbotina_burckart_muddiman_gusev_hercules_starzl_venkataramanan_2009, title={Species-dependent hepatic metabolism of immunosuppressive agent tacrolimus (FK-506)}, volume={39}, ISSN={0049-8254 1366-5928}, url={http://dx.doi.org/10.1080/00498250903114478}, DOI={10.1080/00498250903114478}, abstractNote={The current study aims to investigate species-related differences in the in-vitro hepatic metabolism of tacroliums using liver microsomes obtained from rat, hamster, guinea pig, rabbit, pig, dog, baboon and humans. Tacrolimus metabolism was characterized using high-performance liquid chromatography- ultraviolet light (HPLC-UV) and two soft ionization mass spectrometric techniques; matrix-assisted lasers desorption/ionization (MALDI) and time-of-flight-secondary ion mass spectrometry (TOF-SIMS). The extent of tacrolimus metabolism, when normalized to the cytochrome P-450 content, was in the order: rat < hamster < rabbit < pig < guinea pig < dog < human < baboon. Tacrolimus metabolism exhibited significant qualitative and quantitative differences between the animal species tested. Desmethyl- (MI–MIII), didesmethyl- (MIV–MVI), monohydroxy- (MVII), dihydroxy- (MVIII), epoxide- (MIX), dihydrodiol- (MX), monodesmethyl and monohydroxy- (MXI–MXIII), and didesmethyl and monohydroxy- (MXIV–MXVI) tacroliums metabolites were identified in the species tested. MI–MX were identified in all the species tested; MXI–MXVI were identified in all species except rat, rabbit and guinea pig; and MXIV–MXVI were identified only in baboon. The current investigation was unable to detect any phase II metabolites due to the limitations of the test system used. The analytical methods were not able to differentiate optical and positional isomers of metabolites due to the nature of the analytical tools used, therefore groups of metabolites were identified based on their molecular weights and available information. From the current in-vitro metabolism studies, the pattern of tacroliums metabolism in baboons closely resembled that in humans and thus it is ideal for studying tacroliums metabolism-related work of clinical relevance.}, number={10}, journal={Xenobiotica}, publisher={Informa UK Limited}, author={Tata, P. N. V. and Subbotina, N. and Burckart, G. J. and Muddiman, D. C. and Gusev, A. I. and Hercules, D. M. and Starzl, T. E. and Venkataramanan, R.}, year={2009}, month={Jul}, pages={757–765} }
 @article{yang_northrop_zheng_ghosh_lyndon_muddiman_stang_2009, title={Synthesis of Six-Component Metallodendrimers via [3+3] Coordination-Driven Self-Assembly}, volume={74}, ISSN={["0022-3263"]}, DOI={10.1021/jo900067v}, abstractNote={A new class of 120 degrees dendritic di-Pt(II) acceptor subunits has been designed and synthesized, from which six-component hexagonal metallodendrimers were easily formed with 120 degrees dendritic dipyridine donors via [3 + 3] coordination-driven self-assembly. The structures of all metallodendrimers are confirmed by multinuclear NMR, ESI-TOF-MS/ESI-FTMS, and elemental analysis. MMFF force-field simulations indicates that all metallodendrimers have a hexagonal ring with an internal radius of approximately 1.4 nm.}, number={9}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Yang, Hai-Bo and Northrop, Brian H. and Zheng, Yao-Ron and Ghosh, Koushik and Lyndon, Matthew M. and Muddiman, David C. and Stang, Peter J.}, year={2009}, month={May}, pages={3524–3527} }
 @article{fields-zinna_sampson_crowe_tracy_parker_deney_muddiman_murray_2009, title={Tandem Mass Spectrometry of Thiolate-Protected Au Nanoparticles NaxAu25(SC2H4Ph)(18-y)(S(C2H4O)(5)CH3)(y)}, volume={131}, ISSN={["0002-7863"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000270186600057&KeyUID=WOS:000270186600057}, DOI={10.1021/ja905787y}, abstractNote={We report the first collision-induced dissociation tandem mass spectrometry (CID MS/MS) of a thiolate-protected Au nanoparticle that has a crystallographically determined structure. CID spectra assert that dissociation pathways for the mixed monolayer Na(x)Au(25)(SC(2)H(4)Ph)(18-y)(S(C(2)H(4)O)(5)CH(3))(y) centrally involve the semi-ring Au(2)L(3) coordination (L = some combination of the two thiolate ligands) that constitutes the nanoparticle's protecting structure. The data additionally confirm charge state assignments in the mass spectra. Prominent among the fragments is [Na(2)AuL(2)](1+), one precursor of which is identified as another nanoparticle fragment in the higher m/z region. Another detected fragment, [Na(2)Au(2)L(3)](1+), represents a mass loss equivalent to an entire semi-ring, whereas others suggest involvement (fragmentation/rearrangement) of multiple semi-rings, e.g., [NaAu(3)L(3)](1+) and [NaAu(4)L(4)](1+). The detailed dissociation/rearrangement mechanisms of these species are not established, but they are observed in other mass spectrometry experiments, including those under non-CID conditions, namely, electrospray ionization mass spectrometry (ESI-MS) with both time-of-flight (TOF) and FT-ICR analyzers. The latter, previously unreported results show that even soft ionization sources can result in Au nanoparticle fragmentation, including that yielding Au(4)L(4) in ESI-TOF of a much larger thiolate-protected Au(144) nanoparticle under non-CID conditions.}, number={38}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Fields-Zinna, Christina A. and Sampson, Jason S. and Crowe, Matthew C. and Tracy, Joseph B. and Parker, Joseph F. and deNey, Alexander M. and Muddiman, David C. and Murray, Royce W.}, year={2009}, month={Sep}, pages={13844–13851} }
 @article{williams_kovach_muddiman_hanck_2009, title={Utilizing Artificial Neural Networks in MATLAB to Achieve Parts-Per-Billion Mass Measurement Accuracy with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer}, volume={20}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2009.02.030}, abstractNote={Fourier transform ion cyclotron resonance mass spectrometry has the ability to realize exceptional mass measurement accuracy (MMA); MMA is one of the most significant attributes of mass spectrometric measurements as it affords extraordinary molecular specificity. However, due to space-charge effects, the achievable MMA significantly depends on the total number of ions trapped in the ICR cell for a particular measurement, as well as relative ion abundance of a given species. Artificial neural network calibration in conjunction with automatic gain control (AGC) is utilized in these experiments to formally account for the differences in total ion population in the ICR cell between the external calibration spectra and experimental spectra. In addition, artificial neural network calibration is used to account for both differences in total ion population in the ICR cell as well as relative ion abundance of a given species, which also affords mean MMA values at the parts-per-billion level.}, number={7}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Williams, D. Keith, Jr. and Kovach, Alexander L. and Muddiman, David C. and Hanck, Kenneth W.}, year={2009}, month={Jul}, pages={1303–1310} }
 @article{yang_ghosh_zhao_northrop_lyndon_muddiman_white_stang_2008, title={A new family of multiferrocene complexes with enhanced control of structure and stoichiometry via coordination-driven self-assembly and their electrochemistry}, volume={130}, ISSN={["1520-5126"]}, DOI={10.1021/ja710349j}, abstractNote={The design and synthesis of a new family of multiferrocene complexes with enhanced control of structure and stoichimetry via coordination-driven self-assembly is described. Insight into the structure and electronic properties of all supramolecules was obtained by electrochemical studies. The collective results provide an enhanced understanding of the influence of structural factors on the electrochemistry of multifunctional electroactive supramolecular architectures.}, number={3}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Yang, Hai-Bo and Ghosh, Koushik and Zhao, Yue and Northrop, Brian H. and Lyndon, Matthew M. and Muddiman, David C. and White, Henry S. and Stang, Peter J.}, year={2008}, month={Jan}, pages={839-+} }
 @article{dixon_sampson_hawkridge_muddiman_2008, title={Ambient aerodynamic ionization source for remote analyte sampling and mass spectrometric analysis}, volume={80}, ISSN={["1520-6882"]}, DOI={10.1021/ac800289f}, abstractNote={The use of aerodynamic devices in ambient ionization source development has become increasingly prevalent in the field of mass spectrometry. In this study, an air ejector has been constructed from inexpensive, commercially available components to incorporate an electrospray ionization emitter within the exhaust jet of the device. This novel aerodynamic device, herein termed remote analyte sampling, transport, and ionization relay (RASTIR) was used to remotely sample neutral species in the ambient and entrain them into an electrospray plume where they were subsequently ionized and detected using a linear ion trap Fourier transform mass spectrometer. Two sets of experiments were performed in the ambient environment to demonstrate the device's utility. The first involved the remote (approximately 1 ft) vacuum collection of pure sample particulates (i.e., dry powder) from a glass slide, entrainment and ionization at the ESI emitter, and mass spectrometric detection. The second experiment involved the capture (vacuum collection) of matrix-assisted laser desorbed proteins followed by entrainment in the ESI emitter plume, multiple charging, and mass spectrometric detection. This approach is in principle a RASTIR-assisted matrix-assisted laser desorption electrospray ionization source (Sampson, J. S.; Hawkridge, A. M.; Muddiman, D. C. J. Am. Soc. Mass Spectrom. 2006, 17, 1712-1716; Rapid Commun. Mass Spectrom. 2007, 21, 1150-1154.). A detailed description of the device construction, operational parameters, and preliminary small molecule and protein data are presented.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Dixon, R. Brent and Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2008}, month={Jul}, pages={5266–5271} }
 @article{williams_chadwick_williams_muddiman_2008, title={Calibration laws based on multiple linear regression applied to matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={43}, ISSN={["1096-9888"]}, url={http://europepmc.org/abstract/med/18563853}, DOI={10.1002/jms.1451}, abstractNote={AbstractOperation of any mass spectrometer requires implementation of mass calibration laws to translate experimentally measured physical quantities into a m/z range. While internal calibration in Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS) offers several attractive features, including exposure of calibrant and analyte ions to identical experimental conditions (e.g. space charge), external calibration affords simpler pulse sequences and higher throughput. The automatic gain control method used in hybrid linear trap quadrupole (LTQ) FT‐ICR‐MS to consistently obtain the same ion population is not readily amenable to matrix‐assisted laser desorption/ionization (MALDI) FT‐ICR‐MS, due to the heterogeneous nature and poor spot‐to‐spot reproducibility of MALDI. This can be compensated for by taking external calibration laws into account that consider magnetic and electric fields, as well as relative and total ion abundances. Herein, an evaluation of external mass calibration laws applied to MALDI‐FT‐ICR‐MS is performed to achieve higher mass measurement accuracy (MMA). Copyright © 2008 John Wiley & Sons, Ltd.}, number={12}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Williams, D. Keith, Jr. and Chadwick, M. Ashley and Williams, Taufika Islam and Muddiman, David C.}, year={2008}, month={Dec}, pages={1659–1663} }
 @article{sampson_hawkridge_muddiman_2008, title={Construction of a versatile high precision ambient Ionization source for direct analysis and imaging}, volume={19}, DOI={10.1016/j.jasms.2008.06.013}, abstractNote={The design and construction of a high precision ambient ionization source matrix-assisted laser desorption electrospray ionization (MALDESI) are described in full detail, including a complete parts list. The computer controlled high precision motion control system and high repetition rate Explorer laser are demonstrated during MALDESI-FT-ICR analysis of peptides and proteins ranging from 1 to 17 kDa. The high stability ionization source platform described herein demonstrates both the advantages of the new MALDESI source and versatility for application to numerous desorption and ionization techniques.}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, author={Sampson, J. S. and Hawkridge, A. M. and Muddiman, David}, year={2008}, pages={1527–1534} }
 @article{caskey_yamamoto_addicott_shoemaker_vacek_hawkridge_muddiman_kottas_michl_stang_2008, title={Coordination-driven face-directed self-assembly of trigonal prisms. Face-based conformational chirality}, volume={130}, ISSN={["1520-5126"]}, DOI={10.1021/ja710715e}, abstractNote={The coordination-driven self-assembly of four different trigonal prisms from 3 equiv of one of four different tetrapyridyl star connectors and 6 equiv of a platinum linker dication in nitromethane is presented. This face-directed approach affords high yields without template assistance. The prisms have been characterized by multinuclear and DOSY NMR and dual ESI-FT-ICR mass spectrometry. The use of a conformationally chiral star connector leads to a conformationally chiral prism when connector arm ends attached to a vertex have a strongly correlated twist sense and chirality is communicated across polyhedral faces, edges, and vertices. Molecular mechanics results suggest that in the smallest prism 3d collective effects dominate and the all-P and all-M conformers are strongly favored. NMR data prove that the two edges of the pyridine rings in the triflate salts of 3a-3d are distinct. An Eyring plot of rates obtained from line-shape analysis and 1-D EXCHSY NMR yields an activation enthalpy DeltaH(double dagger) of approximately 12 kcal/mol and activation entropy DeltaS(double dagger) of approximately -15 cal/mol x K for the edge interconversion process, compatible with pyridine rotation around the Pt-N bond. For 3c, this behavior is observed only up to approximately 318 K. At higher temperatures, the Eyring plot is again linear but follows a very different straight line, with a DeltaH(double dagger) of approximately 35 kcal/mol and DeltaS(double dagger) of approximately 60 cal/mol x K. This highly unusual result is further investigated and discussed in the following companion paper.}, number={24}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Caskey, Douglas C. and Yamamoto, Takuya and Addicott, Chris and Shoemaker, Richard K. and Vacek, Jaroslav and Hawkridge, Adam M. and Muddiman, David C. and Kottas, Gregg S. and Michl, Josef and Stang, Peter J.}, year={2008}, month={Jun}, pages={7620–7628} }
 @misc{ghosh_yang_northrop_lyndon_zheng_muddiman_stang_2008, title={Coordination-driven self-assembly of cavity-cored multiple crown ether derivatives and poly[2]pseudorotaxanes}, volume={130}, ISSN={["1520-5126"]}, DOI={10.1021/ja711502t}, abstractNote={The synthesis of a new 120 degree diplatinum(II) acceptor unit and the self-assembly of a series of two-dimensional metallacyclic polypseudorotaxanes that utilize both metal-ligand and crown ether-dialkylammonium noncovalent interactions are described. Judiciously combining complementary diplatinum(II) acceptors with bispyridyl donor building blocks, with an acceptor and/or donor possessing a pendant dibenzo[24]crown-8 (DB24C8) moiety, allows for the formation of three new rhomboidal bis-DB24C8, one new hexagonal tris-DB24C8, and four new hexakis-DB24C8 metallacyclic polygons in quantitative yields. The size and shape of each assembly, as well as the location and stoichiometry of the DB24C8 macrocycle, can be precisely controlled. Each polygon is able to complex two, three, or six dibenzylammonium ions without disrupting the underlying metallacyclic polygons, thus producing eight different poly[2]pseudorotaxanes and demonstrating the utility and scope of this orthogonal self-assembly technique. The assemblies are characterized with one-dimensional multinuclear ((1)H and (31)P) and two-dimensional ((1)H-(1)H COSY and NOESY) NMR spectroscopy as well as mass spectrometry (ESI-MS). Further analysis of the size and shape of each assembly is obtained through molecular force-field simulations. (1)H NMR titration experiments are used to establish thermodynamic binding constants and poly[2]pseudorotaxane/dibenzylammonium stoichiometries. Factors influencing the efficiency of poly[2]pseudorotaxane formation are discussed.}, number={15}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Ghosh, Koushik and Yang, Hai-Bo and Northrop, Brian H. and Lyndon, Matthew M. and Zheng, Yao-Rong and Muddiman, David C. and Stang, Peter J.}, year={2008}, month={Apr}, pages={5320–5334} }
 @article{sampson_hawkridge_muddiman_2008, title={Development and characterization of an ionization technique for analysis of biological macromolecules: Liquid matrix-assisted laser desorption electrospray ionization}, volume={80}, ISSN={["0003-2700"]}, DOI={10.1021/ac8001935}, abstractNote={We have developed an atmospheric pressure ionization technique called liquid matrix-assisted laser desorption electrospray ionization (liq-MALDESI) for the generation of multiply charged ions by laser desorption from liquid samples deposited onto a stainless steel sample target biased at a high potential. This variant of our previously reported MALDESI source does not utilize an ESI emitter to postionize neutrals. Conversely, we report desorption and ionization from a macroscopic charged droplet. We demonstrate high mass resolving power single-acquisition FT-ICR-MS analysis of peptides and proteins ranging from 1 to 8.6 kDa at atmospheric pressure. The liquid sample acts as a macroscopic charged droplet similar to those generated by electrospray ionization, whereby laser irradiation desorbs analyte from organic matrix containing charged droplets generating multiply charged ions. We have observed a singly charged radical cation of an electrochemically active species indicating oxidation occurs for analytes and therefore water; the latter would play a key role in the mechanism of ionization. Moreover, we demonstrate an increase in ion abundance and a concurrent decrease in surface tension with an increase in the applied potential.}, number={17}, journal={ANALYTICAL CHEMISTRY}, author={Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2008}, month={Sep}, pages={6773–6778} }
 @article{bereman_williams_muddiman_2009, title={Development of a nanoLC LTQ Orbitrap Mass Spectrometric Method for Profiling Glycans Derived from Plasma from Healthy, Benign Tumor Control, and Epithelial Ovarian Cancer Patients}, volume={81}, ISSN={["1520-6882"]}, url={http://europepmc.org/abstract/med/19113831}, DOI={10.1021/ac802262w}, abstractNote={We report the development of split-less nano-flow liquid chromatography mass spectrometric analysis of glycans chemically cleaved from glycoproteins in plasma. Porous graphitized carbon operating under reverse-phase conditions and an amide-based stationary phase operating under hydrophilic interaction conditions are quantitatively compared for glycan separation. Both stationary phases demonstrated similar column efficiencies and excellent retention time reproducibility without an internal standard to correct for retention time shift. The 95% confidence intervals of the mean retention times were +/-4 s across 5 days of analysis for both stationary phases; however, the amide stationary phase was observed to be more robust. The high mass measurement accuracy of less than 2 ppm and fragmentation spectra provided highly confident identifications along with structural information. In addition, data are compared among samples derived from 10 healthy controls, 10 controls with a differential diagnosis of benign gynecologic tumors, and 10 diseased epithelial ovarian cancer patients (EOC). Two fucosylated glycans were found to be up-regulated in healthy controls and provided an accurate diagnostic value with an area under the receiver operator characteristic curve of 0.87. However, these same glycans provided a significantly less diagnostic value when used to differentiate EOC from benign tumor control samples with an area under the curve of 0.73.}, number={3}, journal={ANALYTICAL CHEMISTRY}, author={Bereman, Michael S. and Williams, Taufika Islam and Muddiman, David C.}, year={2009}, month={Feb}, pages={1130–1136} }
 @article{hawkridge_muddiman_hebulein_cataliotti_burnett_2008, title={Effect of Plasma Protein Depletion on BNP-32 Recovery}, volume={54}, DOI={https://doi.org/10.1373/clinchem.2007.098038}, abstractNote={Depletion of abundant proteins from plasma and serum is an important initial step in many biomarker discovery platforms(1). Decreasing the concentrations of highly abundant proteins (e.g., albumin, IgG, and antitrypsin) facilitates the use of contemporary proteomics technologies, such as gel electrophoresis and mass spectrometry, for detection and identification of low-abundant proteins. Furthermore, decreasing abundant protein concentrations may also improve immunoprecipitation recovery efficiencies for targeted low-abundant species by decreasing nonspecific binding (i.e., shielding the antigen-binding domain) to the antibody and/or solid supports. A notable pitfall to depletion strategies is the potential for unintentionally removing low-abundant plasma or serum proteins. These low-abundant species may be bound specifically or nonspecifically to the depletion ligand, depletion target protein (e.g., carrier proteins), or the solid support(s). Thus, it is important to critically evaluate the effectiveness of abundant plasma protein depletion for enhancing the study of low-abundant protein biomarker(s).

We have been actively developing a targeted biomarker discovery platform for characterizing the circulating forms of B-type natriuretic peptide (BNP) that includes protein depletion strategies, immunoprecipitation, gel electrophoresis, isotope dilution (absolute quantification), and nanoflow liquid chromatography coupled to high-performance hybrid Fourier transform mass …}, number={5}, journal={Clinical Chemistry}, author={Hawkridge, A.M. and Muddiman, D.C. and Hebulein, D.M. and Cataliotti, A and Burnett, J.C., Jr}, year={2008}, month={May}, pages={933–934} }
 @misc{hawkridge_muddiman_helmlein_cataliotti_burnett_2008, title={Effect of plasma protein depletion on BNP-32 recovery}, volume={54}, ISSN={["0009-9147"]}, DOI={10.1373/clinchem.2007.098038}, abstractNote={Depletion of abundant proteins from plasma and serum is an important initial step in many biomarker discovery platforms(1). Decreasing the concentrations of highly abundant proteins (e.g., albumin, IgG, and antitrypsin) facilitates the use of contemporary proteomics technologies, such as gel electrophoresis and mass spectrometry, for detection and identification of low-abundant proteins. Furthermore, decreasing abundant protein concentrations may also improve immunoprecipitation recovery efficiencies for targeted low-abundant species by decreasing nonspecific binding (i.e., shielding the antigen-binding domain) to the antibody and/or solid supports. A notable pitfall to depletion strategies is the potential for unintentionally removing low-abundant plasma or serum proteins. These low-abundant species may be bound specifically or nonspecifically to the depletion ligand, depletion target protein (e.g., carrier proteins), or the solid support(s). Thus, it is important to critically evaluate the effectiveness of abundant plasma protein depletion for enhancing the study of low-abundant protein biomarker(s).

We have been actively developing a targeted biomarker discovery platform for characterizing the circulating forms of B-type natriuretic peptide (BNP) that includes protein depletion strategies, immunoprecipitation, gel electrophoresis, isotope dilution (absolute quantification), and nanoflow liquid chromatography coupled to high-performance hybrid Fourier transform mass …}, number={5}, journal={CLINICAL CHEMISTRY}, author={Hawkridge, Adam M. and Muddiman, David C. and Helmlein, Denise M. and Cataliotti, Alessandro and Burnett, John C., Jr.}, year={2008}, month={May}, pages={933–934} }
 @article{dixon_sampson_muddiman_2009, title={Generation of Multiply Charged Peptides and Proteins by Radio Frequency Acoustic Desorption and Ionization for Mass Spectrometric Detection}, volume={20}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2008.11.024}, abstractNote={The design and implementation of a radio frequency acoustic desorption ionization (RADIO) source has been demonstrated for the analysis of multiply charged peptides and proteins. One µL aliquots of melittin, BNP-32, and ubiquitin (∼1 µg of analyte) were deposited onto a quartz crystal microbalance (QCM) electrode before radio frequency actuation for desorption. Continuous electrospray parallel to/above the sampling surface enabled the ionization of desorbed species. Detection by a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer confirmed the intact and dissociated species observed during MS and MS/MS experiments, respectively.}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Dixon, R. Brent and Sampson, Jason S. and Muddiman, David C.}, year={2009}, month={Apr}, pages={597–600} }
 @article{mathivanan_ahmed_ahn_alexandre_amanchy_andrews_bader_balgley_bantscheff_bennett_et al._2008, title={Human Proteinpedia enables sharing of human protein data}, volume={26}, ISSN={1087-0156 1546-1696}, url={http://dx.doi.org/10.1038/nbt0208-164}, DOI={10.1038/nbt0208-164}, abstractNote={Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories.}, number={2}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Mathivanan, Suresh and Ahmed, Mukhtar and Ahn, Natalie G and Alexandre, Hainard and Amanchy, Ramars and Andrews, Philip C and Bader, Joel S and Balgley, Brian M and Bantscheff, Marcus and Bennett, Keiryn L and et al.}, year={2008}, month={Feb}, pages={164–167} }
 @misc{mathivanan_ahmed_ahn_alexandre_amanchy_andrews_bader_balgley_bantscheff_bennett_et al._2008, title={Human Proteinpedia enables sharing of human protein data}, volume={26}, number={2}, journal={Nature Biotechnology}, author={Mathivanan, S. and Ahmed, M. and Ahn, N. G. and Alexandre, H. and Amanchy, R. and Andrews, P. C. and Bader, J. S. and Balgley, B. M. and Bantscheff, M. and Bennett, K. L. and et al.}, year={2008}, pages={164–167} }
 @article{sampson_murray_muddiman_2009, title={Intact and Top-Down Characterization of Biomolecules and Direct Analysis Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Coupled to FT-ICR, Mass Spectrometry}, volume={20}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2008.12.003}, abstractNote={We report the implementation of an infrared laser onto our previously reported matrix-assisted laser desorption electrospray ionization (MALDESI) source with ESI post-ionization yielding multiply charged peptides and proteins. Infrared (IR)-MALDESI is demonstrated for atmospheric pressure desorption and ionization of biological molecules ranging in molecular weight from 1.2 to 17 kDa. High resolving power, high mass accuracy single-acquisition Fourier transform ion cyclotron resonance (FT-ICR) mass spectra were generated from liquid- and solid-state peptide and protein samples by desorption with an infrared laser (2.94 mum) followed by ESI post-ionization. Intact and top-down analysis of equine myoglobin (17 kDa) desorbed from the solid state with ESI post-ionization demonstrates the sequencing capabilities using IR-MALDESI coupled to FT-ICR mass spectrometry. Carbohydrates and lipids were detected through direct analysis of milk and egg yolk using both UV- and IR-MALDESI with minimal sample preparation. Three of the four classes of biological macromolecules (proteins, carbohydrates, and lipids) have been ionized and detected using MALDESI with minimal sample preparation. Sequencing of O-linked glycans, cleaved from mucin using reductive beta-elimination chemistry, is also demonstrated.}, number={4}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Sampson, Jason S. and Murray, Kermit K. and Muddiman, David C.}, year={2009}, month={Apr}, pages={667–673} }
 @article{williams_saggese_toups_frahm_an_li_lebrilla_muddiman_2008, title={Investigations with O-linked protein glycosylations by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={43}, ISSN={["1076-5174"]}, url={http://europepmc.org/abstract/med/18324610}, DOI={10.1002/jms.1398}, abstractNote={AbstractPosttranslational modifications such as glycosylation can play a fundamental role in signaling pathways that transform an ordinary cell into a malignant one. The development of a protocol to detect these changes in the preliminary stages of disease can lead to a sensitive and specific diagnostic for the early detection of malignancies such as ovarian cancer in which differential glycan patterns are linked to etiology and progression. Small variations in instrument parameters and sample preparation techniques are known to have significant influence on the outcome of an experiment. For an experiment to be effective and reproducible, these parameters must be optimized for the analyte(s) under study. We present a detailed examination of sample preparation and matrix‐assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI‐FT‐ICR‐MS) analysis of O‐linked glycans globally cleaved from mucin glycoproteins. Experiments with stable isotope‐labeled biomolecules allowed for the establishment of appropriate acquisition times and excitation voltages for MALDI‐FT‐ICR‐MS of oligosaccharides. Quadrupole ion guide optimization studies with mucin glycans identified conditions for the comprehensive analysis of the entire mass range of O‐linked carbohydrates in this glycoprotein. Separately optimized experimental parameters were integrated in a method that allowed for the effective study of O‐linked glycans. Copyright © 2008 John Wiley & Sons, Ltd.}, number={9}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Williams, Taufika Islam and Saggese, Diana A. and Toups, Kristina L. and Frahm, Jennifer L. and An, Hyun Joo and Li, Bensheng and Lebrilla, Carlito B. and Muddiman, David C.}, year={2008}, month={Sep}, pages={1215–1223} }
 @article{bereman_lyndon_dixon_muddiman_2008, title={Mass measurement accuracy comparisons between a double-focusing magnetic sector and a time-of-flight mass analyzer}, volume={22}, ISSN={["0951-4198"]}, DOI={10.1002/rcm.3544}, abstractNote={AbstractWe report a direct comparison of the mass measurement accuracies (MMAs) obtained on different mass spectrometry instrument types; a magnetic sector as the ‘gold standard’ and an electrospray ionization time‐of‐flight (ESI‐TOF) instrument. Sixty samples, obtained from the Department of Chemistry at North Carolina State University, were analyzed on each instrument. Data are presented and compared between the different instruments. The average absolute MMAs achieved for the magnetic sector and Agilent ESI‐TOF mass spectrometers were 3.0 and 1.1 ppm, respectively. Copyright © 2008 John Wiley & Sons, Ltd.}, number={10}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bereman, Michael S. and Lyndon, Matthew M. and Dixon, R. Brent and Muddiman, David C.}, year={2008}, month={May}, pages={1563–1566} }
 @article{williams_saggese_muddiman_2008, title={Studying O-linked protein glycosylations in human plasma}, volume={7}, ISSN={["1535-3893"]}, url={http://europepmc.org/abstract/med/18422354}, DOI={10.1021/pr800066e}, abstractNote={Recent investigations have implicated aberrant glycosylations in various malignancies, including epithelial ovarian cancer (EOC). The protocol here identifies O-linked carbohydrate patterns in EOC plasma glycoproteins through chemical cleavage and purification of these glycans. Dialyzed plasma is subjected to reductive beta-elimination with alkaline borohydride to release O-linked oligosaccharides from glycoproteins. Enrichment of released glycans, as well as removal of peptide and other contaminants, is followed by carbohydrate pattern analysis with MALDI-FT-ICR-MS.}, number={6}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Williams, Taufika Islam and Saggese, Diana A. and Muddiman, David C.}, year={2008}, month={Jun}, pages={2562–2568} }
 @article{williams_meadows_bori_hawkridge_comins_muddiman_2008, title={Synthesis, Characterization, and Application of Iodoacetamide Derivatives Utilized for the ALiPHAT Strategy}, volume={130}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja076849y}, DOI={10.1021/ja076849y}, abstractNote={Hydrophobic tags, derived from iodoacetamide, were synthesized, characterized, and utilized to alkylate peptide E-76, a known inhibitor of coagulation factor VIIIa, and two other cysteine containing peptides. The electrospray response of each tagged peptide was compared against the same peptide alkylated with iodoacetamide. E-76 peptide alkylated with the synthesized tags demonstrated an increase in electrospray response of up to 429 times when compared to that alkylated with iodoacetamide.}, number={7}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Williams, D. Keith and Meadows, Corey W. and Bori, Ibrahim D. and Hawkridge, Adam M. and Comins, Daniel L. and Muddiman, David C.}, year={2008}, month={Feb}, pages={2122–2123} }
 @article{williams_meadows_bori_hawkridge_comins_muddiman_2008, title={Synthesis, characterization, and application of lodoacetamide derivatives utilized for the ALiPHAT strategy}, volume={130}, DOI={10.1021/jao076849y}, number={7}, journal={Journal of the American Chemical Society}, author={Williams, D. K. and Meadows, C. W. and Bori, I. D. and Hawkridge, A. M. and Comins, D. L. and Muddiman, David}, year={2008}, pages={2122-} }
 @article{georgianna_hawkridge_muddiman_payne_2008, title={Temperature-dependent regulation of proteins in Aspergillus flavus: Whole organism stable isotope labeling by amino acids}, volume={7}, ISSN={["1535-3907"]}, DOI={10.1021/pr8001047}, abstractNote={Stable isotope labeling by amino acids in cell culture (SILAC) has been used in many different organisms including yeast, mammalian cells, and Arabidopsis cell culture. We present an adaptation of this method to quickly quantify protein changes in response to environmental stimuli regulating biosynthesis of the carcinogen aflatoxin in the fungus Aspergillus flavus. Changes in relative protein concentrations in response to temperature were quantified and compared to changes in aflatoxin biosynthesis and the transcription of the aflatoxin biosynthetic genes. In a comparison between conducive (28 degrees C) and nonconducive (37 degrees C) temperatures for aflatoxin biosynthesis, 31 proteins were found to be more abundant at 37 degrees C and 18 more abundant at 28 degrees C. The change in expression of the aflatoxin pathway enzymes closely followed the strong repression of both aflatoxin biosynthesis and transcription of the aflatoxin pathway genes observed at 37 degrees C. Transcripts corresponding to the 379 proteins quantified by SILAC were analyzed using microarrays, but their expression did not always correlate well with transcript levels of encoding genes. This is the first reported labeling of a multicellular free-living prototroph using the SILAC procedure to compare (13)C(6)-arginine-labeled samples to (12)C(6)-arginine-labeled samples for quantitative proteomics. The data presented shows the utility of this procedure in quantifying changes in protein expression in response to environmental stimuli.}, number={7}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Georgianna, D. Ryan and Hawkridge, Adam M. and Muddiman, David C. and Payne, Gary A.}, year={2008}, month={Jul}, pages={2973–2979} }
 @article{collier_hawkridge_georgianna_payne_muddiman_2008, title={Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer}, volume={80}, ISSN={["1520-6882"]}, DOI={10.1021/ac800254z}, abstractNote={Online liquid chromatography-mass spectrometric (LC-MS) analysis of intact proteins (i.e., top-down proteomics) is a growing area of research in the mass spectrometry community. A major advantage of top-down MS characterization of proteins is that the information of the intact protein is retained over the vastly more common bottom-up approach that uses protease-generated peptides to search genomic databases for protein identification. Concurrent to the emergence of top-down MS characterization of proteins has been the development and implementation of the stable isotope labeling of amino acids in cell culture (SILAC) method for relative quantification of proteins by LC-MS. Herein we describe the qualitative and quantitative top-down characterization of proteins derived from SILAC-labeled Aspergillus flavus using nanoflow reversed-phase liquid chromatography directly coupled to a linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FTICR-MS). A. flavus is a toxic filamentous fungus that significantly impacts the agricultural economy and human health. SILAC labeling improved the confidence of protein identification, and we observed 1318 unique protein masses corresponding to 659 SILAC pairs, of which 22 were confidently identified. However, we have observed some limiting issues with regard to protein quantification using top-down MS/MS analyses of SILAC-labeled proteins. The role of SILAC labeling in the presence of competing endogenously produced amino acid residues and its impact on quantification of intact species are discussed in detail.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Collier, Timothy S. and Hawkridge, Adam M. and Georgianna, D. Ryan and Payne, Gary A. and Muddiman, David C.}, year={2008}, month={Jul}, pages={4994–5001} }
 @article{yang_ghosh_northrop_zheng_lyndon_muddiman_stang_2007, title={A highly efficient approach to the self-assembly of hexagonal cavity-cored tris[2]pseudorotaxanes from several components via multiple noncovalent interactions}, volume={129}, ISSN={["1520-5126"]}, DOI={10.1021/ja073744m}, abstractNote={A method of incorporating both metal−ligand and crown ether−dialkylammonium self-assembly techniques in the efficient synthesis of metallacyclic tris[2]pseudorotaxanes is described. These multifunctional supramolecules can be prepared by the stepwise or one-pot assembly of nine separate components on account of the orthogonality of the two noncovalent assembly strategies employed. This methodology demonstrates the power of orthogonal self-assembly and may be expanded beyond the use of two recognition motifs in hopes of mimicking the complex multifunctionality of biological systems.}, number={46}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Yang, Hai-Bo and Ghosh, Koushik and Northrop, Brian H. and Zheng, Yao-Rong and Lyndon, Matthew M. and Muddiman, David C. and Stang, Peter J.}, year={2007}, month={Nov}, pages={14187-+} }
 @article{mason_therneau_eckel-passow_johnson_oberg_olson_nair_muddiman_bergen_2007, title={A method for automatically interpreting mass spectra of 180-labeled isotopic clusters}, volume={6}, ISSN={["1535-9476"]}, DOI={10.1074/mcp.M600148-MCP200}, abstractNote={16O/18O labeling is one differential proteomics technology among many that promises diagnostic and prognostic biomarkers of disease. Although the incorporation of 18O in the C-terminal carboxyl group during endoproteinase digestion in the presence of H218O makes the process of labeling facile, the ease and effectiveness of label incorporation have in some regards been outweighed by the difficulties in interpreting the resulting spectra. Complex isotope patterns result from the composition of unlabeled (18O0), singly labeled (18O1), and doubly labeled species (18O2) as well as contributions from the naturally occurring isotopes (e.g.13C and 15N). Moreover because labeling is enzymatic, the number of 18O atoms incorporated can vary from peptide to peptide. Finally it is difficult to distinguish highly up-regulated from highly down-regulated or C-terminal peptides. We have developed an algorithm entitled regression analysis applied to mass spectrometry (RAAMS) that automatically, rapidly, and confidently interprets spectra of 18O-labeled peptides without requiring chemical composition information derived from product ion spectra. The algorithm is able to measure the effective 18O incorporation rate due to variable enzyme substrate specificity of the pseudosubstrate during the isotope exchange reaction and corrects for the 18O0 abundance that remains in the labeled sample when using a two-step digestion/labeling procedure. We have also incorporated a method for distinguishing pure 18O0 from pure 18O2 peptides utilizing impure H218O. The algorithm operates on centroided peak lists and is therefore very fast: nine chromatograms of, on average, 1,168 spectra and containing, on average, 6,761 isotopic clusters were interpreted in, on average, 45 s per chromatogram. RAAMS is fast enough (average, 38 ms/spectrum) to allow the possibility of performing information-dependent MS/MS on a chromatographic time scale on species exceeding predetermined ratio thresholds. We describe in detail the operation of the algorithm and demonstrate its use on datasets with known and unknown ratios.}, number={2}, journal={MOLECULAR & CELLULAR PROTEOMICS}, author={Mason, Christopher J. and Therneau, Terry M. and Eckel-Passow, Jeanete E. and Johnson, Kenneth L. and Oberg, Ann L. and Olson, Janet E. and Nair, K. Sreekumaran and Muddiman, David C. and Bergen, H. Robert, III}, year={2007}, month={Feb}, pages={305–318} }
 @article{frahm_bori_comins_hawkridge_muddiman_2007, title={Achieving augmented limits of detection for peptides with hydrophobic alkyl tags}, volume={79}, ISSN={["0003-2700"]}, DOI={10.1021/ac070558q}, abstractNote={The wide range of protein concentrations found in biological matrixes presents a formidable analytical challenge in proteomics experiments. It is predicted that low-abundance proteins are the likely clinically relevant targets in disease-based proteomics analyses. To effectively analyze low-abundance proteins by electrospray ionization mass spectrometry, limits of detection must be improved upon. Previous studies have demonstrated hydrophobicity is a main determinant of the electrospray ionization response. One would expect to improve the electrospray ionization response of a hydrophilic peptide by making it more hydrophobic, thus increasing the molecule's affinity for the surface of the electrospray droplet, thereby allowing the molecule to more effectively compete for charge. In this report, we demonstrate a strategy to increase the electrospray ionization response of cysteine-containing peptides with the addition of an octylcarboxyamidomethyl modification via alkylation chemistry, which we name the ALiPHAT strategy (augmented limits of detection for peptides with hydrophobic alkyl tags). We demonstrate the relative increase in electrospray ionization response of peptides with an octylcarboxyamidomethyl modification compared to carboxyamidomethyl-modified peptides upon LC-MS analysis. Furthermore, we show the octylcarboxyamidomethyl group does not fragment or undergo neutral loss during collision-induced dissociation. Collectively, our results demonstrate the feasibility of the octylcarboxyamidomethyl modification to improve limits of detection for cysteine-containing peptides.}, number={11}, journal={ANALYTICAL CHEMISTRY}, author={Frahm, Jennifer L. and Bori, Ibrahim D. and Comins, Daniel L. and Hawkridge, Adam M. and Muddiman, David C.}, year={2007}, month={Jun}, pages={3989–3995} }
 @article{bereman_williams_muddiman_2007, title={Carbohydrate analysis by desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={79}, ISSN={["0003-2700"]}, url={http://europepmc.org/abstract/med/17918969}, DOI={10.1021/ac0713858}, abstractNote={We report the use of desorption electrospray ionization hybrid Fourier transform ion cyclotron resonance mass spectrometry (DESI-FT-ICR-MS) for the analysis of carbohydrates. Spectra of neat carbohydrates are presented along with their mass measurement accuracies and limits of detection. Furthermore, a comparison is made between the analyses of O-linked glycans from mucin by DESI-FT-ICR-MS and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Finally, glycans from mucin are identified by using the high mass measurement accuracy and tandem MS capabilities afforded by the hybrid FT-ICR-MS platform.}, number={22}, journal={ANALYTICAL CHEMISTRY}, author={Bereman, Michael S. and Williams, Taufika Islam and Muddiman, David C.}, year={2007}, month={Nov}, pages={8812–8815} }
 @article{hoye_dvornikovs_fine_anderson_jeffrey_muddiman_shao_sorensen_wang_2007, title={Details of the Structure Determination of the Sulfated Steroids PSDS and PADS:  New Components of the Sea Lamprey (Petromyzonmarinus) Migratory Pheromone}, volume={72}, ISSN={0022-3263 1520-6904}, url={http://dx.doi.org/10.1021/jo070957l}, DOI={10.1021/jo070957l}, abstractNote={The discovery of two new components of the migratory pheromone used by sea lamprey to guide adults to spawning grounds was recently reported. These hold promise for use in a pheromone-based control program for this species, an invasive pest in the Great Lakes. Details of the structure determination of these steroidal bis-sulfates [petromyzosterol disulfate (PSDS, 2) and petromyzonamine disulfate (PADS, 3)] are described here. Pattern matching of 1H NMR data was particularly valuable. This involved comparison of spectra of the natural samples of 2 and 3 with those of appropriate steroidal analogues [e.g., petromyzonol sulfate (PS, 1, a previously known sea lamprey bile acid derivative that is a third component of the migratory pheromone), cholesterol sulfate (6), and squalamine (8)] and model compounds containing the unprecedented aminolactam substructure present in 3. The logic underlying the iterative analyses used is presented.}, number={20}, journal={The Journal of Organic Chemistry}, publisher={American Chemical Society (ACS)}, author={Hoye, Thomas R. and Dvornikovs, Vadims and Fine, Jared M. and Anderson, Kari R. and Jeffrey, Christopher S. and Muddiman, David C. and Shao, Feng and Sorensen, Peter W. and Wang, Jizhou}, year={2007}, month={Sep}, pages={7544–7550} }
 @article{hoye_dvornikovs_fine_anderson_jeffrey_muddiman_shao_sorensen_wang_2007, title={Details of the structure determination of the sulfated steroids PSDS and PADS: New components of the sea lamprey (Petromyzon marinus) migratory pheromone}, volume={72}, DOI={10.1021/jo0709571}, number={20}, journal={Journal of Organic Chemistry}, author={Hoye, T. R. and Dvornikovs, V. and Fine, J. M. and Anderson, K. R. and Jeffrey, C. S. and Muddiman, David and Shao, F. and Sorensen, P. W. and Wang, J.}, year={2007}, pages={7544–7550} }
 @article{bereman_muddiman_2007, title={Detection of attomole amounts of analyte by desorption electrospray ionization mass spectrometry (DESI-MS) determined using fluorescence spectroscopy}, volume={18}, ISSN={["1044-0305"]}, DOI={10.1016/j.jasms.2007.03.006}, abstractNote={We report the use of fluorescence spectroscopy to investigate the amount of material removed from a PTFE surface and detected during desorption electrospray ionization (DESI) mass spectrometry measurements. The fluorescence intensity before and after DESI analysis of rhodamine 6G is used to determine the amount of material removed from the surface per mass spectrum. Calculations indicate low attomole amounts are removed per linear ion trap mass spectrum.}, number={6}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Bereman, Michael S. and Muddiman, David C.}, year={2007}, month={Jun}, pages={1093–1096} }
 @article{ogata_charlesworth_higgins_keegan_vernino_muddiman_2007, title={Differential protein expression in male and female human lumbar cerebrospinal fluid using iTRAQ reagents after abundant protein depletion}, volume={7}, ISSN={["1615-9861"]}, DOI={10.1002/pmic.200700455}, abstractNote={AbstractCerebrospinal fluid (CSF) has become one of the most frequently used biological medium for physiological studies for neurological disorders due to its proximity to the brain and clinical availability; however, before undertaking a rational approach to biomarker discovery or diagnostics, it is crucial to understand the underlying characteristics of CSF proteome in subpopulations. In this study, we examined the differential expression of proteins in pooled male and female CSF utilizing isobaric tags for relative and absolute quantification (iTRAQ™) reagents after the depletion of six high abundant proteins using a multiple affinity removal system (MARS). A total of 219 proteins were identified (95% confidence level), and 12 proteins showed difference in expression levels. Eleven out of 12 differentially expressed proteins showed ratios of male/female between 1.15 and 1.29 (duplicate average), indicating a remarkable similarity between male and female CSF. One notable exception was the slightly lower expression level of ceruloplasmin (ferroxidase) in male CSF (0.81), a copper containing protein that catalyzes the conversion of ferrous iron to ferric iron with antioxidant properties. We also examined the levels of ceruloplasmin in each individual patient sample which constituted the pooled CSF using Western blot analysis which confirmed the lower expression levels of ceruloplasmin in male CSF.}, number={20}, journal={PROTEOMICS}, author={Ogata, Yuko and Charlesworth, M. Cristine and Higgins, LeeAnn and Keegan, B. Mark and Vernino, Steven and Muddiman, David C.}, year={2007}, month={Oct}, pages={3726–3734} }
 @article{sampson_hawkridge_muddiman_2007, title={Direct characterization of intact polypeptides by matrix-assisted laser desorption electrospray ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometry}, volume={21}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.2947}, abstractNote={AbstractWe report the characterization of a recently introduced hybrid ionization source, matrix‐assisted laser desorption electrospray ionization (MALDESI), coupled to a quadrupole Fourier transform ion cyclotron resonance mass spectrometry (QFT‐ICR‐MS) system. We first demonstrate the ability of MALDESI‐QFT‐ICR MS to directly analyze and provide high mass measurement accuracy (∼1 part‐per‐million) of a polypeptide using internal calibration. Second, we show the potential of MALDESI‐QFT‐ICR MS for the top‐down characterization of multiply charged polypeptide cations. Finally, we demonstrate sub‐femtomole detection limits in MALDESI‐QFT‐ICR MS using a combination of naturally occurring peptides and their respective stable isotope labeled forms. The results presented herein demonstrate the feasibility of several potential applications for MALDESI‐QFT‐ICR MS for the direct analysis of intact biological molecules. Copyright © 2007 John Wiley & Sons, Ltd.}, number={7}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2007}, pages={1150–1154} }
 @article{williams_mcalister_good_coon_muddiman_2007, title={Dual electrospray ion source for electron-transfer dissociation on a hybrid linear ion trap-orbitrap mass spectrometer}, volume={79}, ISSN={["1520-6882"]}, DOI={10.1021/ac071444h}, abstractNote={A dual electrospray ionization source (ESI) has been modified to simultaneously produce cations and anions, one from each emitter, for performing rapid electron-transfer dissociation (ETD) ion/ion reactions on a hybrid linear ion trap-orbitrap mass spectrometer. Unlike the pulsed dual ESI sources that were used to generate ETD reagent ions, this source separates the emitters in space, rather than time, by physically switching which one is in front of the atmospheric inlet. The new arrangement allows for substantially enhanced spray stability and decreased switching times (<or=30 ms), allowing for more tandem-MS spectra per unit time. Herein, we demonstrate the stability of the ETD anion population and the ability to identify several c- and z-type product ions from multiply protonated peptide cations.}, number={20}, journal={ANALYTICAL CHEMISTRY}, author={Williams, D. Keith, Jr. and McAlister, Graeme C. and Good, David M. and Coon, Joshua J. and Muddiman, David C.}, year={2007}, month={Oct}, pages={7916–7919} }
 @article{williams_saggese_wilcox_martin_muddiman_2007, title={Effect of matrix crystal structure on ion abundance of carbohydrates by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={21}, ISSN={["0951-4198"]}, url={http://europepmc.org/abstract/med/17279479}, DOI={10.1002/rcm.2904}, abstractNote={AbstractSample preparation techniques for carbohydrate analysis using matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) are explored, with particular emphasis on analyte/matrix co‐crystallization procedures. While carbohydrates are known to prefer 2,5‐dihydroxybenzoic acid (2,5‐DHB) as the matrix of choice, these analytes are quite specific about matrix crystal structure, which in turn is dependent on the rate of drying of analyte/matrix spots on the MALDI target. With N‐acetylglucosamine (GlcNAc) and N‐acetylneuraminic acid (sialic acid or NeuAc) as test monosaccharides, significant increases in ion abundances are demonstrated with 2,5‐DHB/NeuAc spots (>10‐fold improvement) and 2,5‐DHB/GlcNAc spots (∼5‐fold improvement) with active drying. The fine structure of crystals generated in active and passive drying was investigated using powder diffraction. Passively dried samples were shown to consist of an ordered polymorph, crystallizing in the space group P21/a, while the actively dried samples produced a disordered phase crystallizing in the space group Pa. These data provide the wherewithal to engineer a matrix best suited for carbohydrate analyses. Copyright © 2007 John Wiley & Sons, Ltd.}, number={5}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Williams, Taufika Islam and Saggese, Diana A. and Wilcox, Robert J. and Martin, James D. and Muddiman, David C.}, year={2007}, pages={807–811} }
 @article{ogata_heppelmann_charlesworth_madden_miller_kalli_cilby_bergen_saggese_muddiman_2007, title={Elevated Levels of Phosphorylated Fibrinogen-α-Iso-forms and Differential Expression of Other Post-Translationally Modified Proteins in the Plasma of Ovarian Cancer PatientsJ. Proteome Res.2006,5, 3318−3325.}, volume={6}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr078005j}, DOI={10.1021/pr078005j}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVAdditions & Corr...Additions & CorrectionsORIGINAL ARTICLEThis notice is a correctionElevated Levels of Phosphorylated Fibrinogen-α-Iso-forms and Differential Expression of Other Post-Translationally Modified Proteins in the Plasma of Ovarian Cancer Patients J. Proteome Res. 2006, 5, 3318−3325.Yuko Ogata, Carrie J. Heppelmann, M. Cristine Charlesworth, Benjamin J. Madden, Melinda N. Miller, Kimberly R. Kalli, William A. Cilby, H. Robert Bergen, Diana A. Saggese, and David C. MuddimanCite this: J. Proteome Res. 2007, 6, 4, 1615Publication Date (Web):March 7, 2007Publication History Published online7 March 2007Published inissue 1 April 2007https://pubs.acs.org/doi/10.1021/pr078005jhttps://doi.org/10.1021/pr078005jcorrectionACS PublicationsCopyright © 2007 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views265Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (43 KB) Get e-AlertscloseSUBJECTS:Cancer,Peptides and proteins,Plasma,Protein dynamics Get e-Alerts}, number={4}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Ogata, Yuko and Heppelmann, Carrie J. and Charlesworth, M. Cristine and Madden, Benjamin J. and Miller, Melinda N. and Kalli, Kimberly R. and Cilby, William A. and Bergen, H. Robert and Saggese, Diana A. and Muddiman, David C.}, year={2007}, month={Apr}, pages={1615–1615} }
 @misc{williams_toups_saggese_kalli_cliby_muddiman_2007, title={Epithelial ovarian cancer: Disease etiology, treatment, detection, and investigational gene, metabolite, and protein biomarkers}, volume={6}, ISSN={["1535-3907"]}, url={http://europepmc.org/abstract/med/17583933}, DOI={10.1021/pr070041v}, abstractNote={Cancer research in recent years has immensely benefited from the development of novel technologies that enable scientists to perform detailed investigations of genomes, transcriptomes, proteomes, and metabolomes. This has invariably furthered knowledge of tumorigenesis and etiology of cancer. The resulting information can, in the foreseeable future, effect a significant change in the pace of cancer research, thereby producing improvements in patient care. Ovarian cancer in particular has received the interest of the scientific community, being the most frequent cause of death from gynecological cancers, characterized by few early symptoms, diagnosis at an advanced stage, as well as poor prognosis. Ovarian cancer is a malignancy in which normal ovarian cells begin to grow in an uncontrolled, abnormal manner and produce tumors in one or both ovaries. Epithelial cancers, the most common ovarian cancers (>80%), develop from cells lining the ovarian surface. Most ovarian cancer research is primarily focused on the early detection and treatment of epithelial ovarian cancer, the more common ovarian malignancy. This review offers an introduction to ovarian cancer, with particular emphasis on human epithelial ovarian cancer. Current methods of detection and therapy are discussed. A survey of promising new protein, gene, and metabolite biomarkers on the horizon is provided. Future prospects for improved diagnosis are offered.}, number={8}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Williams, Taufika Islam and Toups, Kristina L. and Saggese, Diana A. and Kalli, Kimberly R. and Cliby, William A. and Muddiman, David C.}, year={2007}, month={Aug}, pages={2936–2962} }
 @article{yang_hawkridge_huang_das_bunge_muddiman_stang_2007, title={New cavity rules}, volume={6}, ISSN={["1476-1122"]}, DOI={10.1021/ja066804h}, abstractNote={The design and self-assembly of novel cavity-cored metallodendrimers via noncovalent interactions are described. By employing [G0]-[G3] 120 degrees ditopic donor linkers substituted with Fréchet-type dendrons and appropriate rigid di-Pt(II) acceptor subunits, [G0]-[G3]-rhomboidal metallodendrimers and [G0]-[G3]-hexagonal, "snowflake-shaped" metallodendrimers with well-defined shape and size were prepared under mild conditions in high yields. The assemblies were characterized with multinuclear NMR ((1)H and (31)P), mass spectrometry (ESI-MS and ESI-FT-ICR-MS), and elemental analysis. Isotopically resolved mass spectrometry data support the existence of the metallodendrimers with rhomboidal and hexagonal cavities, and NMR data are consistent with the formation of all ensembles. The structures of [G0]- and [G1]-rhomboidal metallodendrimers were unambiguously confirmed via single-crystal X-ray crystallography. The shape and size of two [G3]-hexagonal metallodendrimers were investigated with MM2 force-field modeling.}, number={3}, journal={NATURE MATERIALS}, author={Yang, H. B. and Hawkridge, A. M. and Huang, S. P. D. and Das, N. and Bunge, S. D. and Muddiman, David and Stang, P. J.}, year={2007}, month={Mar}, pages={171–171} }
 @article{williams_muddiman_2007, title={Parts-per-billion mass measurement accuracy achieved through the combination of multiple linear regression and automatic gain control in a Fourier transform ion cyclotron resonance mass spectrometer}, volume={79}, ISSN={["1520-6882"]}, DOI={10.1021/ac0704210}, abstractNote={Fourier transform ion cyclotron resonance mass spectrometry has the ability to achieve unprecedented mass measurement accuracy (MMA); MMA is one of the most significant attributes of mass spectrometric measurements as it affords extraordinary molecular specificity. However, due to space-charge effects, the achievable MMA significantly depends on the total number of ions trapped in the ion cyclotron resonance (ICR) cell for a particular measurement. Even through the use of automatic gain control (AGC), the total ion population is not constant between spectra. Multiple linear regression calibration in conjunction with AGC is utilized in these experiments to formally account for the differences in total ion population in the ICR cell between the external calibration spectra and experimental spectra. This ability allows for the extension of dynamic range of the instrument and for the mean MMA values to remain less than 1 part-per-million (ppm). In addition, multiple linear regression calibration is used to account for both differences in total ion population in the ICR cell as well as relative ion abundance of a given species, which also affords mean MMA values at the parts-per-billion (ppb) level.}, number={13}, journal={ANALYTICAL CHEMISTRY}, author={Williams, D. Keith, Jr. and Muddiman, David C.}, year={2007}, month={Jul}, pages={5058–5063} }
 @article{dixon_muddiman_hawkridge_fedorov_2007, title={Probing the mechanisms of an air amplifier using a LTQ-FT-ICR-MS and fluorescence spectroscopy}, volume={18}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2007.08.006}, abstractNote={We report the first quantitative assessment of electrosprayed droplet/ion focusing enabled by the use of a voltage-assisted air amplifier between an electrospray ionization emitter and a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (ESI-LTQ-FT-ICR-MS). A solution of fluorescent dye was electrosprayed with a stainless steel mesh screen placed in front of the MS inlet capillary acting as a gas-permeable imaging plate for fluorescence spectroscopy. Without use of the air amplifier, no detectable FT-ICR signal was observed, as well as no detectable fluorescence on the screen upon imaging using a fluorescence scanner. When the air amplifier was turned ON while electrospraying the fluorescent dye, FT-ICR mass spectra with high signal to noise ratio were obtained with an average ion injection time of 21 ms for an AGC target value of 5 × 105. Imaging of the screen using a fluorescence scanner produced a distinct spot of cross-sectional area ∼33.5 mm2 in front of the MS inlet capillary. These experimental results provide direct evidence of aerodynamic focusing of electrosprayed droplets/ions enabled by an air amplifier, resulting in improved electrospray droplet/ion capture efficiency and reduced ion injection time. A second set of experiments was carried out to explore whether the air amplifier assists in desolvation. By electrospraying a mix of quaternary amines, ratios of increasingly hydrophobic molecules were obtained. Observation of the solvophobic effect associated with electrospray ionization resulted in a higher abundance of the hydrophobic molecule. This bias was eliminated when the air amplifier was turned ON and a response indicative of the respective component concentrations of the molecules in the bulk solution was observed.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Dixon, R. Brent and Muddiman, David C. and Hawkridge, Adam M. and Fedorov, A. G.}, year={2007}, month={Nov}, pages={1909–1913} }
 @article{dixon_muddiman_2007, title={Quantitative comparison of a flared and a standard heated metal capillary inlet with a voltage-assisted air amplifier on an electrospray ionization linear ion trap mass spectrometer}, volume={21}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.3206}, abstractNote={AbstractThe performance characteristics (i.e., ion abundance and electrospray ion current) of a flared and blunt‐ended heated metal capillary were evaluated with a voltage‐assisted air amplifier on a linear ion trap mass spectrometer (LTQ‐MS). The results demonstrated that a standard capillary afforded higher ion abundance than a flared capillary, thus further work is necessary to investigate conditions for which significant benefits with the flared capillary will be observed. The compatibility of a voltage‐assisted air amplifier is explored for both types of capillaries and in all cases resulted in improved ion abundance and spray current. Copyright © 2007 John Wiley & Sons, Ltd.}, number={19}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Dixon, R. Brent and Muddiman, David C.}, year={2007}, pages={3207–3212} }
 @article{dixon_bereman_muddiman_hawkridge_2007, title={Remote mass spectrometric sampling of electrospray- and desorption electrospra-generated ions using an air ejector}, volume={18}, DOI={10.1016/i.jasms.2007.07.024}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, author={Dixon, R. B. and Bereman, M. S. and Muddiman, David and Hawkridge, A. M.}, year={2007}, pages={1844–1847} }
 @article{dixon_bereman_muddiman_hawkridge_2007, title={Remote mass spectrometric sampling of electrospray- and desorption electrospray-generated ions using an air ejector}, volume={18}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/j.jasms.2007.07.024}, DOI={10.1016/j.jasms.2007.07.024}, abstractNote={A commercial air ejector was coupled to an electrospray ionization linear ion trap mass spectrometer (LTQ) to transport remotely generated ions from both electrospray (ESI) and desorption electrospray ionization (DESI) sources. We demonstrate the remote analysis of a series of analyte ions that range from small molecules and polymers to polypeptides using the AE-LTQ interface. The details of the ESI-AE-LTQ and DESI-AE-LTQ experimental configurations are described and preliminary mass spectrometric data are presented.}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Dixon, R. Brent and Bereman, Michael S. and Muddiman, David C. and Hawkridge, Adam M.}, year={2007}, month={Oct}, pages={1844–1847} }
 @article{williams_hawkridge_muddiman_2007, title={Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometer}, volume={18}, ISSN={["1044-0305"]}, DOI={10.1016/j.jasms.2006.08.014}, abstractNote={High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from −2.0 ppm to 1.1 ppm, with an average of −0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.}, number={1}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Williams, Keith, Jr. and Hawkridge, Adam M. and Muddiman, David C.}, year={2007}, month={Jan}, pages={1–7} }
 @article{frahm_capo velez_muddiman_2007, title={Understanding the influence of post-excite radius and axial confinement on quantitative proteomic measurements using Fourier transform ion cyclotron resonance mass spectrometry}, volume={21}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.2957}, abstractNote={AbstractEarly studies of Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry (MS) explored many of the fundamental issues surrounding the potential of the technique to provide quantitative data. Improvements in instrument technology and the analysis of larger molecules in increasingly complex mixtures warrant not only a revisit to some of these earlier studies, but a more comprehensive examination of the influence of various instrument parameters on quantitative (absolute and relative) measurements in proteomics. We present a detailed examination of the role that acquisition time, excite voltage (i.e. excite radius), trapping voltage, and the type of excitation waveform have on the ability of FT‐ICR to accurately quantify biological molecules. The use of a stable‐isotope‐labeled and unlabeled phenyl isocyanate derivatized peptide allows us to ascribe the effects of FT‐ICR‐MS on quantification, thus eliminating the contribution of ionization differences to ion abundance. To adequately assess the multiple parameters in the large dataset, we develop a multiplicative quality factor that encompasses the total ion abundance, as well as the accuracy and the precision of abundance ratios. This assessment allows facile determination of optimal instrument parameters for quantitative measurements. Copyright © 2007 John Wiley & Sons, Ltd.}, number={7}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Frahm, Jennifer L. and Capo Velez, Coral M. and Muddiman, David C.}, year={2007}, pages={1196–1204} }
 @article{muddiman_2006, title={"Lewis and Clark" proteomics}, volume={5}, ISSN={["1535-3893"]}, DOI={10.1021/pr0626886}, abstractNote={ADVERTISEMENT RETURN TO ISSUEEDITORIALNEXT"Lewis & Clark" ProteomicsDavid C. MuddimanCite this: J. Proteome Res. 2006, 5, 2, 221–222Publication Date (Web):February 3, 2006Publication History Published online3 February 2006Published inissue 1 February 2006https://pubs.acs.org/doi/10.1021/pr0626886https://doi.org/10.1021/pr0626886newsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views223Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (72 KB) Get e-Alertsclose SUBJECTS:Proteomics Get e-Alerts}, number={2}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Muddiman, DC}, year={2006}, month={Feb}, pages={221–222} }
 @article{frahm_howard_heber_muddiman_2006, title={Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry}, volume={41}, ISSN={["1096-9888"]}, DOI={10.1002/jms.1024}, abstractNote={AbstractThe number and wide dynamic range of components found in biological matrixes present several challenges for global proteomics. In this perspective, we will examine the potential of zero‐dimensional (0D), one‐dimensional (1D), and two‐dimensional (2D) separations coupled with Fourier‐transform ion cyclotron resonance (FT‐ICR) and time‐of‐flight (TOF) mass spectrometry (MS) for the analysis of complex mixtures. We describe and further develop previous reports on the space occupied by peptides, to calculate the theoretical peak capacity available to each separations‐mass spectrometry method examined. Briefly, the peak capacity attainable by each of the mass analyzers was determined from the mass resolving power (RP) and the m/z space occupied by peptides considered from the mass distribution of tryptic peptides from National Center for Biotechnology Information's (NCBI's) nonredundant database. Our results indicate that reverse‐phase‐nanoHPLC (RP‐nHPLC) separation coupled with FT‐ICR MS offers an order of magnitude improvement in peak capacity over RP‐nHPLC separation coupled with TOF MS. The addition of an orthogonal separation method, strong cation exchange (SCX), for 2D LC‐MS demonstrates an additional 10‐fold improvement in peak capacity over 1D LC‐MS methods. Peak capacity calculations for 0D LC, two different 1D RP‐HPLC methods, and 2D LC (with various numbers of SCX fractions) for both RP‐HPLC methods coupled to FT‐ICR and TOF MS are examined in detail. Peak capacity production rates, which take into account the total analysis time, are also considered for each of the methods. Furthermore, the significance of the space occupied by peptides is discussed. Copyright © 2006 John Wiley & Sons, Ltd.}, number={3}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Frahm, JL and Howard, BE and Heber, S and Muddiman, DC}, year={2006}, month={Mar}, pages={281–288} }
 @article{zhou_madden_muddiman_zhang_2006, title={Chromatin Assembly Factor 1 Interacts with Histone H3 Methylated at Lysine 79 in the Processes of Epigenetic Silencing and DNA Repair†}, volume={45}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi0521083}, DOI={10.1021/bi0521083}, abstractNote={In eukaryotic cells, chromatin is classified into euchromatin, which is active in transcription, and heterochromatin that silences transcription. Histones in these two domains contain distinct modifications. Chromatin assembly factor 1 (CAF-1) is a highly conserved protein that functions in DNA replication, DNA repair, and heterochromatin silencing. CAF-1 binds histones H3 and H4 and deposits histones onto DNA to form nucleosomes. However, modifications on H3 and H4 associated with CAF-1 are not known. Here, we have purified a complex containing CAF-1 and H3 and H4 from yeast cells and determined the modifications present on these histones using linear ion trap FT-ICR mass spectrometry. H4 that copurified with CAF-1 was a mixture of isoforms acetylated at lysines 5, 8, 12, and 16, whereas an H3 peptide methylated at lysine 79 and an H3 peptide acetylated at lysine 56 were detected. In yeast cell extracts, these two H3 modifications peaked in the late S phase with different kinetics. Moreover, the association of CAF-1 with H3 methylated at lysine 79 appeared to occur in the late S phase. Finally, cells lacking both Dot1p, the methyltransferase that methylates H3 lysine 79, and Cac1p, the large subunit of CAF-1, exhibited a dramatic loss of telomeric silencing and increased sensitivity to DNA damaging agents. Together, these data indicate that CAF-1 interacts with H3 methylated at lysine 79 during the processes of epigenetic silencing and DNA repair.}, number={9}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Zhou, Hui and Madden, Benjamin J. and Muddiman, David C. and Zhang, Zhiguo}, year={2006}, month={Mar}, pages={2852–2861} }
 @article{bereman_nyadong_fernandez_muddiman_2006, title={Direct high-resolution peptide and protein analysis by desorption electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={20}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.2759}, DOI={10.1002/rcm.2759}, abstractNote={AbstractWe report the first coupling of a desorption electrospray ionization (DESI) ion source to Fourier transform ion cyclotron resonance mass spectrometry (ESI‐FT‐ICR‐MS) for high‐resolution protein analysis. The DESI FT‐ICR‐MS source design is described in detail along with preliminary data obtained on peptides and proteins ranging from 1 to 5.7 kDa. Copyright © 2006 John Wiley & Sons, Ltd.}, number={22}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Bereman, Michael S. and Nyadong, Leonard and Fernandez, Facundo M. and Muddiman, David C.}, year={2006}, pages={3409–3411} }
 @article{ogata_hepplmann_charlesworth_madden_miller_kalli_cilby_bergen_saggese_muddiman_2006, title={Elevated levels of phosphorylated fibrinogen-alpha-isoforms and differential expression of other post-translationally modified proteins in the plasma of ovarian cancer patients}, volume={5}, ISSN={["1535-3907"]}, DOI={10.1021/pr060344+}, abstractNote={We evaluated the differentially expressed proteins in the plasma of ovarian cancer (OVC) patients using 2-D SDS-polyacrylamide gel electrophoresis (SDS-PAGE) with post-translational modification (P...}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Ogata, Yuko and Hepplmann, Carrie J. and Charlesworth, M. Cristine and Madden, Benjamin J. and Miller, Melinda N. and Kalli, Kimberly R. and Cilby, William A. and Bergen, H. Robert, III and Saggese, Diana A. and Muddiman, David C.}, year={2006}, month={Dec}, pages={3318–3325} }
 @article{limbach_muddiman_2006, title={Focus in Honor of James A. McCloskey, Recipient of the 2005 ASMS award for a distinguished contribution in mass spectrometry}, volume={17}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/J.JASMS.2006.07.003}, DOI={10.1016/J.JASMS.2006.07.003}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVEditorialFocus in Honor of James A. McCloskey, Recipient of the 2005 ASMS award for a distinguished contribution in mass spectrometryPat LimbachPat LimbachMore by Pat Limbach and Dave MuddimanDave MuddimanMore by Dave MuddimanCite this: The official journal of The American Society for Mass Spectrometry 2006, 17, 10, I1–I2Publication Date (Web):October 1, 2006Publication History Published online1 October 2006Published inissue 1 October 2006https://pubs.acs.org/doi/10.1016/j.jasms.2006.07.003https://doi.org/10.1016/j.jasms.2006.07.003editorialACS PublicationsCopyright © 2006 © American Society for Mass Spectrometry 2006. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views19Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (96 KB) Get e-Alerts}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Limbach, Pat and Muddiman, Dave}, year={2006}, month={Oct}, pages={I1–I2} }
 @article{sampson_hawkridge_muddiman_2006, title={Generation and detection of multiply-charged peptides and proteins by matrix-assisted laser desorption electrospray ionization (MALDESI) Fourier transform ion cyclotron resonance mass spectrometry}, volume={17}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2006.08.003}, abstractNote={We report the coupling of a hybrid ionization source, matrix-assisted laser desorption electrospray ionization (MALDESI), to a Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR MS). The details of the source design and initial data are presented. Analysis of peptides and proteins ranging from 1 to 8.6 kDa resulted in high resolving power single-acquisition FT-ICR mass spectra with average charge-states highly correlated to those obtained by nanoESI, thus, providing strong evidence that the ESI process dictates the observed charge-state distribution. Importantly, unlike the recently introduced electrospray assisted laser desorption ionization (ELDI) source reported by Shiea and coworkers [1, 2], the data we have obtained to date rely on the use of an organic acid matrix. The results presented herein provide insight into the charging mechanism of this emerging ionization approach, while also expanding the utility of FT-ICR MS for top-down protein and complex mixture analysis.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Sampson, Jason S. and Hawkridge, Adam M. and Muddiman, David C.}, year={2006}, month={Dec}, pages={1712–1716} }
 @article{kang_hawkridge_johnson_muddiman_prevelige_2006, title={Identification of Subunit−Subunit Interactions in Bacteriophage P22 Procapsids by Chemical Cross-linking and Mass Spectrometry}, volume={5}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr050356f}, DOI={10.1021/pr050356f}, abstractNote={Viral capsids are dynamic structures which self-assemble and undergo a series of structural transformations to form infectious viruses. The dsDNA bacteriophage P22 is used as a model system to study the assembly and maturation of icosahedral dsDNA viruses. The P22 procapsid, which is the viral capsid precursor, is assembled from coat protein with the aid of scaffolding protein. Upon DNA packaging, the capsid lattice expands and becomes a stable virion. Chemical cross-linking analyzed by mass spectrometry was used to identify residue specific inter- and intra-subunit interactions in the P22 procapsids. All the intersubunit cross-links occurred between residues clustered in a loop region (residues 157-207) which was previously identified by mass spectrometry based on hydrogen/deuterium exchange and biochemical experiments. DSP and BS3 which have similar distance constraints (12 angstroms and 11.4 angstroms, respectively) cross-linked the same residues between two subunits in the procapsids (K183-K183), whereas DST, a shorter cross-linker, cross-linked lysine 175 in one subunit to lysine 183 in another subunit. The replacement of threonine with a cysteine at residue 182 immediately adjacent to the K183 cross-linking site resulted in slow spontaneous disulfide bond formation in the procapsids without perturbing capsid integrity, thus suggesting flexibility within the loop region and close proximity between neighboring loop regions. To build a detailed structure model, we have predicted the secondary structure elements of the P22 coat protein, and attempted to thread the prediction onto identified helical elements of cryoEM 3D reconstruction. In this model, the loop regions where chemical cross-linkings occurred correspond to the extra density (ED) regions which protrude upward from the outside of the capsids and face one another around the symmetry axes.}, number={2}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Kang, Sebyung and Hawkridge, Adam M. and Johnson, Kenneth L. and Muddiman, David C. and Prevelige, Peter E.}, year={2006}, month={Feb}, pages={370–377} }
 @article{yang_das_huang_hawkridge_diaz_arif_finn_muddiman_stang_2006, title={Incorporation of 2,6-di(4,4 '-dipyridyl)-9-thiabicyclo[3.3.1] nonane into discrete 2D supramolecules via coordination-driven self-assembly}, volume={71}, ISSN={["0022-3263"]}, DOI={10.1021/jo0608117}, abstractNote={The synthesis and characterization of three new supramolecular complexes 6-8 (a rhomboid and two hexagons) via coordination-driven self-assembly are reported in excellent yields (>90%). These assemblies have 2,6-di(4,4'-dipyridyl)-9-thiabicyclo[3.3.1]nonane 2 as the bridging tecton. All assemblies were characterized by multinuclear NMR (1H and 31P), mass spectrometry (ESI-MS and ESI-FT-ICR), and elemental analysis. The X-ray structure of the 120 degrees tecton 2 is also discussed.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Yang, Hai-Bo and Das, Neeladri and Huang, Feihe and Hawkridge, Adam M. and Diaz, David D. and Arif, Atta M. and Finn, M. G. and Muddiman, David C. and Stang, Peter J.}, year={2006}, month={Aug}, pages={6644–6647} }
 @article{yang_das_huang_hawkridge_muddiman_stang_2006, title={Molecular Architecture via Coordination:  Self-Assembly of Nanoscale Hexagonal Metallodendrimers with Designed Building Blocks}, volume={128}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja063377z}, DOI={10.1021/ja063377z}, abstractNote={The first self-assembly of nanoscale metallodendrimers that have a hexagonal cavity as a core via the directional-bonding approach is reported. All metallodendrimers were characterized by multinuclear NMR (1H and 31P), mass spectrometry (ESI-MS and ESI-FT-ICR), and elemental analysis.}, number={31}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Yang, Hai-Bo and Das, Neeladri and Huang, Feihe and Hawkridge, Adam M. and Muddiman, David C. and Stang, Peter J.}, year={2006}, month={Aug}, pages={10014–10015} }
 @article{yang_das_huang_hawkridge_muddiman_stang_2006, title={Molecular Architecture via Coordination:  Self-Assembly of Nanoscale Hexagonal Metallodendrimers with Designed Building Blocks}, volume={128}, DOI={https://doi.org/10.1021/ja063377z}, abstractNote={The first self-assembly of nanoscale metallodendrimers that have a hexagonal cavity as a core via the directional-bonding approach is reported. All metallodendrimers were characterized by multinuclear NMR (1H and 31P), mass spectrometry (ESI-MS and ESI-FT-ICR), and elemental analysis.}, number={31}, journal={Journal of American Chemical Society}, author={Yang, H. and Das, N. and Huang, F. and Hawkridge, A.M. and Muddiman, D.C. and Stang, P.J.}, year={2006}, month={Jul}, pages={10014–10015} }
 @article{johnson_ovsyannikova_madden_poland_muddiman_2005, title={Accurate mass precursor ion data and tandem mass spectrometry identify a class I human leukocyte antigen A*0201-presented peptide originating from vaccinia virus}, volume={16}, ISSN={["1879-1123"]}, DOI={10.1016/j.jasms.2005.07.015}, abstractNote={We have used accurate mass precursor ion data generated on a hybrid linear-ion trap-Fourier transform ion cyclotron resonance mass spectrometer to augment tandem mass spectrometry (MS/MS) data generated on two different instrument types. Results from these experiments have allowed us for the first time to identify a naturally processed peptide presented by a class I human leukocyte antigen allele (HLA-A*0201) that was isolated from B cells infected by live vaccinia, the viral agent of the smallpox vaccine. The accurate mass data, in conjunction with MS/MS data, was able to identify the sequence IVIEAIHTV (aa 187–195) from the protein thymidylate kinase of vaccinia, distinguishing it from a similar sequence IVLEAIAEH: a "self-peptide" from the human protein phospholipase Cβ3. Accurate mass data for the doubly charged species from the naturally processed and presented peptide was 497.8006, which was within 0.8 ppm of the calculated m/z of 497.8002, while being −37.3 ppm from the calculated m/z (497.7820) of the second-ranked peptide sequence IVLEAIAEH. Accurate mass data ranged from less than 0.1 to 1.2 ppm for other peptides identified in this sample. A BLAST search shows this sequence, IVIEAIHTV, is conserved in the same protein of a number of other orthopoxviruses, including the variola (smallpox) virus. Additionally, accurate mass data were able to uncover a false positive search result that was not distinguished by scoring of the match to the MS/MS data.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Johnson, KL and Ovsyannikova, IG and Madden, BJ and Poland, GA and Muddiman, DC}, year={2005}, month={Nov}, pages={1812–1817} }
 @article{jude_disteldorf_fischer_wedge_hawkridge_arif_hawthorne_muddiman_stang_2005, title={Coordination-Driven Self-Assemblies with a Carborane Backbone}, volume={127}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja053050i}, DOI={10.1021/ja053050i}, abstractNote={The design and self-assembly of five new supramolecular complexes (a rectangle, a triangle, a hexagon, and two squares) are described. These assemblies incorporate carborane building blocks and were prepared in excellent yields (>85%). The assemblies and building blocks were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectrometry, and elemental analysis. Isotopically resolved mass spectrometry data confirm the existence of the rectangle, triangle, and hexagon, and NMR data are consistent with the formation of all five assemblies. The X-ray structures of two linear carborane building blocks, 1,12-(4-CC(C(5)H(4)N)(2)-p-C(2)B(10)H(10) (1) and 1,12-(trans-(Pt(PEt(3))(2)I)CC)(2)-p-C(2)B(10)H(10) (2), are reported: 1 is monoclinic, P2(1)/c, a = 10.6791(4) A, b = 8.0091(14) A, c = 11.6796(4) A, beta = 107.8461(15) degrees , V = 950.89(5) A(3), Z = 2; 2 is monoclinic, C2/c, a = 62.1128(10) A, b = 22.0071(3) A, c = 14.0494(2) A, beta = 89.9411(8) degrees , V = 19204.4(5) A(3), Z = 16. Crystals of the linear linker 1 exhibit close pi-pi pyridine and pyridine-B(carborane) interactions, which are discussed.}, number={34}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Jude, Hershel and Disteldorf, Hendrik and Fischer, Sonja and Wedge, Tim and Hawkridge, Adam M. and Arif, Atta M. and Hawthorne, M. Frederick and Muddiman, David C. and Stang, Peter J.}, year={2005}, month={Aug}, pages={12131–12139} }
 @article{kramp_dewitt_flora_muddiman_slunt_houston_2005, title={Derivatives of pentamidine designed to target the Leishmania lipophosphoglycan}, volume={46}, ISSN={0040-4039}, url={http://dx.doi.org/10.1016/j.tetlet.2004.11.112}, DOI={10.1016/j.tetlet.2004.11.112}, abstractNote={The Leishmania lipophosphoglycan (LPG) is the most abundant cell surface glycoconjugate of a family of infectious protozoa. Pentamidine, a common drug used in the treatment of Leishmania infections, has been modified with boronic acids so that it might bind more selectively to the phosphodisaccharide repeating unit of the LPG. This could serve to target the drug to the protozoan surface and increase its efficacy in vivo.}, number={4}, journal={Tetrahedron Letters}, publisher={Elsevier BV}, author={Kramp, Kari L. and DeWitt, Kristin and Flora, Jason W. and Muddiman, David C. and Slunt, Kelli M. and Houston, Todd A.}, year={2005}, month={Jan}, pages={695–698} }
 @article{swanson_pittelkow_benson_hawkridge_muddiman_2005, title={Déjà Vu All Over Again: Skin Cap Still Contains a High-Potency Glucocorticosteroid}, volume={141}, ISSN={0003-987X}, url={http://dx.doi.org/10.1001/archderm.141.6.801}, DOI={10.1001/archderm.141.6.801}, number={6}, journal={Archives of Dermatology}, publisher={American Medical Association (AMA)}, author={Swanson, David L. and Pittelkow, Mark R. and Benson, Linda M. and Hawkridge, Adam M. and Muddiman, David C.}, year={2005}, month={Jun} }
 @article{hawkridge_nepomuceno_lovik_mason_muddiman_2005, title={Effect of post-excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry}, volume={19}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.1871}, DOI={10.1002/rcm.1871}, abstractNote={AbstractWe report an evaluation of a modern Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS) instrument to determine the general trend of post‐excitation radius on total ion abundance, mass measurement accuracy, and isotopic distributions for internally calibrated mass spectra. The optimum post‐excitation radius was determined using total ion abundance, mass measurement accuracy (MMA), and isotope ratios. However, despite the utility of internal calibration for achieving ultimate MMA, the internal calibrant ions were insufficient for compensating for sub‐optimum ICR cell conditions. The findings presented herein underscore the importance of determining the optimal post‐excitation radius in FT‐ICR‐MS to achieve high ion abundance (low limits of detection), high MMA, and valid isotopic distributions. Copyright © 2005 John Wiley & Sons, Ltd.}, number={7}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Hawkridge, Adam M. and Nepomuceno, Angelito I. and Lovik, Stephanie L. and Mason, Christopher J. and Muddiman, David C.}, year={2005}, pages={915–918} }
 @article{ogata_charlesworth_muddiman_2005, title={Evaluation of Protein Depletion Methods for the Analysis of Total-, Phospho- and Glycoproteins in Lumbar Cerebrospinal Fluid}, volume={4}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr049750o}, DOI={10.1021/pr049750o}, abstractNote={A proper sample preparation, in particular, abundant protein removal is crucial in the characterization of low-abundance proteins including those harboring post-translational modifications. In human cerebrospinal fluid (CSF), approximately 80% of proteins originate from serum, and removal of major proteins is necessary to study brain-derived proteins that are present at low concentrations for successful biomarker and therapeutic target discoveries for neurological disorders. In this study, phospho- and glycoprotein specific fluorescent stains and mass spectrometry were used to map proteins from CSF on two-dimensional gel electropherograms after immunoaffinity based protein removal. Two protein removal methods were evaluated: batch mode with avian IgY antibody microbeads using spin filters and HPLC multiple affinity removal column. Six abundant proteins were removed from CSF: human serum albumin (HSA), transferrin, IgG, IgA, IgM, and fibrinogen with batch mode, and HSA, transferrin, IgG, IgA, antitrypsin, and haptoglobin with column chromatography. 2D gels were compared after staining for phospho-, glyco- and total proteins. The column format removed the major proteins more effectively and approximately 50% more spots were visualized when compared to the 2D gel of CSF without protein depletion. After protein depletion, selected phospho- and glycoprotein spots were identified using mass spectrometry in addition to some of the spots that were not visualized previously in nondepleted CSF. Fifty proteins were identified from 66 spots, and among them, 12 proteins (24%) have not been annotated in previously published 2D gels.}, number={3}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Ogata, Yuko and Charlesworth, M. Cristine and Muddiman, David C.}, year={2005}, month={Jun}, pages={837–845} }
 @article{yang_cooks_ouyang_hawkridge_muddiman_2005, title={Gentle Protein Ionization Assisted by High-Velocity Gas Flow}, volume={77}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac050711l}, DOI={10.1021/ac050711l}, abstractNote={Gentle protein electrospray ionization is achieved using the high-velocity gas flow of an air amplifier to improve desolvation in conventional ESI and generate intact folded protein ions in the gas phase. Comparisons are made between the ESI spectra of a number of model proteins, including ubiquitin, cytochrome c, lysozyme, and myoglobin, over a range of pH values under optimized conditions, with and without using an air amplifier to achieve high-velocity gas flow. Previously reported increased ion signals are confirmed. In addition, the peaks recorded using the air amplifier are shown to be narrower, corresponding to more complete desolvation. Significant changes in the charge-state distribution also are observed, with a shift to lower charge state at high-velocity flow. The relationship between the observed charge-state distribution and protein conformation was explored by comparing the charge-state shifts and the distributions of charge states for proteins that are or are not stable in their native conformations in low pH solutions. The data suggest retention of native or nativelike protein conformations using the air amplifier in all cases examined. This is explained by a mechanism in which the air amplifier rapidly creates small droplets from the original large ESI droplets and these microdroplets then desolvate without a significant decrease in pH, resulting in retention of the folded protein conformations. Furthermore, the holoform of ionized myoglobin is visible at pH 3.5, a much lower value than the minimum needed to see this form in conventional ESI. These results provide evidence for the importance of the conditions used in the desolvation process for the preservation of the protein conformation and suggest that the conditions achieved when using high-velocity gas flows to assist droplet evaporation and ion desolvation are much gentler than those in conventional ESI experiments.}, number={19}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Yang, Pengxiang and Cooks, R. Graham and Ouyang, Zheng and Hawkridge, Adam M. and Muddiman, David C.}, year={2005}, month={Oct}, pages={6174–6183} }
 @article{johnson_ovsyannikova_poland_muddiman_2005, title={Identification of class IIHLA-DBR1*03-bound measles virus peptides by 2D-liquid chromatography tandem mass spectrometry}, volume={4}, ISSN={["1535-3907"]}, DOI={10.1021/pr0501416}, abstractNote={Two-dimensional liquid chromatography (2D-LC), combined with gas phase fractionation tandem mass spectrometry, was used to identify 13 naturally processed peptides originating from measles virus that were presented by HLA-DRB1*03 class II molecules. The peptides are from three of the six measles structural proteins: phosphoprotein, nucleocapsid, and hemagglutinin. These peptides provide an important first step toward understanding the mechanism of immune response to measles virus and development of a new generation of peptide-based vaccines.}, number={6}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Johnson, KL and Ovsyannikova, IG and Poland, GA and Muddiman, DC}, year={2005}, pages={2243–2249} }
 @article{frahm_muddiman_burke_2005, title={Leveling response factors in the electrospray ionization process using a heated capillary interface}, volume={16}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/j.jasms.2005.02.002}, DOI={10.1016/j.jasms.2005.02.002}, abstractNote={Several investigators have observed a discrepancy in electrospray response of complementary strands from denatured DNA, which has been attributed to the difference in hydrophobicity between the two strands; the more hydrophobic species tend to have higher ion abundances. The implementation of a heated electrospray source has allowed us to "level" the electrospray response for two equimolar complementary strands with different hydrophobicities. As the temperature was increased, the ratio of ion abundances of the less hydrophobic noncoding strand to the more hydrophobic coding strand approached unity. Furthermore, the heated electrospray source was used to denature amplicons containing 7-deaza purines, which can be used to facilitate sequencing by mass spectrometry.}, number={5}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Frahm, Jennifer L. and Muddiman, David C. and Burke, Michael J.}, year={2005}, month={May}, pages={772–778} }
 @article{mccormick_holmes_muddiman_madden_2005, title={Mapping Sites of Protein Phosphorylation by Mass Spectrometry Utilizing a Chemical-Enzymatic Approach:  Characterization of Products from α-S1Casein Phosphopeptides}, volume={4}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr049804u}, DOI={10.1021/pr049804u}, abstractNote={A novel chemical-enzymatic approach was developed to facilitate identification of phosphorylation sites in isolated phosphoproteins. ESI-TOF mass spectrometry was used to characterize products from the chemical-enzymatic cleavage of specific phosphorylation sites in bovine alpha-S1 casein and synthetic phosphopeptides containing substitutions at a single phosphorylation site. Further refinements to this approach for identification of protein phosphorylation sites and its utility for the quantification of phosphopeptides by isotope-dilution mass spectrometry are presented.}, number={2}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={McCormick, Daniel J. and Holmes, Michael W. and Muddiman, David C. and Madden, Benjamin J.}, year={2005}, month={Apr}, pages={424–434} }
 @article{bergen_muddiman_o'brien_hoyer_2005, title={Normalization of relative peptide ratios derived from in-gel digests: applications to protein variant analysis at the peptide level}, volume={19}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.2134}, DOI={10.1002/rcm.2134}, abstractNote={AbstractThe ability to detect protein variants and post‐translational modifications by mass spectrometry has become increasingly important. Unfortunately, the ability to detect variants in large intact proteins (>80 000 Da) is limited. Even in the analysis of smaller proteins, algorithms are required to determine the presence of a 2 Da mass shift in an intact 13 kDa protein because the isotopic distribution of the multiply charged ions of the variant overlaps the wild‐type distribution. Fortunately, most modern instruments are capable of detecting variants in tryptic peptides derived from intact proteins. If a single common variant protein is known, the presence of a variant tryptic peptide can be easily demonstrated. A more difficult issue is the case where a multiplicity of peptides with multiple amino acid substitutions can be associated with pathology. In these cases a decrease in the relative amount of a variant peptide relative to other internal tryptic fragments would be diagnostic. However, the variability associated with the analysis of in‐gel or solution digests of proteins, related to efficiencies in digestion, extraction and ionization, confounds variant analysis at the peptide level. A strategy was developed to normalize for this variability by utilizing multiple isotopically labeled internal standards for multiple peptides derived from the same protein. Erythrocyte spectrin from 36 normal and 25 abnormal osmotic fragility samples was analyzed as a test case. Three isotopically labeled target peptides comprising the α/β‐spectrin self‐association sites were added to purified digested α‐spectrin. The utilization of multiple internal standards demonstrates the capability to normalize for sample variability due to ionization efficiency, solvent effects, digestion and extraction efficiency. Copyright © 2005 John Wiley & Sons, Ltd.}, number={19}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Bergen, H. Robert and Muddiman, David C. and O'Brien, John F. and Hoyer, James D.}, year={2005}, pages={2871–2877} }
 @article{frahm_muddiman_2005, title={Nucleic Acid Analysis by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at the Beginning of the Twenty-First Century}, volume={11}, ISSN={1381-6128}, url={http://dx.doi.org/10.2174/1381612054546905}, DOI={10.2174/1381612054546905}, abstractNote={Mass spectrometers measure an intrinsic property (i.e., mass) of a molecule, which makes it an ideal platform for nucleic acid analysis. Importantly, the unparalleled capabilities of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry further extend its usefulness for nucleic acid analysis. The beginning of the twenty-first century has been marked with notable advances in the field of FT-ICR mass spectrometry analysis of nucleic acids. Some of these accomplishments include fundamental studies of nucleic acid properties, improvements in sample clean up and preparation, better methods to obtain higher mass measurement accuracy, analysis of noncovalent complexes, tandem mass spectrometry, and characterization of peptide nucleic acids. This diverse range of studies will be presented herein.}, number={20}, journal={Current Pharmaceutical Design}, publisher={Bentham Science Publishers Ltd.}, author={Frahm, J. and Muddiman, D.}, year={2005}, month={Aug}, pages={2593–2613} }
 @article{fautsch_howell_vrabel_charlesworth_muddiman_johnson_2005, title={Primary Trabecular Meshwork Cells Incubated in Human Aqueous Humor Differ from Cells Incubated in Serum Supplements}, volume={46}, ISSN={1552-5783}, url={http://dx.doi.org/10.1167/iovs.05-0101}, DOI={10.1167/iovs.05-0101}, abstractNote={PURPOSE
To determine whether aqueous humor, the in vivo source of nutrients for trabecular meshwork cells, alters cellular and molecular characteristics in primary trabecular monolayer cell cultures when compared with standard culture conditions.


METHODS
Human primary trabecular meshwork cell cultures were grown in DMEM supplemented with 50% human aqueous humor (DMEM-AH), heat-denatured DMEM-AH, 10% fetal bovine serum (DMEM-FBS, the standard culture supplement), or heat-denatured DMEM-FBS. Confluent trabecular cells were assayed for cell propagation and morphology for 21 days. Protein expression profiles of trabecular cell lysates were analyzed by two-dimensional polyacrylamide gel electrophoresis. Western blot analysis was used to determine the protein expression of myocilin and TIMP-1 in conditioned media collected from trabecular cells at 5, 10, 15, and 21 days. Myocilin expression was also analyzed by Western immunoblots after addition of dexamethasone (10(-7) M) or ascorbic acid (29 mg/dL).


RESULTS
Trabecular cells supplemented with DMEM-AH for 21 days showed decreased cell proliferation when compared with DMEM-FBS (11% vs. 141%). Cellular morphology was also altered: Trabecular cells incubated in DMEM-AH showed larger-, broader-, and flatter-appearing cells than did the more spindle-shaped cells grown in DMEM-FBS. Protein profiles of trabecular cell lysates isolated from cells incubated in DMEM-AH differed from those incubated in DMEM-FBS. In DMEM-AH-conditioned medium, myocilin expression was increased and TIMP-1 expression was decreased at day 21. Induction of myocilin by dexamethasone was observed in conditioned medium isolated from cells treated with DMEM-FBS (442%), but only a 10% increase in myocilin was observed beyond the normal induction in DMEM-AH. Daily administration of ascorbic acid to DMEM-AH failed to increase myocilin expression beyond that obtained with DMEM-AH.


CONCLUSIONS
Addition of human aqueous humor rather than FBS to trabecular monolayer cell cultures triggers significant changes in cellular and molecular characteristics. The protein component of aqueous humor is responsible for these changes. Aqueous humor supplementation may maintain cultured trabecular cells in a more physiologic state.}, number={8}, journal={Investigative Opthalmology & Visual Science}, publisher={Association for Research in Vision and Ophthalmology (ARVO)}, author={Fautsch, Michael P. and Howell, Kyle G. and Vrabel, Anne M. and Charlesworth, M. Cristine and Muddiman, David C. and Johnson, Douglas H.}, year={2005}, month={Aug}, pages={2848} }
 @article{barnidge_tschumper_jelinek_muddiman_kay_2005, title={Protein expression profiling of CLL B cells using replicate off-line strong cation exchange chromatography and LC–MS/MS}, volume={819}, ISSN={1570-0232}, url={http://dx.doi.org/10.1016/j.jchromb.2005.01.021}, DOI={10.1016/j.jchromb.2005.01.021}, abstractNote={In this study we use replicate 2D-LC-MS/MS analyses of crude membranes from B cells derived from a patient with chronic lymphocytic leukemia (CLL) to examine the protein expression profile of CLL B cells. Protein identifications made by replicate 2D-LC-MS/MS analysis of tryptic peptides from detergent solubilized B cell membrane proteins, as well as replicate LC-MS/MS analysis of single off-line strong cation exchange chromatography (SCX) fractions, were analyzed. We show that despite the variance in SCX, capillary LC, and the data-dependent selection of precursor ions, an overlap of 64% between proteins identified in replicate runs was achieved for this system.}, number={1}, journal={Journal of Chromatography B}, publisher={Elsevier BV}, author={Barnidge, David R. and Tschumper, Renee C. and Jelinek, Diane F. and Muddiman, David C. and Kay, Neil E.}, year={2005}, month={May}, pages={33–39} }
 @article{barnidge_jelinek_muddiman_kay_2005, title={Quantitative Protein Expression Analysis Of CLL B Cells from Mutated and Unmutated IgVHSubgroups Using Acid-Cleavable Isotope-Coded Affinity Tag Reagents}, volume={4}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr050028f}, DOI={10.1021/pr050028f}, abstractNote={Relative protein expression levels were compared in leukemic B cells from two patients with chronic lymphocytic leukemia (CLL) having either mutated (M-CLL) or unmutated (UM-CLL) immunoglobulin variable heavy chain genes (IgV(H)). Cells were separated into cytosol and membrane protein fractions then labeled with acid-cleavable ICAT reagents (cICAT). Labeled proteins were digested with trypsin then subjected to SCX and affinity chromatography followed by LC-ESI-MS/MS analysis on a linear ion trap mass spectrometer. A total of 9 proteins from the cytosol fraction and 4 from the membrane fraction showed a 3-fold or greater difference between M-CLL and UM-CLL and a subset of these were examined by Western blot where results concurred with cICAT abundance ratios. The abundance of one of the proteins in particular, the mitochondrial membrane protein cytochrome c oxidase subunit COX G was examined in 6 M-CLL and 6 UM-CLL patients using western blot and results showed significantly greater levels (P < 0.001) in M-CLL patients vs UM-CLL patients. These results demonstrate that stable isotope labeling and mass spectrometry can complement 2D gel electrophoresis and gene microarray technologies for identifying putative and perhaps unique prognostic markers in CLL.}, number={4}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Barnidge, David R. and Jelinek, Diane F. and Muddiman, David C. and Kay, Neil E.}, year={2005}, month={Aug}, pages={1310–1317} }
 @article{hawkridge_heublein_bergen_cataliotti_burnett_muddiman_2005, title={Quantitative mass spectral evidence for the absence of circulating brain natriuretic peptide (BNP-32) in severe human heart failure}, volume={102}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0508782102}, DOI={10.1073/pnas.0508782102}, abstractNote={
            C-terminal brain (B-type) natriuretic peptide (BNP)-32 is a widely used clinical biomarker for the diagnosis, prognosis, and treatment of heart failure (HF). The 32-aa peptide is synthesized primarily in the atrial and ventricular myocardium and constitutes the mature biologically active form of immature BNP (pro-BNP). There has been mounting evidence that suggests BNP circulates in different structural forms that impact HF diagnosis and
            in vivo
            activity. Herein, we have developed and used an immunoaffinity purification assay to isolate endogenous BNP-32 from New York Heart Association class IV patient plasma for subsequent analysis by nano-liquid chromatography (LC) electrospray ionization Fourier transform ion cyclotron resonance (FT-ICR) MS. We have introduced stable isotope-labeled BNP-32 to the assayed plasma to enable quantification of endogenous levels of BNP-32. Unlike the chemically nonspecific point-of-care tests (POCTs) and RIAs used worldwide to quantify BNP-32 from plasma, FT-ICR-MS (unprecedented mass measurement accuracy) coupled with LC (retention time) affords extraordinary molecular specificity, and when combined with the use of internal standards is able to confidently identify and quantify BNP-32. The significance of this work is despite exceedingly high circulating levels of BNP-32 in the New York Heart Association class IV patients as determined by POCTs (>290 fmol/ml) nano-LC-electrospray ionization-FT-ICR-MS data did not reveal any endogenous BNP-32. These results provide molecularly specific evidence for the absence of circulating BNP-32 in advanced-stage HF patients and suggest the existence of altered forms of BNP that are contributing to the POCT values.
          }, number={48}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Hawkridge, A. M. and Heublein, D. M. and Bergen, H. R. and Cataliotti, A. and Burnett, J. C. and Muddiman, D. C.}, year={2005}, month={Nov}, pages={17442–17447} }
 @article{muddiman_mason_johnson_2005, title={Reproducibility of Retention Time using a Splitless nanoLC Coupled to an ESI-FTICR Mass Spectrometer}, volume={16, 4}, journal={Journal of Biomolecular Techniques}, author={Muddiman, D.C. and Mason, C.J. and Johnson, K.L.}, year={2005}, month={Dec}, pages={414–422} }
 @article{muddiman_oberg_2005, title={Statistical Evaluation of Internal and External Mass Calibration Laws Utilized in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry}, volume={77}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac048258l}, DOI={10.1021/ac048258l}, abstractNote={The statistical evaluation of two common and three new calibration laws utilized in Fourier transform ion cyclotron resonance mass spectrometry are presented. Electrospray ionization was used to prepare a series of mass spectra of ammonium-adducted polypropylene glycol (PPG) with an average molecular weight of 1000 Da. The singly charged PPG-1000 oligomers allowed for the description of a broad range of m/z and abundance values within each mass spectrum. The hexapole accumulation time was varied to afford a range of total ion abundance values of about an order of magnitude. To examine each of the calibration laws, we utilized cross-validation both "within-spectrum" and "between-spectra" for internally and externally calibrated data, respectively. In addition, we used t-statistics to ensure that each calibration coefficient was statistically significant and necessary to accurately describe the variation in the data. In comparison to commonly used calibration laws for internal calibration, our new calibration law based on multiple linear regression offered a 2-fold improvement in mass measurement accuracy (MMA). In comparison to external calibration laws without automatic gain control, our new calibration law using multiple regression improved the MMA by >10-fold; this improvement would increase further as the dynamic range of the measurement increases (e.g., a biological system). For both our internal and external calibration laws, the median MMA was less than 1 part-per-million. Furthermore, we investigate the number of calibrant ions as well as their required m/z range in order to successfully achieve high MMA.}, number={8}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Oberg, Ann L.}, year={2005}, month={Apr}, pages={2406–2414} }
 @article{johnson_muddiman_2004, title={A method for calculating 16o/18o peptide ion ratios for the relative quantification of proteomes}, volume={15}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/j.jasms.2003.11.016}, DOI={10.1016/j.jasms.2003.11.016}, abstractNote={A method is described for the identification and relative quantification of proteomes using accurate mass tags (AMT) generated by nLC-dual ESI-FT-ICR-MS on a 7T instrument in conjunction with stable isotope labeling using 16O/18O ratios. AMTs were used for putative peptide identification, followed by confirmation of peptide identity by tandem mass spectrometry. For a combined set of 58 tryptic peptides from bovine serum albumin (BSA) and human transferrin, a mean mass measurement accuracy of 1.9 ppm ±0.94 ppm (CIM99%) was obtained. This subset of tryptic peptides was used to measure 16O/18O ratios of 0.36±0.09 (CIM99%) for BSA (μ=0.33) and 1.48±0.47 (CIM99%) for transferrin (μ=1.0) using a method for calculating 16O/18O ratios from overlapping isotopic multiplets arising from mixtures of 16O, 18O1, and 18O2 labeled C-termini. The model amino acid averagine was used to calculate a representative molecular formula for estimating and subtracting the contributions of naturally occurring isotopes solely as a function of peptide molecular weight. The method was tested against simulated composite 16O/18O spectra where peptide molecular weight, 16O/18O ratio, 18O1/18O2 ratios, and number of sulfur atoms were varied. Relative errors of 20% or less were incurred when the 16O/18O ratios were less than three, even for peptides where the number of sulfur atoms was over- or under-estimated. These data demonstrate that for biomarker discovery, it is advantageous to label the proteome representing the disease state with 18O; and the method is not sensitive to variations in 18O1/18O2 ratio. This approach allows a comprehensive differentiation of expression levels and tentative identification via AMTs, followed by targeted analysis of over- and under-expressed peptides using tandem mass spectrometry, for applications such as the discovery of disease biomarkers.}, number={4}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Johnson, Kenneth L. and Muddiman, David C.}, year={2004}, month={Apr}, pages={437–445} }
 @article{barnidge_goodmanson_klee_muddiman_2004, title={Absolute Quantification of the Model Biomarker Prostate-Specific Antigen in Serum by LC−MS/MS Using Protein Cleavage and Isotope Dilution Mass Spectrometry}, volume={3}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr049963d}, DOI={10.1021/pr049963d}, abstractNote={Protein cleavage-isotope dilution mass spectrometry (PC-IDMS) can be used to quantify proteins, with an isotope-labeled analogue of the peptide fragment used as an internal standard. Here, we investigate use of a standard LC-MS/MS platform for quantifying a model biomarker directly from serum by this technique. We synthesized a peptide (IVGGWECEK) identical to the N-terminal tryptic fragment of PSA but with each glycine containing two 13C atoms and one 15N atom. PSA-free human serum was denatured with urea followed by the introduction of PSA standard and the stable isotope labeled internal standard peptide. The sample was then proteolyzed with trypsin and subjected to quantification using LC-MS/ MS on a triple quadrupole mass spectrometer. A linear least squares calibration curve made from five different concentrations of PSA added to serum and digested (each made in triplicate and randomly injected three times) had a mean slope of 0.973 (SE = 0.023), intercept of -0.003 (SE = 0.022), and R2 of 0.971. Recovery of calibrators ranged from 70 to 85% with a mean run-to-run CV of 13% and a mean within-run CV of 5.7%. PC-IDMS is a promising technique for quantifying proteins covering a broad range of applications from standardizing immunoassays to monitoring post-translational modifications to quantifying newly discovered biomarkers prior to the development and implementation of an immunoassay, just to name a few. Issues surrounding the application of PC-IDMS for the absolute quantification of proteins include selection of a proteolytic fragment for quantification that can be cleaved and isolated reproducibly over a broad dynamic range, stable isotope labeled synthetic peptide standards that give consistent results, and LC-MS/MS methods that provide adequate sensitivity and reproducibility without creating impractical analysis times. The results presented here show that absolute quantification can be performed on the model biomarker PSA introduced into denatured serum when analyzed by LC-MS/MS. However, concerns still exist regarding sensitivity compared to existing immunoassays as well as the reproducibility of PC-IDMS performed in different matrixes.}, number={3}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Barnidge, David R. and Goodmanson, Marcia K. and Klee, George G. and Muddiman, David C.}, year={2004}, month={Jun}, pages={644–652} }
 @inproceedings{klein_kim_dyck_zeldenrust_bergen_o'brien_nepomuceno_butz_thibodeau_muddiman_et al._2004, title={Accurate and Expedited Diagnosis of Amyloidotic Transthyretin Neuropathy: Proteomic and Genomic Approach}, volume={56}, number={S8}, booktitle={Annals of Neurology}, author={Klein, C.J. and Kim, C.H. and Dyck, P.J. and Zeldenrust, S.R. and Bergen, H.R. and O'Brien, J.F. and Nepomuceno, A.I. and Butz, M.L. and Thibodeau, S.I. and Muddiman, D.C. and et al.}, year={2004}, pages={29} }
 @article{johnson_mason_muddiman_eckel_2004, title={Analysis of the Low Molecular Weight Fraction of Serum by LC-Dual ESI-FT-ICR Mass Spectrometry:  Precision of Retention Time, Mass, and Ion Abundance}, volume={76}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac0497003}, DOI={10.1021/ac0497003}, abstractNote={This study quantifies the experimental uncertainty for LC retention time, mass measurement precision, and ion abundance obtained from replicate nLC-dual ESI-FT-ICR analyses of the low molecular weight fraction of serum. We used ultrafiltration to enrich the < 10-kDa fraction of components from the high-abundance proteins in a pooled serum sample derived from ovarian cancer patients. The THRASH algorithm for isotope cluster detection was applied to five replicate nLC-dual ESI-FT-ICR chromatograms. A simple two-level grouping algorithm was applied to the more than 7000 isotope clusters found in each replicate and identified 497 molecular species that appeared in at least four of the replicates. In addition, a representative set of 231 isotope clusters, corresponding to 188 unique molecular species, were manually interpreted to verify the automated algorithm and to set its tolerances. For nLC retention time reproducibility, 95% of the 497 species had a 95% confidence interval of the mean of +/- 0.9 min or less without the use of chromatographic alignment procedures. Furthermore, 95% of the 497 species had a mass measurement precision of < or = 3.2 and < or = 6.3 ppm for internally and externally calibrated spectra, respectively. Moreover, 95% of replicate ion abundance measurements, covering an ion abundance range of approximately 3 orders of magnitude, had a coefficient of variation of less than 62% without using any normalization functions. The variability of ion abundance was independent of LC retention time, mass, and ion abundance quartile. These measures of analytical reproducibility establish a statistical rationale for differentiating healthy and disease patient populations for the elucidation of biomarkers in the low molecular fraction of serum.}, number={17}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Johnson, Kenneth L. and Mason, Christopher J. and Muddiman, David C. and Eckel, Jeanette E.}, year={2004}, month={Sep}, pages={5097–5103} }
 @article{hawkridge_zhou_lee_muddiman_2004, title={Analytical Performance of a Venturi Device Integrated into an Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Analysis of Nucleic Acids}, volume={76}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac049677l}, DOI={10.1021/ac049677l}, abstractNote={A voltage-assisted venturi device modeled after an industrial air amplifier was used to improve the ion transmission efficiency of a 16.2 kDa oligonucleotide and a 53-mer PCR product in the high-pressure region between an electrospray ionization (ESI) emitter and the sampling orifices of two Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR-MS). The venturi device increased the total ion abundance of the oligonucleotide and the PCR product by more than 6-fold relative to the best achievable signal without the device. Furthermore, the average charge states of the oligonucleotide and PCR product shifted from 12.5- to 14.5- and 10.9- to 12.6-, respectively, with the addition of the venturi device. Specific to FT-ICR mass spectrometry, this increase in the charge state directly translates to an increase in theoretical mass resolving power (>10000 full width half-maximum for the results presented here at 7 T). Adduction was still observed while using the device, suggesting that it is "soft" relative to other high-pressure ion focusing methods.}, number={14}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Hawkridge, Adam M. and Zhou, Li and Lee, Milton L. and Muddiman, David C.}, year={2004}, month={Jul}, pages={4118–4122} }
 @article{huang_muddiman_tindall_2004, title={Androgens Negatively Regulate Forkhead Transcription Factor FKHR (FOXO1) through a Proteolytic Mechanism in Prostate Cancer Cells}, volume={279}, ISSN={0021-9258 1083-351X}, url={http://dx.doi.org/10.1074/jbc.M314143200}, DOI={10.1074/jbc.M314143200}, abstractNote={The ability of androgens to inhibit apoptosis in both normal and malignant prostatic cells has been well documented. However, the underlying mechanisms are understood poorly. Here we demonstrated that forkhead transcription factor FKHR (FOXO1)-induced death of LNCaP cells was blocked by a synthetic androgen R1881. Androgen treatment also resulted in a reduction in transcriptional activity of FKHR in these cells. Moreover, treatment of LNCaP cells with R1881 led to a decrease in the intact FKHR protein (70 kDa) and an increase in a faster migrating protein band (60 kDa). Androgen-enhanced appearance of the 60-kDa protein was diminished specifically by lysosomal acidic cysteine protease inhibitors. Mass spectrometry analyses of the purified FLAG-tagged 70- and 60-kDa proteins demonstrated that the 60-kDa species is a FKHR protein product that lacks about 120 amino acid residues of the C-terminal end. Mutagenesis of the basic amino acid Arg537 in the protease cleavage region, as suggested by mass spectrometry, abrogated both the androgen-induced accumulation of the 60-kDa product and decrease in cell death induced by FKHR, suggesting that the residue Arg537 is a potential protease cleavage site. Finally, ectopic expression of the first 537 amino acids of FKHR produced an inhibitory effect on transcriptional activity of the intact protein. Together, these results suggest that androgens induce increased activity of an acidic cysteine protease, which in turn cleaves FKHR. This provides a mechanism by which androgens protect prostate cancer cells from the killing effect of FKHR.}, number={14}, journal={Journal of Biological Chemistry}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Huang, Haojie and Muddiman, David C. and Tindall, Donald J.}, year={2004}, month={Jan}, pages={13866–13877} }
 @article{nepomuceno_mason_muddiman_bergen_zeldenrust_2004, title={Detection of Genetic Variants of Transthyretin by Liquid Chromatography–Dual Electrospray Ionization Fourier-Transform Ion-Cyclotron-Resonance Mass Spectrometry}, volume={50}, ISSN={0009-9147 1530-8561}, url={http://dx.doi.org/10.1373/clinchem.2004.033274}, DOI={10.1373/clinchem.2004.033274}, abstractNote={AbstractBackground: One of the numerous proteins causing amyloidosis is transthyretin (TTR), a protein usually responsible for the transport of thyroxine and retinol-binding protein. Variants within TTR cause it to aggregate and form insoluble fibers that accumulate in tissue, leading to organ dysfunction.Methods: TTR was immunoprecipitated from serum by use of a polyclonal antibody and subsequently reduced with tris(2-carboxyethyl)phosphine. The purified TTR was then analyzed by fast-gradient liquid chromatography–dual-electrospray ionization Fourier-transform ion-cyclotron-resonance (FT-ICR) mass spectrometry. DNA sequencing was performed on all samples used in this study.Results: Because of the inherent limitations in achieving high mass measurement accuracy based on the most abundant isotopic mass, we applied a fitting procedure that allowed determination of monoisotopic mass. Wild-type TTR (mean molecular mass, 13 761 Da) and its associated variant forms could be distinguished because of the high molecular mass accuracy afforded by FT-ICR (≤3 ppm) except for instances involving isobaric species or when isotopic distributions overlapped significantly. The [M + 11 H+]11+ charge state for all samples was used to determine the mass accuracies for both wild-type and variant forms of the protein. We correctly assigned seven of seven TTR variants. Moreover, using a combination of proteomic and genomic technologies, we discovered and characterized a previously unreported cis double mutation with a mass only 2 Da different from wild-type TTR. Furthermore, DNA sequencing of the TTR gene for all individuals in this study completely agreed with the intact protein measurements.Conclusions: FT-ICR mass spectrometry has sufficient mass accuracy to identify genetic variants of immunoaffinity-purified TTR. We believe that 91% of known TTR variants could be detected by this technique.}, number={9}, journal={Clinical Chemistry}, publisher={Oxford University Press (OUP)}, author={Nepomuceno, Angelito I and Mason, Christopher J and Muddiman, David C and Bergen, H Robert, III and Zeldenrust, Steven R}, year={2004}, month={Sep}, pages={1535–1543} }
 @article{flora_muddiman_2004, title={Determination of the relative energies of activation for the dissociation of aromatic versus aliphatic phosphopeptides by ESI-FTICR-MS and IRMPD}, volume={15}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/j.jasms.2003.10.004}, DOI={10.1016/j.jasms.2003.10.004}, abstractNote={Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (ESI-FTICR-MS) coupled with infrared multiphoton dissociation (IRMPD) is potentially a powerful method for rapid phosphopeptide mapping of complex proteolytic digests. The dissociation of deprotonated phosphopeptides by IRMPD is energetically favorable over unmodified deprotonated peptides because of a lower energy of activation and a higher internal energy under identical irradiation conditions. The energies of activation for dissociation are determined for model peptides phosphorylated on an aliphatic side chain (serine) and an aromatic side chain (tyrosine). The determination of phosphorylation location provides important biochemical information identifying the kinase involved in specific phosphorylation mechanisms. The data presented in this manuscript also support the theory that for phosphopeptides, the phosphate moiety's P-O stretch is in direct resonance with the infrared laser (10.6 microm), thus increasing the relative absorptivity of the modified species. A greater extinction coefficient affords more extensive photon absorption and subsequently a greater internal energy at the rapid exchange limit.}, number={1}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Flora, Jason W. and Muddiman, David C.}, year={2004}, month={Jan}, pages={121–127} }
 @article{bergen_vasmatzis_cliby_johnson_oberg_muddiman_2004, title={Discovery of Ovarian Cancer Biomarkers in Serum Using NanoLC Electrospray Ionization TOF and FT-ICR Mass Spectrometry}, volume={19}, ISSN={0278-0240 1875-8630}, url={http://dx.doi.org/10.1155/2004/797204}, DOI={10.1155/2004/797204}, abstractNote={Treatment of cancer patients is greatly facilitated by detection of the cancer prior to metastasis. One of the obstacles to early cancer detection is the lack of availability of biomarkers with sufficient specificity. With modern differential proteomic techniques, the potential exists to identify high specificity cancer biomarkers. We have delineated a set of protocols for the isolation and identification of serum biomarkers for ovarian cancer that exist in the low molecular weight serum fraction. After isolation of the low molecular weight fraction by ultrafiltration, the potential biomarkers are separated by reversed phase nano liquid chromatography. Detection via TOF or FT-ICR yields a data set for each sample. We compared stage III/IV ovarian cancer serum with postmenopausal age-matched controls. Using bioinformatics tools developed at Mayo, we normalized each sample for intensity and chromatographic alignment. Normalized data sets are subsequently compared and potential biomarkers identified. Several candidate biomarkers were found. One of these contains the sequence of fibrinopeptide-A known to be elevated in many types of cancer including ovarian cancer. The protocols utilized will be examined and would be applicable to a wide variety of cancers or disease states.}, number={4-5}, journal={Disease Markers}, publisher={Hindawi Limited}, author={Bergen, H. Robert and Vasmatzis, George and Cliby, William A. and Johnson, Kenneth L. and Oberg, Ann L. and Muddiman, David C.}, year={2004}, pages={239–249} }
 @article{barnidge_hall_stocker_muddiman_2004, title={Evaluation of a Cleavable Stable Isotope Labeled Synthetic Peptide for Absolute Protein Quantification Using LC−MS/MS}, volume={3}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr034124x}, DOI={10.1021/pr034124x}, abstractNote={Protein cleavage coupled with isotope dilution mass spectrometry (PC-IDMS) has the potential to provide the absolute concentration of a specific protein, or multiple proteins, in complex mixtures. However, PC-IDMS differs from standard IDMS since the internal standard is a different molecule than the analyte at the start of the experiment, more specifically, the internal standard is a peptide and the analyte is a protein prior to cleavage. It is not until after the cleavage process that the stable isotope labeled synthetic peptide has the same physicochemical behavior as the peptide cleaved from the protein. The work presented here evaluates the use of tryptic cleavage sites incorporated into the internal standard synthetic peptide in an attempt to create an internal standard that has cleavage characteristics more similar to the protein being quantified. Results presented here suggest that an internal standard synthetic peptide incorporating internal cleavage sites does not improve the accuracy and precision of the values obtained when performing PC-IDMS.}, number={3}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Barnidge, David R. and Hall, Gregory D. and Stocker, Jeanne L. and Muddiman, David C.}, year={2004}, month={Jun}, pages={658–661} }
 @article{ovsyannikova_johnson_muddiman_vierkant_poland_2004, title={Identification and Characterization of Novel, Naturally Processed Measles Virus Class II HLA-DRB1 Peptides}, volume={78}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.78.1.42-51.2004}, DOI={10.1128/jvi.78.1.42-51.2004}, abstractNote={ABSTRACTPreviously, we identified a naturally processed and presented measles virus (MV) 19-amino-acid peptide, ASDVETAEGGEIHELLRLQ (MV-P), derived from the phosphoprotein and eluted from the human leukocyte antigen (HLA) class II molecule by using mass spectrometry. We report here the identification of a 14-amino-acid peptide, SAGKVSSTLASELG, derived from the MV nucleoprotein (MV-N) bound to HLA-DRB1*0301. Peripheral blood mononuclear cells (PBMC) from 281 previously vaccinated measles-mumps-rubella II (MMR-II) subjects (HLA discordant) were studied for peptide recognition by T cells. Significant gamma interferon (IFN-γ) responses to MV-P and MV-N peptides were observed in 55.9 and 15.3% of subjects, respectively. MV-P- and MV-N-specific interleukin-4 (IL-4) responses were detected in 19.2 and 23.1%, respectively, of PBMC samples. Peptide-specific cytokine responses and HLA-DRB1 allele associations revealed that, for the MV-P peptide, the allele with the strongest association with both IFN-γ (P= 0.02) and IL-4 (P= 0.03) secretion was DRB1*0301. For MV-N, the allele with the strongest association with IFN-γ secretion was DRB1*1501 (P= 0.04), and the alleles with the strongest associations with IL-4 secretion were DRB1*1103 and DRB1*1303 (P= 0.01). These results indicate that HLA class II MV proteins can be processed, presented, and identified, and the ability to generate cell-mediated immune responses can be demonstrated. This information is promising for new vaccine design strategies with peptide-based vaccines.}, number={1}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Ovsyannikova, Inna G. and Johnson, Kenneth L. and Muddiman, David C. and Vierkant, Robert A. and Poland, Gregory A.}, year={2004}, month={Jan}, pages={42–51} }
 @article{bergen_zeldenrust_butz_snow_dyck_dyck_klein_o’brien_thibodeau_muddiman_2004, title={Identification of Transthyretin Variants by Sequential Proteomic and Genomic Analysis}, volume={50}, ISSN={0009-9147 1530-8561}, url={http://dx.doi.org/10.1373/clinchem.2004.033266}, DOI={10.1373/clinchem.2004.033266}, abstractNote={Abstract
               Background: Transthyretin-associated hereditary amyloidosis (ATTR) is an inherited disease in which variants in the primary structure of transthyretin (TTR; prealbumin) lead to the extracellular polymerization of insoluble protein fibrils, causing organ failure and ultimately death when major organs are involved. We have developed an integrated approach to molecular diagnosis with initial analysis of intact plasma TTR by electrospray ionization mass spectrometry (MS) and referral of positive samples for DNA sequence analysis and real-time PCR to confirm the common Gly6Ser polymorphism.
               Methods: Samples from 6 patients previously diagnosed with ATTR and from 25 controls with (n = 15) or without (n = 10) polyneuropathy were analyzed in a blinded fashion for the presence of variant TTR. TTR protein was extracted with an immunoaffinity resin from 20 μL of archived plasma samples. The purified TTR was reduced with tris(2-carboxyethyl)phosphine and analyzed by MS. The appearance of two peaks (or a single peak shifted in mass indicative of a homozygous variant), including the wild-type mass of 13 761 Da, was indicative of the presence of a variant, and the individual was referred for DNA sequence analysis.
               Results: MS analysis of intact reduced TTR correctly identified each of six samples known to contain variant TTR. These results were corroborated by subsequent DNA sequence analysis. Additionally, all Gly6Ser polymorphisms were correctly called based on the +30 mass shift and an equal relative abundance of the +30 polymorphism relative to wild-type TTR. No false-positive results were seen.
               Conclusions: This referral method eliminates the necessity of sequencing most samples and allows screening for the familial forms of amyloidosis in a broad patient population in a timely fashion. This method correctly identified all previously known variants and also identified a novel variant, Val94Ala.}, number={9}, journal={Clinical Chemistry}, publisher={Oxford University Press (OUP)}, author={Bergen, H Robert, III and Zeldenrust, Steven R and Butz, Malinda L and Snow, Denise S and Dyck, Peter J and Dyck, P James B and Klein, Christopher J and O’Brien, John F and Thibodeau, Stephen N and Muddiman, David C}, year={2004}, month={Sep}, pages={1544–1552} }
 @article{bergen_klug_bolander_muddiman_2004, title={Informed use of proteolytic inhibitors in biomarker discovery}, volume={18}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.1439}, DOI={10.1002/rcm.1439}, abstractNote={Rapid Communications in Mass SpectrometryVolume 18, Issue 9 p. 1001-1002 Letter to the Editor Informed use of proteolytic inhibitors in biomarker discovery H. Robert Bergen III, H. Robert Bergen III W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMichael G. Klug, Michael G. Klug W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMark E. Bolander, Mark E. Bolander Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorDavid C. Muddiman, Corresponding Author David C. Muddiman [email protected] W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USAMedical Science Building 3-115, Mayo Clinic College of Medicine, 200 First Street, SW, Rochester, MN 55905, USA.Search for more papers by this author H. Robert Bergen III, H. Robert Bergen III W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMichael G. Klug, Michael G. Klug W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorMark E. Bolander, Mark E. Bolander Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Rochester, MN 55905, USASearch for more papers by this authorDavid C. Muddiman, Corresponding Author David C. Muddiman [email protected] W. M. Keck FT-ICR Mass Spectrometry Laboratory, Mayo Proteomics Research Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USAMedical Science Building 3-115, Mayo Clinic College of Medicine, 200 First Street, SW, Rochester, MN 55905, USA.Search for more papers by this author First published: 01 April 2004 https://doi.org/10.1002/rcm.1439Citations: 5Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. REFERENCES 1 Bergen HR III, Zeldenrust SR, Naylor S. Amyloid 2003; 10: 190. 2 Riordan JF, Vallee BL. Methods Enzymol. 1972; 25: 449. 3 Brewer C, Riehm J. Anal. Biochem. 1967; 18: 248. 4 Bergen HR III, Vasmatzis G, Cliby WA, Johnson KL, Oberg AL, Muddiman DC. Dis. Markers 2004; in press. Citing Literature Volume18, Issue915 May 2004Pages 1001-1002 ReferencesRelatedInformation}, number={9}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Bergen, H. Robert and Klug, Michael G. and Bolander, Mark E. and Muddiman, David C.}, year={2004}, month={Apr}, pages={1001–1002} }
 @article{frahm_mason_muddiman_2004, title={Utility of accurate monoisotopic mass measurements to confidently identify lambda exonuclease generated single-stranded amplicons containing 7-deaza analogs by electrospray ionization FT-ICR mass spectrometry}, volume={234}, ISSN={1387-3806}, url={http://dx.doi.org/10.1016/j.ijms.2004.02.004}, DOI={10.1016/j.ijms.2004.02.004}, abstractNote={A 53-base pair region on the long arm of chromosome 22 was amplified using PCR with 7-deaza-modified deoxynucleotides. Increased amplification efficiency was achieved by doubling the concentration of the modified deoxynucleotide triphosphates. Incorporation of 7-deaza purines has been previously shown to selectively eliminate fragmentation pathways during gas-phase sequencing of nucleic acids by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) and infrared multiphoton dissociation. However, 7-deaza analogs result in significant duplex stability precluding interrogation of the single-stranded species by tandem mass spectrometry. Herein, we demonstrate the use of lambda exonuclease to successfully overcome this problem and are able to obtain single-stranded PCR products containing 7-deaza adenine and guanine nucleobases. Mass accuracy was used as our metric to determine complete incorporation of 7-deaza residues in PCR products>15 kDa; ≤ 3 ppm neutral monoisotopic mass measurement accuracies were routinely achieved. High mass measurement accuracy was obtained using a dual electrospray source and subsequently, using an isotopic fitting algorithm, the best fit between the theoretical and experimental isotopic distributions was determined using a chi-square value. Theoretical isotopic distributions were generated using an average nucleotide (averatide) chemical formula developed herein which was based on the relative frequencies of AT and GC base pairs in the human genome. Single-stranded PCR products were fragmented using SORI-CID and as expected, cleavage at the 7-deaza modified sites was not observed. Collectively, this integrated approach can facilitate top–down sequencing of PCR products by a variety of tandem mass spectrometry methods.}, number={1-3}, journal={International Journal of Mass Spectrometry}, publisher={Elsevier BV}, author={Frahm, Jennifer L and Mason, Christopher J and Muddiman, David C}, year={2004}, month={May}, pages={79–87} }
 @article{stringfield_somayajula_muddiman_flora_shepherd_2003, title={1H NMR and electrospray mass spectrometry of the mono-ionized bis(2,2′-bis(4,5-dimethylimidazole)chloronitrosylruthenium(II) complex ([Ru(NO)Cl(LH2)2]+, LH2=2,2′-bis(4,5-dimethylimidazole)}, volume={343}, ISSN={0020-1693}, url={http://dx.doi.org/10.1016/s0020-1693(02)01243-4}, DOI={10.1016/s0020-1693(02)01243-4}, abstractNote={The reaction of RuCl3(NO)(H2O)2 with 2 equiv. of LH2=2,2′-bis(4,5-dimethylimidazole) in refluxing ethanol generates cis-[Ru(NO)Cl(LH2)2]2+ (1), analogous in structure to cis-[Ru(NO)Cl(bpy)2]2+, as the chloride salt. In 1, the methyl groups are differentiated into eight different 1H NMR magnetic environments. Substitution of 4,5-dimethyl-2,2′-biimidazole (L′H2), an 11.1% impurity in commercial LH2, occurred randomly with the undecorated ring diminishing the intensity of all eight resonances equally. The methyl group of the “out-of-plane” ring that hangs over the π orbitals of the NO+ ligand (CH3(6)) is shifted most upfield from 2.19 ppm of free LH2 and is assigned to the 1.23 ppm resonance. With the aid of 2-D NMR methods, we assign the following shifts. The ring donor opposite the {Ru(NO)}3+, CH3(7), should experience the greatest withdrawing influence, and is assigned as the origin of the 2.50 ppm resonance. Its ring partner, CH3(5), placed below another ring current, is assigned to the resonance at 2.13 ppm. 2-D NMR methods support the assignments of 1.39 ppm to CH3(1) and 2.09 ppm to CH3(2), the “in-plane-near” CH3 groups; 2.36 and 2.34 ppm to “in-plane-remote” CH3(3) and CH3(4); a 2.47 ppm shift is assigned to the remaining CH3(8). Because of the presence of the impurity L′H2 which has a substitution rate advantage (ca. 2.14-fold) due to a lower steric barrier for the unmethylated ring, the isolated product contained 62.4% (1a) [Ru(NO)Cl(LH2)2]Cl2, 31.9% (1b) [Ru(NO)Cl(LH2)(L′H2)]Cl2, and 5.7% (1c) [Ru(NO)Cl(L′H2)2]Cl2. The ESI MS spectrum exhibits parent 1+ ions (2a–c) in which one of the imidazole rings has been deprotonated. Thus, eight-line patterns for RuCl-containing fragments appear for m/z with z=1+ centered about 546 (2a), 518 (2b) and 490 (2c) in the intensity ratios of 1.000:0.511:0.091, respectively. The atomic composition for 2a was shown to be RuC20H27N9OCl (m/z=540.109049) by checking the “540” line of the isotopic bundle around m/z=546. The atomic composition of 2b was established from the “512” mass as RuC18H23N9OCl (m/z=512.077748) from the isotopic bundle around m/z=518. 2a–c undergo the loss of LH2 or L′H2 with low efficiency, but few other fragmentations were observed. Notably, the loss of NO or HCl are absent. 2a–c have good π-donating imidazole and imidazolato functionalities which suppress NO loss. IR laser loss experiments on 2a in the mass spectral cavity were unable to identify a frequency value that selectively dissociates NO. Rather, complete fragmentation of the complexes 2a–c occurred at energies sufficient to induce any ligand dissociation; the parent ions being very robust. The 1H NMR data are supported by an MMFF94 energy-minimized structure for 1 and its theoretical trans isomer.}, journal={Inorganica Chimica Acta}, publisher={Elsevier BV}, author={Stringfield, Thomas W and Somayajula, Kasi V and Muddiman, David C and Flora, Jason W and Shepherd, Rex E}, year={2003}, month={Jan}, pages={317–328} }
 @article{benson_null_muddiman_2003, title={Advantages of Thermococcus kodakaraenis (KOD) DNA Polymerase for PCR-mass spectrometry based analyses}, volume={14}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(03)00148-x}, DOI={10.1016/s1044-0305(03)00148-x}, abstractNote={The advantages of the thermostable DNA polymerase from Thermococcus kodakaraensis (KOD) are demonstrated for PCR amplification with subsequent detection by mass spectrometry. Commonly used DNA polymerases for PCR amplification include those from Thermus aquaticus (Taq) and Pyrococcus furiosus (Pfu). A 116 base-pair PCR product derived from a vWA locus was amplified by Taq, Pfu, or KOD DNA polymerase and compared by agarose gel electrophoresis and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). KOD DNA polymerase demonstrated a 2- to 3-fold increase in PCR product formation compared to Pfu or Taq, respectively, and generated blunt-ended PCR product which allows facile interpretation of the mass spectrum. Additionally, we demonstrate the advantage of using high magnetic fields to obtain unit resolution of the same 116 base pair (approximately 72 kDa) PCR product at high m/z.}, number={6}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Benson, Linda M. and Null, Allison P. and Muddiman, David C.}, year={2003}, month={Jun}, pages={601–604} }
 @article{muddiman_cliby_bergen_2003, title={Cancer Biomarkers: How Proteomics is Leading to the Discovery of New Markers}, volume={29}, journal={Clinical Laboratory News}, author={Muddiman, D.C. and Cliby, W.A. and Bergen, H.R., III}, year={2003}, pages={12–16} }
 @article{kryschenko_seidel_muddiman_nepomuceno_stang_2003, title={Coordination-Driven Self-Assembly of Supramolecular Cages:  Heteroatom-Containing and Complementary Trigonal Prisms}, volume={125}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja030209n}, DOI={10.1021/ja030209n}, abstractNote={The self-assembly of three nanoscopic prisms of approximate size 1 x 4 nm is reported. Tetrahedral carbon, silicon, and phosphorus were used as structure-defining elements in these coordination-based cages. A carbon-based assembly completes a pair of nanoscopic complementary 3-D structures. The formation of the structures is supported by multinuclear NMR, ESI FT-ICR mass spectrometry, and elemental analysis data.}, number={32}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Kryschenko, Yury K. and Seidel, S. Russell and Muddiman, David C. and Nepomuceno, Angelito I. and Stang, Peter J.}, year={2003}, month={Aug}, pages={9647–9652} }
 @article{null_muddiman_2003, title={Determination of a correction to improve mass measurement accuracy of isotopically unresolved polymerase chain reaction amplicons by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={17}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.1111}, DOI={10.1002/rcm.1111}, abstractNote={AbstractThe experimental determination of average mass by mass spectrometry is limited for large molecules due to the negative bias introduced by the natural distribution of isotopic abundances. This results in the measurement of the top‐of‐centroid (ToC) as opposed to the true centroid. We have developed a practical correction factor that is applied to the ToC measurement to largely remove the systematic bias introduced by nature. The correction factor is calculated easily using the average molecular mass (<100 kDa) of the analyte molecule and the full‐width half maximum resolving power (<3500) of the measurement. In addition, an approach to calculating resolving power is described that accurately predicts resolving power achievable for Fourier transform ion cyclotron resonance (FT‐ICR) mass analysis of large molecules. A combination of internal calibration with a dual‐electrospray source and application of the correction factor to average mass measurements improved the mass error from 192.5 to −35.0 ppm for a 44 kDa PCR amplicon. Copyright © 2003 John Wiley & Sons, Ltd.}, number={15}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Null, Allison P. and Muddiman, David C.}, year={2003}, pages={1714–1722} }
 @article{nepomuceno_muddiman_bergen_craighead_burke_caskey_allan_2003, title={Dual Electrospray Ionization Source for Confident Generation of Accurate Mass Tags Using Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometry}, volume={75}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac0342471}, DOI={10.1021/ac0342471}, abstractNote={Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) has rapidly established a prominent role in proteomics because of its unparalleled resolving power, sensitivity and ability to achieve high mass measurement accuracy (MMA) simultaneously. However, space-charge effects must be quantitatively, routinely, and confidently corrected because they are known to profoundly influence MMA. We argue that the most effective way to account for space-charge effects is to introduce an internal mass calibrant (IMC) using a dual electrospray ionization (ESI) source where the IMC is added from a separate ESI emitter. The major disadvantage of our initial dual ESI source to achieve high MMA, and arguably the only one, was the time required to switch between the analyte emitter and IMC emitter (i.e., >300 ms). While this "switching time" was acceptable for direct infusion experiments, it did not lend itself to high-throughput applications or when conducting on-line liquid separations. In this report, we completely redesigned the dual ESI source and demonstrate several key attributes. First, the new design allows for facile alignment of ESI emitters, undetectable vibration, and the ability to extend to multiple emitters. Second, the switching time was reduced to <50 ms, which allowed the analyte and IMC to be accumulated "simultaneously" in the external ion reservoir and injected as a single ion packet into the ion cyclotron resonance cell, eliminating the need for a separate accumulation and ion injection event for the IMC. Third, by using a high concentration of the IMC, the residence time on this emitter could be reduced to approximately 80 ms, allowing for more time spent accumulating analyte ions of significantly lower concentration. Fourth, multiplexed on-line separations can be carried out providing increased throughput. Specifically, the new dual ESI source has demonstrated its ability to produce a stable ion current over a 45-min time period at 7 T resulting in mass accuracies of 1.08 ppm +/- 0.11 ppm (mean +/- confidence interval of the mean at 95% confidence; N = 160). In addition, the analysis of a tryptic digest of apomyoglobin by nanoLC-dual ESI-FT-ICR afforded an average MMA of -1.09 versus -74.5 ppm for externally calibrated data. Furthermore, we demonstrate that the amplitude of a peptide being electrosprayed at 25 nM can be linearly increased, ultimately allowing for dynamic analyte/IMC abundance modulation. Finally, we demonstrate that this source can reliably be used for multiplexing measurements from two (eventually more) flow streams.}, number={14}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Nepomuceno, Angelito I. and Muddiman, David C. and Bergen, H. Robert and Craighead, James R. and Burke, Michael J. and Caskey, Patrick E. and Allan, Jonathan A.}, year={2003}, month={Jul}, pages={3411–3418} }
 @article{null_benson_muddiman_2003, title={Enzymatic strategies for the characterization of nucleic acids by electrospray ionization mass spectrometry}, volume={17}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.1255}, DOI={10.1002/rcm.1255}, abstractNote={AbstractElectrospray ionization mass spectrometry (ESI‐MS) is a powerful technique used for the identification and characterization of DNA polymorphisms. Continual improvement in instrument design assures high mass measurement accuracy, sensitivity, and resolving power. This work describes an eclectic array of enzymatic strategies we have invoked in order to detect single‐nucleotide polymorphisms by ESI‐MS, although other applications may be envisioned. One strategy combines the use of two enzymes, exonuclease III and lambda exonuclease, to provide a ladder of single‐stranded DNA fragments for straightforward sequence identification by mass spectrometry. A second strategy combines restriction enzymes to screen for polymorphisms present within specific amplicons. Finally, we describe the use of stable‐isotope‐labeled nucleotides for the determination of length and base composition of a PCR product. Copyright © 2003 John Wiley & Sons, Ltd.}, number={24}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Null, Allison P. and Benson, Linda M. and Muddiman, David C.}, year={2003}, pages={2699–2706} }
 @article{null_nepomuceno_muddiman_2003, title={Implications of Hydrophobicity and Free Energy of Solvation for Characterization of Nucleic Acids by Electrospray Ionization Mass Spectrometry}, volume={75}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac026217o}, DOI={10.1021/ac026217o}, abstractNote={Electrospray ionization (ESI) is a dynamic process that, when coupled with mass spectrometry (MS), serves as an invaluable tool for analysis of biomolecules. Our group, as well as others, has observed that there is a bias in signal intensity for one strand of a PCR amplicon over the complementary strand in an ESI mass spectrum. In this report, we have investigated the contributions of hydrophobicity and free energy of solvation to relative signal intensities in ESI-MS spectra of nucleic acids. We developed approaches for predicting which strand of the PCR amplicon will be the most intense: one based on a rate equation for calculating ion flux using values from the literature for hydrophobicity and free energy of solvation and the other based on the percentage of the relatively hydrophilic guanines present in the strand. A trend in signal intensity for deoxyribonucleotide triphosphates, oligonucleotides, and PCR amplicons was observed that was consistent with our model. On the basis of the observation that increased hydrophobicity correlates with greater signal intensity, we selectively enhanced the signal intensity of a 20-mer with the addition of an alkyl chain to the 5' terminus, which subsequently improved the limit of detection to 1 nM, an improvement by 1 order of magnitude. This was extended to a 53-bp PCR amplicon by modifying one primer with the hydrophobic moiety, which resulted in a 16% increase in signal intensity. We capitalized on this result to determine allele frequencies from pooled DNA for single-nucleotide polymorphisms down to 1%.}, number={6}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Null, Allison P. and Nepomuceno, Angelito I. and Muddiman, David C.}, year={2003}, month={Mar}, pages={1331–1339} }
 @article{bergen_ajtai_burghardt_nepomuceno_muddiman_2003, title={Mass spectral determination of skeletal/cardiac actin isoform ratios in cardiac muscle}, volume={17}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.1075}, DOI={10.1002/rcm.1075}, abstractNote={AbstractSkeletal and cardiac muscle contains actin isoforms that vary by two juxtaposed amino acids and two amino acid substitutions (Met299Leu and Ser358Thr). This close sequence homology does not allow cardiac and skeletal actin isoforms to be resolved in traditional SDS‐PAGE analysis as the molecular weights (Δmass = 32 Da) are not significantly different and the pIs are identical (5.2). Although cardiac actin is the predominant form in cardiac muscle, there appears to be a specific skeletal/cardiac actin ratio in a normal heart that may vary in a compromised or diseased heart. In an effort to ascertain the validity of this hypothesis we developed a mass spectrometric technique to measure the ratio of skeletal to cardiac actin. The technique involves purification of muscle actin and subsequent liquid chromatography coupled with electrospray ionization Fourier transform ion cylcotron resonance (LC/FTICR‐MS) mass spectrometry. A 7 Tesla FTICR mass spectrometer was utilized to compare skeletal/cardiac actin isoform ratios. Additionally, a new dual electrospray ionization source was employed to determine accurate masses of the α‐skeletal and α‐cardiac actins. Copyright © 2003 John Wiley & Sons, Ltd.}, number={13}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Bergen, H. Robert and Ajtai, Katalin and Burghardt, Thomas P. and Nepomuceno, Angelito I. and Muddiman, David C.}, year={2003}, pages={1467–1471} }
 @article{ovsyannikova_johnson_naylor_muddiman_poland_2003, title={Naturally processed measles virus peptide eluted from class II HLA-DRB1*03 recognized by T lymphocytes from human blood}, volume={312}, ISSN={0042-6822}, url={http://dx.doi.org/10.1016/s0042-6822(03)00281-2}, DOI={10.1016/s0042-6822(03)00281-2}, abstractNote={This is the first report of the direct identification of a HLA-DRB1*03 measles-derived peptide from measles virus infected EBV-transformed B cells. We purified HLA-DR3-peptide complexes from EBV-B cells infected with measles virus (Edmonston strain) and sequenced the HLA-DR3-peptides by mass spectrometry. A class II peptide, derived from a measles phosphoprotein, ASDVETAEGGEIHELLRLQ (P1, residues 179–197), exhibited the capacity to stimulate peripheral blood mononuclear cells to proliferate. Our data provides direct evidence that the antigenic peptide of measles virus was processed by antigen-presenting cells, presented in the context of HLA class II molecules, and was recognized by peripheral blood T cells from healthy individuals previously immunized with measles vaccine. The approach described herein provides a useful methodology for the future identification of HLA-presented pathogen-derived epitopes using mass spectrometry. The study of cell-mediated immune responses to the measles-derived peptide in immune persons should provide significant insight into the design and development of new vaccines.}, number={2}, journal={Virology}, publisher={Elsevier BV}, author={Ovsyannikova, Inna G and Johnson, Kenneth L and Naylor, Stephen and Muddiman, David C and Poland, Gregory A}, year={2003}, month={Aug}, pages={495–506} }
 @article{null_muddiman_2002, title={CEPH family 1362 STR database: An online resource for characterization of PCR products using electrospray ionization mass spectrometry}, volume={13}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(01)00326-9}, DOI={10.1016/s1044-0305(01)00326-9}, abstractNote={An online database has been established in order to validate electrospray ionization mass spectrometry (ESI-MS) for genotyping and to publicize the procedures developed in our laboratory for the characterization of PCR products by ESI-MS. Genotypes derived from short tandem repeat (STR) loci that were obtained using ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) have been posted for fifteen members of the CEPH family 1362 pedigree. The website provides specific information such as PCR parameters, PCR product cleanup approaches, and ESI solution compositions to enable other laboratories to reproduce our data. Links are provided to related websites in an effort to integrate information regarding the CEPH family, STR genotyping, and mass spectrometry. The database, currently available at http://www.people.vcu.edu/~dcmuddim/genotype/ will be routinely updated with genotypes from additional STR loci including PCR parameters as well as PCR cleanup strategies as further developments are completed.}, number={1}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Null, Allison P. and Muddiman, David C.}, year={2002}, month={Jan}, pages={89–90} }
 @article{flora_null_muddiman_2002, title={Dual-micro-ESI source for precise mass determination on a quadrupole time-of-flight mass spectrometer for genomic and proteomic applications}, volume={373}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/s00216-002-1357-0}, DOI={10.1007/s00216-002-1357-0}, abstractNote={A universal dual-electrospray (ESI) source is demonstrated on a quadrupole orthogonal-accelerated time-of-flight mass spectrometer (Q-ToF-MS) for both genomic and proteomic applications. This facile source modification enables internal calibration for consistent mass measurements by a mainstream MS platform and requires no mixing of analyte and calibrant prior to ion formation. In this report, the dual-sprayer is demonstrated in the negative-ion mode for internal calibration of polymerase chain reaction (PCR) amplicons generated from synthetic and genomic templates as well as a proteolytic digest of a naturally phosphorylated protein. For all PCR amplicons, experimentally determined average mass measurements are well within the instrument specifications of better than 0.01%. For the proteolytic fragments of the phosphoprotein, average mass errors of the isotopically resolved peptides are better than 10 ppm.}, number={7}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Flora, Jason W. and Null, Allison P. and Muddiman, David C.}, year={2002}, month={Jun}, pages={538–546} }
 @article{null_george_muddiman_2002, title={Evaluation of sample preparation techniques for mass measurements of PCR products using ESI-FT-ICR mass spectrometry}, volume={13}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(02)00342-2}, DOI={10.1016/s1044-0305(02)00342-2}, abstractNote={Elimination of PCR buffer components and alkali metal cations (i.e., Na+, K+) is of critical importance to allow for accurate mass measurements of PCR products for genotyping and sequencing applications. Ethanol precipitation followed by microdialysis has been repeatedly shown to efficiently desalt PCR products for analysis by mass spectrometry and is considered the gold standard. Alternative cleanup techniques that are compatible with automation are explored here with the intent of expanding the bottleneck that exists between the production of PCR products and analysis by electrospray ionization mass spectrometry (ESI-MS). Numerous combinations of approaches were evaluated that included PCR purification kits and alcohol precipitations. The data shown here support alternative approaches to an ethanol precipitation followed by microdialysis that have comparable desalting efficiency and can be utilized for cleanup of PCR products generated from single reactions.}, number={4}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Null, Allison P. and George, Laura T. and Muddiman, David C.}, year={2002}, month={Apr}, pages={338–344} }
 @article{flora_muddiman_2002, title={Gas-Phase Ion Unimolecular Dissociation for Rapid Phosphopeptide Mapping by IRMPD in a Penning Ion Trap:  An Energetically Favored Process}, volume={124}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja0261170}, DOI={10.1021/ja0261170}, abstractNote={This communication discusses the efficient detection of the most important and common protein modification, phosphorylation, using ESI-FTICR-MS and IRMPD. Preliminary studies have demonstrated that within a complex protein digest, all phosphopeptides can be identified by a single IR laser irradiation event due to preferential dissociation of the modified peptides. This research demonstrates that the energy of activation for dissociation of the phosphopeptides is lower than that of the unmodified analogues providing the basis for the success of this technique. However, the P-O stretch (9.6-11 mum or 1042-909 cm-1) of this posttranslational modification is in direct resonance with the CO2 IR laser (10.6 mum or 943 cm-1) used for IRMPD. Therefore, the vibrational frequency of the phosphate moiety may be an additional factor in the rapid first-order decay of phosphopeptides. Based upon the energetics of dissociation discussed in this manuscript, IRMPD of ions in a Penning ion trap is an ideal platform for rapid phosphopeptide mapping.}, number={23}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Flora, Jason W. and Muddiman, David C.}, year={2002}, month={Jun}, pages={6546–6547} }
 @article{gardella_lytle_muddiman_2002, title={In celebration of the 70th birthday of Dr David M. Hercules}, volume={373}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/s00216-002-1385-9}, DOI={10.1007/s00216-002-1385-9}, number={7}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Gardella, Joseph A. and Lytle, Fred E. and Muddiman, David C.}, year={2002}, month={Jul}, pages={517–518} }
 @article{gardella_lytle_muddiman_2002, title={Memoirs, Hercules lineage, students, visiting scientists and staff}, volume={373}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/s00216-002-1390-z}, DOI={10.1007/s00216-002-1390-z}, number={7}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Gardella, Joseph A., Jr and Lytle, Fred E. and Muddiman, David C.}, year={2002}, month={Jul}, pages={669–675} }
 @article{mangrum_flora_muddiman_2002, title={Solution composition and thermal denaturation for the production of single-stranded PCR amplicons: Piperidine-induced destabilization of the DNA duplex?}, volume={13}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(01)00356-7}, DOI={10.1016/s1044-0305(01)00356-7}, abstractNote={Strategies to produce single-stranded PCR amplicons for detection by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) were investigated using modified electrospray solutions and by thermally denaturing the duplex structures with a resistively heated electrospray ionization source. A synthetic 20-mer oligonucleotide annealed to its complementary strand was used as a model system for initial experiments. Electrospray solutions were altered by varying the relative proportion of aqueous phase in efforts to induce destabilization of the double helix. When the electrospray solution contains a 25% aqueous content, the 20-mer oligonucleotide is detected in its double-stranded form. Increasing the proportion of aqueous phase in the electrospray solution to 60% destabilized the double helix, resulting in the detection of only single-stranded species. This strategy was extended to an 82-bp polymerase chain reaction (PCR) product derived from the human tyrosine hydroxylase gene (HUMTH01). In efforts to destabilize the 82-bp PCR product, electrospray solutions reaching 70% aqueous content were necessary to promote the detection of only single-stranded amplicons. Implementation of the resistively heated transfer line and an electrospray solution in which the oligonucleotide is on the threshold of duplex stability allowed for double-stranded and single-stranded species to be generated from the same ESI solutions at both ambient and elevated transfer line temperatures, respectively, without disruption of the electrospray process. The volatile base piperidine, present at 20 mM concentrations in the electrospray solution, was found to play a critical role in the formation of single-stranded species at the higher aqueous percentages and a duplex destabilization mechanism has been proposed.}, number={3}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Mangrum, John B. and Flora, Jason W. and Muddiman, David C.}, year={2002}, month={Mar}, pages={232–240} }
 @article{hannis_muddiman_2002, title={Tailoring the gas-phase dissociation and determining the relative energy of activation for dissociation of 7-deaza purine modified oligonucleotides containing a repeating motif}, volume={219}, ISSN={1387-3806}, url={http://dx.doi.org/10.1016/s1387-3806(02)00544-4}, DOI={10.1016/s1387-3806(02)00544-4}, abstractNote={7-Deaza purine modified oligonucleotides with a repeating motif have been sequenced by slow heating methods illustrating the ability to alter the preferred unimolecular decomposition pathway. The modified oligonucleotides limited the number of product ions per repeat unit resulting in an increased signal-to-noise ratio for the tandem mass spectrometry data. Loss of 7-deaza purine nucleobases or 7-deaza purine related product ions were not observed. The results illustrate the importance of the N7 position of purine nucleobases for low energy gas-phase decomposition. FRAGMENT results showed that for the 3− charge state of the 16-mer oligonucleotides, 5′-(AATG)4-3′ and 5′-(c7Ac7ATG)4-3′, that the 7-deaza deoxyadenosine modified sequence had a 38% greater relative energy of activation for unimolecular decomposition when compared to the unmodified sequence. For large DNA molecules that have purine-rich repeat units, the multiple sequence sites per repeat can result in a substantial loss of sequence information over large areas due to a reduced signal-to-noise ratio of the product ion spectrum. The incorporation of 7-deaza purines can limit the number of product ions during gas phase sequencing while ensuring sufficient sequence coverage to localize mutations or polymorphisms housed within a specific repeat unit.}, number={1}, journal={International Journal of Mass Spectrometry}, publisher={Elsevier BV}, author={Hannis, James C and Muddiman, David C}, year={2002}, month={Aug}, pages={139–150} }
 @article{flora_muddiman_2001, title={Complete sequencing of mono—deprotonated peptide nucleic acids by sustained off-resonance irradiation collision—induced dissociation}, volume={12}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(01)00259-8}, DOI={10.1016/s1044-0305(01)00259-8}, abstractNote={Complete peptide nucleic acids (PNAs) sequence information is obtained from the unimolecular decomposition of singly-charged PNA oligomers in the negative-ion mode using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) and sustained off-resonance irradiation collision induced dissociation. The 4-mers, n-CATT-c, n-AGCT-c, n-AACT-c, and n-acetylated-AACT-c and two 6-mers, n-AAAAAA-c and n-CCCCCC-c, were investigated to explore the unimolecular decomposition of mixed-nucleobase and homopolymer PNAs representing purine and pyrimidine oligomers, respectively. PNA decomposition is explored using a product-ion appearance curve and double resonance experiments. A decomposition mechanism for sequence ion formation (PNA amide bond cleavage) is proposed.}, number={7}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Flora, Jason W. and Muddiman, David C.}, year={2001}, month={Jul}, pages={805–809} }
 @article{hannis_muddiman_2001, title={Detection of double-stranded PCR amplicons at the attomole level electrosprayed from low nanomolar solutions using FT-ICR mass spectrometry}, volume={369}, ISSN={0937-0633 1432-1130}, url={http://dx.doi.org/10.1007/s002160000612}, DOI={10.1007/s002160000612}, abstractNote={An 82-base-pair polymerase chain reaction (PCR) product was amplified from the tetranucleotide short tandem repeat locus within the human tyrosine hydroxylase gene. PCR amplification was carried out using 100 ng of human nuclear DNA obtained from an individual who is homozygotic for the 9.3 allele resulting in a 50.5 kDa amplicon. To generate sufficient material for these investigations, several reactions were pooled and subsequently purified and quantified using UV-vis spectrophotometry. A serial dilution was carried out from a 2 microM stock solution providing solution concentrations down to 5 nM. Measurements were made using hexapole accumulation and gated trapping strategies in a 4.7 Telsa Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) which facilitated detection of the amplicon at the attomole level when electrosprayed from a 5 nM solution with a single acquisition! The signal-to-noise ratio was determined to be 8.3 for the spectrum derived from the 5 nM solution using the magnitude-mode mass spectral peak height for the most abundant charge-state. This remarkable sensitivity for large PCR amplicons will dramatically improve the ability of electrospray ionization mass spectrometry to address important genetic questions for low copy number genes or when the amount of initial template is limited; the latter issue is commonly encountered in DNA forensics. Furthermore, these data represents over 2 orders of magnitude decrease in detection limits over other existing ESI-MS reports concerning PCR products, including those conducted using FTICR-MS.}, number={3-4}, journal={Fresenius' Journal of Analytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Hannis, James C. and Muddiman, David C.}, year={2001}, month={Feb}, pages={246–251} }
 @article{null_hannis_muddiman_2001, title={Genotyping of Simple and Compound Short Tandem Repeat Loci Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry}, volume={73}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac0103928}, DOI={10.1021/ac0103928}, abstractNote={The utility of electrospray ionization Fourier transform ion cyclotron resonance (ESI-FIICR) mass spectrometry as a new approach for genotyping short tandem repeats (STRs) is demonstrated. STRs are currently valued as a powerful source of genetic information with repeats that range in structure from simple to hypervariable. Two tetranucleotide STR loci were chosen to evaluate ESI-FTICR mass spectrometry as a tool for genotyping: HUM-TH01, a simple STR with nonconsensus alleles, and vWA, a compound STR with nonconsensus alleles. For HUM-TH01, the genotype (i.e., repeat number of each allele) was determined for each of 30 individuals using mass measurements of double-stranded amplicons. Low-intensity peaks observed in the spectra of amplicons derived from heterozygous individuals were identified by mass as heteroduplexes that had formed between nonhomologous strands. Mass measurement of the double-stranded vWA amplicon was not sufficient for determining whether the individual was homozygous for allele subtype 18 or 18' since the amplicons differ by only 0.99 Da. Therefore, single-stranded amplicons were generated by incorporating a phosphorylated primer, prepared using T4 polynucleotide kinase, into the PCR phase and subsequently digesting the bottom strand using lambda-exonuclease. Accurate mass measurements were obtained for the single-stranded amplicons using internal calibration and the addition of a correction factor to adjust for the natural variation of isotopic abundances, confirming that the individual is homozygous for allele 18. Our results clearly demonstrate that ESI-FTICR mass spectrometry is a powerful approach to characterize both simple and compound STRs beyond the capabilities of electrophoretic technologies.}, number={18}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Null, Allison P. and Hannis, James C. and Muddiman, David C.}, year={2001}, month={Sep}, pages={4514–4521} }
 @article{hannis_muddiman_2001, title={Genotyping short tandem repeats using flow injection and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={15}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/rcm.234}, DOI={10.1002/rcm.234}, abstractNote={AbstractCharacterizing polymerase chain reaction (PCR) amplicons has been accomplished for the first time using flow injection analysis coupled to electrospray ionization mass spectrometry (ESI‐MS). The PCR amplicons were amplified at the human tyrosine hydroxylase short tandem repeat locus from an individual homozygotic for the 9.3 allele. One product was amplified using Pfu polymerase and yielded a blunt‐ended amplicon of 82 base‐pairs (bp) in length. The second PCR product was amplified using Taq polymerase that resulted in an amplicon with cohesive termini of 82 bp plus either mono‐ or diadenylation. The two PCR amplicons were alternatively injected using a 0.5‐µL loop at 2 µM for the Pfu amplicon and 1 µM for the Taq amplicon with a flow rate of 200 nL/min during data acquisition. Both PCR amplicons were accurately identified using mass measurements illustrating the compatibility of ESI‐MS for genotyping short tandem repeat sequences and the potential for high‐throughput genotyping of large PCR amplicons. Copyright © 2001 John Wiley & Sons, Ltd.}, number={5}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Hannis, James C. and Muddiman, David C.}, year={2001}, pages={348–350} }
 @article{flora_hannis_muddiman_2001, title={High-Mass Accuracy of Product Ions Produced by SORI-CID Using a Dual Electrospray Ionization Source Coupled with FTICR Mass Spectrometry}, volume={73}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac0011282}, DOI={10.1021/ac0011282}, abstractNote={High-mass accuracy is demonstrated using internal calibration for product ions produced by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) of a 15-mer oligonucleotide, 5'-(CTG)5-3'. Internal calibration for this tandem MS experiment was accomplished using a dual electrospray ionization (ESI) source coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) utilizing hexapole accumulation and gated trapping. The pulse sequence entails injection, trapping, and gas-phase isolation of the precursor ion of interest followed by the SORI-CID of this ion and, subsequently, injection and trapping of the internal mass calibrant (i.e., poly(ethylene glycol) with a 1000 Da average mass). The product ions and the poly(ethylene glycol) ions are then simultaneously excited by a broadband frequency chirp excitation waveform and detected. This technique corrects for space-charge effects on the measurement of an ion's cyclotron frequency experienced when externally calibrated data are used. While external calibration for FTICR-MS can result in mass errors of greater than 100 ppm, this internal standardization method demonstrated significantly more consistent accurate mass measurements with average mass errors ranging from -1.2 to -3.2 ppm for the 15-mer oligonucleotide used in this study. This method requires limited modifications to ESI-FTICR mass spectrometers and is applicable for both positive and negative modes of ionization as well as other sample types (e.g., pharmaceuticals, proteins, etc.).}, number={6}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Flora, Jason W. and Hannis, James C. and Muddiman, David C.}, year={2001}, month={Mar}, pages={1247–1251} }
 @article{chen_hannis_flora_muddiman_charles_yu_povirk_2001, title={Homogeneous Preparations of 3′-Phosphoglycolate-Terminated Oligodeoxynucleotides from Bleomycin-Treated DNA as Verified by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry}, volume={289}, ISSN={0003-2697}, url={http://dx.doi.org/10.1006/abio.2000.4936}, DOI={10.1006/abio.2000.4936}, abstractNote={Single- and double-strand breaks bearing 3'-phosphoglycolate termini are among the most frequent lesions formed in DNA by ionizing radiation and other oxidative mutagens. In order to obtain homogeneous preparations of defined 3'-phosphoglycolate substrates for repair studies, 5'-(32)P-end-labeled partial duplex DNAs were treated with bleomycin, and individual cleavage products were isolated from polyacrylamide gels. The fragments were then treated with alkaline phosphatase and further purified by reverse-phase HPLC. Electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry of the purified oligomers produced molecular ions of the expected masses, with no detectable contaminants. Gas-phase sequencing by tandem mass spectrometry of these single species yielded the expected sequence ions and confirmed the presence of phosphoglycolate on the 3'-terminal fragments only. The fragments could be relabeled with polynucleotide kinase to yield highly purified, high-specific-activity substrates for repair studies.}, number={2}, journal={Analytical Biochemistry}, publisher={Elsevier BV}, author={Chen, Shuang and Hannis, James C. and Flora, Jason W. and Muddiman, David C. and Charles, Kwabena and Yu, Yin and Povirk, Lawrence F.}, year={2001}, month={Feb}, pages={274–280} }
 @article{gordon_muddiman_2001, title={Impact of ion cloud densities on the measurement of relative ion abundances in Fourier transform ion cyclotron resonance mass spectrometry: experimental observations of coulombically induced cyclotron radius perturbations and ion cloud dephasing rates}, volume={36}, ISSN={1076-5174 1096-9888}, url={http://dx.doi.org/10.1002/jms.121}, DOI={10.1002/jms.121}, abstractNote={AbstractFundamental research into the quantitative properties of Fourier transform ion cyclotron resonance mass spectrometry (FTICR‐MS) has yielded interesting observations, especially in terms of factors affecting the accuracy of relative ion abundances. However, most of the previous discussions have focused on theoretical systems, or systems of limited scope. In this paper, we document ion motion attributes of a 30 spectra (six samples, five replicates each) system previously established as linear over two orders of magnitude. Observed behaviors include the perturbation of one charged species (cyclosporin A, CsA) of low ion density to a cyclotron orbit of greater radius than that of an almost identical, but slightly mass‐separated species (CsG) with a higher ion density. This radial perturbation is attributed to the coulombic repulsion between the two ion clouds as they interact during the excitation process, as previously proposed by Uechi and Dunbar. Magnitudes of the perturbation were confirmed by making cyclotron radii determinations utilizing the ratio of the third‐to‐first harmonics for the charged species of interest. It was found that these radial differences can account for as much as a 55% signal bias in favor of CsA for a single sample and a >20% positive bias in the slope of the regressed data set. A second behavior noted that also contributes to the potential inaccuracy of relative ion abundance measurements is the difference in signal decay rates for CsA and CsG. Damping constants and initial time domain signal amplitudes were evaluated using segmented Fourier transforms. Discrepancies in decay rates were not expected from two species that have essentially identical collisional cross‐sections. However, it has been observed that the faster decay rates are observed by the species of lower ion cloud density. We have attributed this differential signal decay phenomenon to the rates of loss of phase coherence for the two ion clouds. Previously, others have reported that less dense ion clouds are more susceptible to shearing and other disruptive forces during the course of their excited cyclotron motion. Our experimental evidence supports that it is the loss of cloud coherence that accounts for the signal loss over time, with the less dense cloud de‐phasing more quickly. As the ion populations of the two investigated species near equivalence, so do their time constants. Copyright © 2001 John Wiley & Sons, Ltd.}, number={2}, journal={Journal of Mass Spectrometry}, publisher={Wiley}, author={Gordon, Eric F. and Muddiman, David C.}, year={2001}, pages={195–203} }
 @article{null_muddiman_2001, title={Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post‐genome era}, volume={36}, DOI={10.1002/jms.172}, abstractNote={AbstractThe recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make‐up; however, the post‐genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs. Copyright © 2001 John Wiley & Sons, Ltd.}, number={6}, journal={Journal of Mass Spectrometry (Special Feature)}, author={Null, A.P. and Muddiman, D.C.}, year={2001}, month={Jun}, pages={589–606} }
 @article{flora_muddiman_2001, title={Selective, Sensitive, and Rapid Phosphopeptide Identification in Enzymatic Digests Using ESI-FTICR-MS with Infrared Multiphoton Dissociation}, volume={73}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac010333u}, DOI={10.1021/ac010333u}, abstractNote={Rapid screening for phosphopeptides within complex proteolytic digests involving electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in the negative ion mode with infrared multiphoton dissociation (IRMPD) accompanied by improved phosphopeptide sensitivity and selectivity is demonstrated with the tryptic digests of the naturally phosphorylated proteins bovine alpha- and beta-casein. All peptides in a complex proteolytic digest can be examined simultaneously for phosphorylation with a 4-s IR laser pulse at 7-11 W where phosphopeptide signature ions form upon irradiation, as the low energy of activation phosphate moiety cleavage transpires without the dissociation of the unphsophorylated peptide population. The tyrosine phosphorylated peptide HGLDN-pY-R, its nonphosphorylated analogue HGLDNYR, the kinase domain of insulin receptor unphosphorylated TRDIYETDYYRK, monophosphorylated TRDIYED-pY-YRK, and triphosphorylated TRDI-pY-ETD-pY-pY-RK were also used as model peptides in this research. The sensitivity and selectivity of phosphopeptides is shown to greatly improve when the volatile base piperidine is used to adjust the pH of th}, number={14}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Flora, Jason W. and Muddiman, David C.}, year={2001}, month={Jul}, pages={3305–3311} }
 @article{hannis_muddiman_2000, title={A dual electrospray ionization source combined with hexapole accumulation to achieve high mass accuracy of biopolymers in Fourier transform ion cyclotron resonance mass spectrometry}, volume={11}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(00)00160-4}, DOI={10.1016/s1044-0305(00)00160-4}, abstractNote={A dual electrospray ionization (ESI) source employed with hexapole accumulation and gated trapping provides a novel method of using an internal standard to achieve high mass accuracies in Fourier transform ion cyclotron resonance mass spectrometry. Two ESI emitters are sequentially positioned in front of the heated metal capillary inlet by a solenoid fitted to an XYZ micromanipulator; one emitter contains the analyte(s) of interest and the other an internal standard. A 5 V transistor-transistor logic pulse from the data station controls the solenoid by means of a solid-state relay so that matching of spectral peak intensities (i.e., analyte and internal standard intensities) can be accomplished by adjusting the hexapole accumulation time for each species. Polythymidine, d(pT)18, was used as the internal standard for all studies reported here. The absolute average error for an internally calibrated 15-mer oligonucleotide (theoretical monoisotopic mass = 4548.769 Da) was -1.1 ppm (external calibration: 41 ppm) with a standard deviation of +/-3.0 ppm (external calibration: +/-24 ppm) for a total of 25 spectra obtained at various hexapole accumulation time ratios. Linear least squares regression analysis was carried out and revealed a linear dependence of the magnitudes of the peak height ratios (analyte/internal standard) vs. hexapole accumulation time ratios (analyte/internal standard) which is described by the following equation: y = 0.45 x - 0.02. The fitted line had a %RSD of the slope of 28% with an R2 of 0.93. The applicability of this methodology was extended to a polymerase chain reaction product with a theoretical average molecular mass of 50,849.20 Da. With the internal standard, d(pT)18, an absolute average error of -8.9 ppm (external calibration: 44 ppm) based on five measurements was achieved with a standard deviation of 11 ppm (external calibration: +/-36 ppm), thus illustrating this method's use for characterizing large biomolecules such as those encountered in genomics and proteomics related research.}, number={10}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Hannis, James C. and Muddiman, David C.}, year={2000}, month={Oct}, pages={876–883} }
 @misc{shuford_muddiman_2000, title={Absolute Quantification of Proteins by Mass Spectrometry}, ISBN={9780470027318 9780471976707}, url={http://dx.doi.org/10.1002/9780470027318.a9311}, DOI={10.1002/9780470027318.a9311}, abstractNote={Abstract
          
            Mass spectrometry (MS) provides unambiguous molecular specificity relative to all other analytical and immunological techniques and, consequently, has great potential to provide unambiguous estimates of absolute protein quantities within complex biological systems. Here, we provide a critical review and discussion of the predominant
            MS
            ‐based technology used for absolute protein quantification, referred to as protein cleavage‐isotope dilution mass spectrometry (
            PC‐IDMS
            ). This technique requires proteolytic conversion of the analyte protein into its quantitative surrogate peptide, which is subsequently quantified using a stable isotope‐labeled (SIL) peptide analog as an internal standard (IS). All phases of the
            PC‐IDMS
            workflow, from the
            SIL
            peptide production platforms to data analysis, are described and characterized in detail. An emphasis is placed on the practical quantitative aspects for each step of the workflow and their implication on quantitative accuracy.
          }, journal={Encyclopedia of Analytical Chemistry}, publisher={John Wiley & Sons, Ltd}, author={Shuford, Christopher M. and Muddiman, David C.}, year={2000}, month={Oct}, pages={1–26} }
 @article{flora_shillady_muddiman_2000, title={An experimental and theoretical study of the gas-phase decomposition of monoprotonated peptide nucleic acids}, volume={11}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/s1044-0305(00)00126-4}, DOI={10.1016/s1044-0305(00)00126-4}, abstractNote={Peptide nucleic acids (PNAs) are DNA/RNA mimics which have recently generated considerable interest due to their potential use as antisense and antigene therapeutics and as diagnostic and molecular biology tools. These synthetic biomolecules were designed with improved properties over corresponding oligonucleotides such as greater binding affinity to complementary nucleic acids, enhanced cellular uptake, and greater stability in biological systems. Because of the stability and unique structure of PNAs, traditional sequence confirmation methods are not effective. Alternatively, electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry shows great potential as a tool for the characterization and structural elucidation of these oligonucleotide analogs. Extensive gasphase fragmentation studies of a mixed nucleobase 4-mer (AACT) and a mixed nucleobase 4-mer with an acetylated N-terminus (N-acetylated AACT) have been performed. Gas-phase collision-induced dissociation of PNAs resulted in water loss, cleavage of the methylene carbonyl linker containing a nucleobase, cleavage of the peptide bond, and the loss of nucleobases. These studies show that the fragmentation behavior of PNAs resembles that of both peptides and oligonucleotides. Molecular mechanics (MM+), semiempirical (AM1), and ab initio (STO-3G) calculations were used to investigate the site of protonation and determine potential low energy conformations. Computational methods were also employed to study prospective intramolecular interactions and provide insight into potential fragmentation mechanisms.}, number={7}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Flora, Jason W. and Shillady, Donald D. and Muddiman, David C.}, year={2000}, month={Jul}, pages={615–625} }
 @article{null_hannis_muddiman_2000, title={Preparation of single-stranded PCR products for electrospray ionization mass spectrometry using the DNA repair enzyme lambda exonuclease}, volume={125}, ISSN={0003-2654 1364-5528}, url={http://dx.doi.org/10.1039/a908022h}, DOI={10.1039/a908022h}, abstractNote={Electrospray ionization mass spectrometry (ESI-MS) has been utilized to obtain accurate mass measurements of intact PCR products; however, single-stranded PCR products are necessary to detect sequence modifications such as base substitutions, additions or deletions. The locations of these modifications can subsequently be determined using additional stages of mass spectrometry. The recombinant enzyme lambda exonuclease selectively digests one strand of a DNA duplex from a 5' phosphorylated end leaving the complementary strand intact. Using this rapid enzymatic step, we were able to produce single-stranded PCR products by digestion of an intact PCR product derived from the Human Tyrosine Hydroxylase (HUMTHO1) gene, which contains a tetrameric repeating motif. The non-template directed 3' adenylation common when using Taq polymerase resulted in three distinct species (blunt-ended, mono-adenylated and di-adenylated), which added complexity to the spectrum of the double-stranded product. The data from the single-stranded products shows that one strand is preferentially adenylated over the other, which cannot be determined from the mass spectrum of the double-stranded PCR product alone. The ESI-FTICR (Fourier transform ion cyclotron resonance) mass spectra of the lambda exonuclease treated PCR products exhibited less than expected signal-to-noise (S/N) ratios. This is attributed to inaccurate concentration calculations due to remaining double-stranded PCR product amplified with unphosphorylated primers, and to matrix effects contributed by the lambda exonuclease reaction buffer. To further test this hypothesis, we investigated and determined the limit of detection to be 0.27 microM using standard curve statistics for single acquisitions of a synthetic 75-mer. The concentrations of the noncoding and coding strands produced by lambda exonuclease digestion were calculated to be 0.29 and 0.37 microM, respectively, taking into account the presence of double-stranded product. The products were electrosprayed from concentrations at the limit of detection requiring the averaging of 5-10 acquisitions to produce a sufficient S/N ratio, indicating that product concentration, base composition and matrix effects play a combined, significant role in detection of lambda exonuclease treated PCR products. Although additional work will be required to further exploit this strategy, lambda exonuclease clearly provides mass spectrometrists with a method to generate single-stranded PCR products.}, number={4}, journal={The Analyst}, publisher={Royal Society of Chemistry (RSC)}, author={Null, Allison P. and Hannis, James C. and Muddiman, David C.}, year={2000}, pages={619–626} }
 @article{hannis_muddiman_1999, title={Accurate characterization of the tyrosine hydroxylase forensic allele 9.3 through development of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={13}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19990530)13:10<954::aid-rcm593>3.0.co;2-r}, DOI={10.1002/(sici)1097-0231(19990530)13:10<954::aid-rcm593>3.0.co;2-r}, abstractNote={Accurate and precise determination of the number of repeats from a short tandem repeat (STR) sequence for a human gene locus is demonstrated for the first time by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). Specifically, the polymorphic human tyrosine hydroxylase (HUMTHO1) gene, a tetranucleotide STR forensic allele, was chosen as a model system to evaluate our approach for future characterization of both STRs and variable number of tandem repeats (VNTRs) by development of an ESI-FTICR-MS approach. The coding and noncoding strands from the HUMTHO1 9.3 allele are simultaneously resolved obtaining accurate (better than 70 ppm) average mass measurements of 25,783.23 and 24,754.55 Da for the coding and noncoding strands, respectively. The mass measurements are used to calculate the number of repeats for each strand, 'n', of 9.75169 and 9.75001 for the coding and noncoding strands, respectively. It will be shown how the value of 'n' can be used to directly determine the number of pure repeats and accurately determine the exact nature of the polymorphism within the repeat (if any). The single nucleotide deletion in the coding strand (adenine) and noncoding strand (thymine) were accurately identified using this approach. Interestingly, we observed the conversion of single-stranded to double-stranded DNA while the PCR product in the ESI buffer was being infused; the issues related to this observation will be presented. Previous results by other researchers investigating the HUMTHO1 9.3 allele using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) are directly compared with our results. Our results indicate that ESI-FTICR-MS is a powerful approach to rapidly and accurately characterize tandem repeating sequences which will ultimately lead towards the understanding of a complex class of diseases and in human identity determination.}, number={10}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Hannis, James C. and Muddiman, David C.}, year={1999}, month={May}, pages={954–962} }
 @article{hannis_muddiman_1999, title={Characterization of a microdialysis approach to prepare polymerase chain reaction products for electrospray ionization mass spectrometry using on-line ultraviolet absorbance measurements and inductively coupled plasma-atomic emission spectroscopy}, volume={13}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19990315)13:5<323::aid-rcm485>3.0.co;2-b}, DOI={10.1002/(sici)1097-0231(19990315)13:5<323::aid-rcm485>3.0.co;2-b}, abstractNote={The desalting efficiencies for microdialysis have been quantitatively determined using inductively coupled plasma atomic emission spectroscopy (ICP-AES) by analyzing samples which mimic polymerase chain reaction (PCR) conditions. Desalting efficiencies for the removal of Mg2+ from samples containing oligonucleotides were typically 99.94% for a single dialysis experiment and 99.98% for a tandem-dialysis experiment. The determination of the molecular weight selectivity of a microdialysis fiber with a 13,000 Da molecular weight cutoff (MWCO) employing a 10 mM NH4OAc countercurrent buffer was accomplished using on-line ultraviolet (UV) absorbance. Results revealed an insensitivity to molecular weight over a broad range represented by dNTPs (ca. 490 Da), PCR primers (ca. 5100 Da), and PCR products (extending to ca. 100 kDa) thus showing the inability of microdialysis to remove unincorporated deoxyribonucleotide 5′-triphosphates (dNTPs) and primers from PCRs. A comparison study conducted utilizing proteins ranging from ca. 1 to 29 kDa produced recoveries dictated by the MWCO of the microdialysis fiber. Recoveries were zero for the smallest proteins tested (ca. 1.3 and 2.9 kDa), but increased to 98% for the largest protein (ca. 29 kDa). The ability of microdialysis to convert double-stranded DNA to single-stranded DNA due to a rapid decrease in the ionic strength was examined along with the effects of buffer concentration, temperature, pH, tandem dialysis, and a denaturing additive, formamide. Melting temperature curves showed that microdialyzed samples remain double stranded while utilizing NH4OAc buffer concentrations of 0 (i.e. pure water) to 10 mM. Adjustment of the buffer up to pH 10.98, temperature increases to 51 °C, tandem dialysis, and the addition of formamide were also unable to produce the conversion of ds-DNA to ss-DNA in detectable amounts. Copyright © 1999 John Wiley & Sons, Ltd.}, number={5}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Hannis, James C. and Muddiman, David C.}, year={1999}, month={Mar}, pages={323–330} }
 @article{kloster_hannis_muddiman_farrell_1999, title={Consequences of Nucleic Acid Conformation on the Binding of a Trinuclear Platinum Drug†}, volume={38}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi991202e}, DOI={10.1021/bi991202e}, abstractNote={BBR3464, a charged trinuclear platinum compound, is the first representative of a new class of anticancer drugs to enter phase I clinical trials. The structure of BBR3464 is characterized by two [trans-PtCl(NH(3))(2)] units linked by a tetraamine [trans-Pt(NH(3))(2)¿H(2)N(CH(2))(6)NH(2)¿(2)] unit. The +4 charge of BBR3464 and the separation of the platinating units indicate that the mode of DNA binding will be distinctly different from those of classical mononuclear drugs such as cisplatin, cis-[PtCl(2)(NH(3))(2)]. The reaction of BBR3464 with three different nucleic acid conformations was assessed by gel electrophoresis. Comparison of single-stranded DNA, RNA, and double-stranded DNA indicated that the reaction of BBR3464 with single-stranded DNA and RNA was faster than that with duplex DNA, and produced more drug-DNA and drug-RNA adducts. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry was used to further characterize the binding modes of BBR3464 with the DNA substrates. BBR3464 binding to different nucleic acid conformations raises the possibility that the adducts of single-stranded DNA and RNA may play a role in the different antitumor efficacies of this novel drug as compared with cisplatin.}, number={45}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Kloster, Miriam B. G. and Hannis, James C. and Muddiman, David C. and Farrell, Nicholas}, year={1999}, month={Nov}, pages={14731–14737} }
 @article{lewis_dawson_hannis_muddiman_macrina_1999, title={Hemoglobinase Activity of the Lysine Gingipain Protease (Kgp) of Porphyromonas gingivalis W83}, volume={181}, ISSN={1098-5530 0021-9193}, url={http://dx.doi.org/10.1128/jb.181.16.4905-4913.1999}, DOI={10.1128/jb.181.16.4905-4913.1999}, abstractNote={ABSTRACT
               
                  Porphyromonas gingivalis, an important periodontal disease pathogen, forms black-pigmented colonies on blood agar. Pigmentation is believed to result from accumulation of iron protoporphyrin IX (FePPIX) derived from erythrocytic hemoglobin. The Lys-X (Lys-gingipain) and Arg-X (Arg-gingipain) cysteine proteases ofP. gingivalis bind and degrade erythrocytes. We have observed that mutations abolishing activity of the Lys-X-specific cysteine protease, Kgp, resulted in loss of black pigmentation ofP. gingivalis W83. Because the hemagglutinating and hemolytic potentials of mutant strains were reduced but not eliminated, we hypothesized that this protease played a role in acquisition of FePPIX from hemoglobin. In contrast to Arg-gingipain, Lys-gingipain was not inhibited by hemin, suggesting that this protease played a role near the cell surface where high concentrations of hemin confer the black pigmentation. Human hemoglobin contains 11 Lys residues in the α chain and 10 Lys residues in the β chain. In contrast, there are only three Arg residues in each of the α and β chains. These observations are consistent with human hemoglobin being a preferred substrate for Lys-gingipain but not Arg-gingipain. The ability of the Lys-gingipain to cleave human hemoglobin at Lys residues was confirmed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry of hemoglobin fragments resulting from digestion with the purified protease. We were able to detect several of the predicted hemoglobin fragments rendered by digestion with purified Lys-gingipain. Thus, we postulate that the Lys-gingipain of P. gingivalisis a hemoglobinase which plays a role in heme and iron uptake by effecting the accumulation of FePPIX on the bacterial cell surface.}, number={16}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Lewis, Janina P. and Dawson, Janet A. and Hannis, James C. and Muddiman, David and Macrina, Francis L.}, year={1999}, month={Aug}, pages={4905–4913} }
 @article{gordon_mansoori_carroll_muddiman_1999, title={Hydropathic influences on the quantification of equine heart cytochromec using relative ion abundance measurements by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={34}, ISSN={1076-5174 1096-9888}, url={http://dx.doi.org/10.1002/(sici)1096-9888(199910)34:10<1055::aid-jms864>3.0.co;2-e}, DOI={10.1002/(sici)1096-9888(199910)34:10<1055::aid-jms864>3.0.co;2-e}, abstractNote={The number of publications documenting the utility of electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) for the analysis of biological molecules has increased in geometric proportion spanning diverse areas of research. Currently, we are investigating the capabilities of ESI-FTICR to quantify relative molecular ion abundances of biopolymers, an area which has not been explored rigorously. We present here the results of an investigation of a two-component system utilizing equine heart cytochrome c (EH) as the analyte and bovine heart cytochrome c (BH) as a constant concentration internal standard. As these compounds are relatively large ( approximately 12 kDa), they will become multiply charged during the electrospray process. Using appropriate solution and instrument conditions, the 7(+) and 8(+) charge states were enhanced for both cytochrome c species. We report that using the average of the ion abundances for the two charge states observed for each species, the linear curve (intensity ratio vs concentration ratio) had a dynamic range of 0.045-2.348 microM (1.7 orders of magnitude). Linear least-squares regression analysis (LLSRA) of these averaged ion abundances (i.e. [(EH + 7H(+))(7+)/(BH + 7H(+))(7+) + (EH + 8H(+))(8+)/(BH + 8H(+))(8+)]/2) yielded the equation y = 1.005x + 0.027. The slope of the line with its calculated precision, reported as one standard deviation, is 1.005 +/- 0.0150, which is statistically ideal (i.e. equal to unity). However, LLSRA of the ion abundances of the two individual charge states were significantly different (i.e. the slope of the (EH + 7H(+))(7+)/(BH + 7H(+))(7+) peak intensity ratio vs molar ratio data was 0.885 +/- 0.0183 and the slope of the (EH + 8H(+))(8+)/(BH + 8H(+))(8+) data was 1.125 +/- 0.0308). We attribute this difference to the variation in primary amino acid sequence for the two cytochrome c species. Both have 104 amino acids, but there are three residue substitutions between EH and BH; one of the substitutions confers an additional basic site to EH. While this extra basic residue may imply an additional charging site, the low charge states observed under the solution conditions employed indicate that most (>66%) basic sites are not protonated. However, the extra basic site also renders EH slightly more hydrophilic. These results present significant considerations when choosing internal standards for the quantification of large proteins by ESI-FTICR-MS and demonstrate that relative molecular ion signals in FTICR can be used to quantify macromolecular species in the nanomolar regime.}, number={10}, journal={Journal of Mass Spectrometry}, publisher={Wiley}, author={Gordon, Eric F. and Mansoori, Bashir A. and Carroll, Charlotte F. and Muddiman, David C.}, year={1999}, month={Oct}, pages={1055–1062} }
 @article{muddiman_null_hannis_1999, title={Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry}, volume={13}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19990630)13:12<1201::aid-rcm643>3.0.co;2-x}, DOI={10.1002/(sici)1097-0231(19990630)13:12<1201::aid-rcm643>3.0.co;2-x}, abstractNote={Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/µL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.}, number={12}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Muddiman, David C. and Null, Allison P. and Hannis, James C.}, year={1999}, month={Jun}, pages={1201–1204} }
 @article{gordon_muddiman_1999, title={Quantification of singly charged biomolecules by electrospray ionization fourier transform ion cyclotron resonance mass spectrometry utilizing an internal standard}, volume={13}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19990215)13:3<164::aid-rcm474>3.0.co;2-l}, DOI={10.1002/(sici)1097-0231(19990215)13:3<164::aid-rcm474>3.0.co;2-l}, abstractNote={The quantification of Cyclosporin A (CsA) and related biological compounds by various mass spectrometric techniques is well established. It is precisely this fact that makes the use of CsA particularly appealing as a model system in evaluating the quantitative properties of electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). Utilizing the internal standard methodology, we have generated a linear calibration curve ranging from 5–250 ng/mL CsA described by the equation y = 0.00503x–0.00958, with a %RSDslope of 0.74% and a correlation coefficient (r0) equal to 0.9992 (N = 30). The internal standard (200 ng/mL Cyclosporin G) was found to be necessary to establish the reported dynamic range, two orders of magnitude based on an experimentally determined detection limit of 2.4 ng/mL CsA, and also significantly improved the overall precision of the method. The data represented in the standard curve were collected as 1.05 s single acquisitions (512 K data points at an ADC rate of 500 kHz) and unapodized prior to the Fourier transformation of the time-domain data. We report that full Hanning apodization has a statistically significant negative effect (F-test at 95% confidence level) on the regression statistics of the curve (i.e. increasing the %RSDslope to 1.33%). Finally, we report that acceptable quantitative properties of an FTICR-MS experiment can be realized as soon as the detection of a second isotopic beat for the targeted species is obtained. This should allow for the practical and effective coupling of on-line separation techniques for quantitative analysis using ESI-FTICR-MS. Copyright © 1999 John Wiley & Sons, Ltd.}, number={3}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Gordon, Eric F. and Muddiman, David C.}, year={1999}, month={Feb}, pages={164–171} }
 @article{flora_muddiman_1998, title={Comprehensive nomenclature for the fragment ions produced from collisional activation of peptide nucleic acids}, volume={12}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19980630)12:12<759::aid-rcm228>3.0.co;2-e}, DOI={10.1002/(sici)1097-0231(19980630)12:12<759::aid-rcm228>3.0.co;2-e}, abstractNote={A relatively new class of DNA mimics, peptide nucleic acids (PNA’s), have generated increasing interest and importance over the last few years. These molecules have a neutral ‘peptide-like’ backbone granting them many advantageous properties which lead to their potential use as antisense and antigene therapeutics. Due to the promising properties possessed by PNA’s, there is a demand for the development of analytical methods for characterization of these molecules. We have been investigating the gas-phase fragmentation pathways of singly and multiply charged PNA’s using electrospray ionization in conjunction with Fourier transform ion cyclotron resonance mass spectrometry. Fragmentations induced by sustained off-resonance irradiation and nozzle–skimmer dissociation have revealed water loss, cleavages of the methylene carbonyl linker (to which the nucleobases are attached), fragmentation along the PNA backbone, and the elimination of single nucleobases. It is becoming increasingly evident that multi-stage MS is especially suited to structural characterization of large bio-molecules such as PNA’s, and herein we propose a comprehensive nomenclature for the product ions produced upon collisional activation of PNA’s, which is based upon extensive experimental studies. © 1998 John Wiley & Sons, Ltd.}, number={12}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Flora, Jason W. and Muddiman, David C.}, year={1998}, month={Jun}, pages={759–762} }
 @article{wunschel_muddiman_fox_fox_smith_1998, title={Heterogeneity inBacillus cereusPCR Products Detected by ESI−FTICR Mass Spectrometry}, volume={70}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac971156t}, DOI={10.1021/ac971156t}, abstractNote={PCR amplification of a segment of the 16/23S rDNA interspace region (ISR) from Bacillus cereus 6464 produced a mixture of products. An 89-bp product was predicted on the basis of the reported sequence. The ESI-FTICR analysis revealed three double-stranded products, differing in size by a single nucleotide corresponding to two homoduplexes of 89 and 88 base pairs and a heteroduplex of 89 and 88 nucleotide strands. These were produced from a single preparation of genomic DNA and a single primer pair. ESI-FTICR analysis of the single strands identified a deletion of a T in the coding strand and a corresponding loss of an A in the noncoding strand of this product. The ESI-FTICR analysis indicated the presence of an unreported sequence variation between rRNA operons in this organism. This report illustrates that PCR products amplified from templates differing by a single nucleotide can be resolved and identified using ESI-FTICR at the 89-bp level. Furthermore, the ESI-FTICR mass measurements provided the identity of the deletion, which is indicative of interoperon variability.}, number={6}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Wunschel, David S. and Muddiman, David C. and Fox, Karen F. and Fox, Alvin and Smith, Richard D.}, year={1998}, month={Mar}, pages={1203–1207} }
 @article{wunschel_muddiman_smith_1998, title={Mass Spectrometric Characterization of DNA for Molecular Biology Applications: Advances using MALDI and ESI}, volume={14}, journal={Advances in Mass Spectrometry}, author={Wunschel, D.S. and Muddiman, D.C. and Smith, R.D.}, year={1998}, pages={377–406} }
 @article{hannis_muddiman_1998, title={Nanoelectrospray mass spectrometry using non-metalized, tapered (50 → 10 μm) fused-silica capillaries}, volume={12}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19980430)12:8<443::aid-rcm183>3.0.co;2-e}, DOI={10.1002/(sici)1097-0231(19980430)12:8<443::aid-rcm183>3.0.co;2-e}, abstractNote={Nanoelectrospray emitter tips, pulled from fused-silica capillaries requiring no chemical treatment or metal coating, have been operated using remote coupling of the electrospray voltage. Using common laboratory implements, 50 μm i.d. fused-silica capillaries were pulled to ca. 10 μm, and attached to a stainless steel capillary via a teflon coupler for the production of nanoelectrospray (i.e. nL/min flowrates). Using a variety of different tips, flowrates were determined to range from 30 to 80 nL/min. Spectra of bovine insulin (ca. 6 kDa) and Angiotensin III (ca. 1 kDa) produced signal-to-noise (S/N) ratios of ca.500 and ca.100, respectively; each analysis consuming ca. 10 femtomoles of sample. Radical cation formation, in addition to the monoprotonated molecule was also observed during nanoelectrospray of angiotensin III which implies that this nanoelectrospray source should be applicable to trace amounts of non-polar compounds. The stability of the ion source is demonstrated by measuring the current of the electrosprayed ions at the shutter of the Fourier transform ion cyclotron resonance mass spectrometer as a function of time. Overall stability of the nanoelectrospray for angiotensin III, using no pressure to initialize or stabilize the electrospray, was determined as 23 pA ± 0.97 pA (4.2 % relative standard deviation) over a 30 minute period. © 1998 John Wiley & Sons, Ltd.}, number={8}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Hannis, James C. and Muddiman, David C.}, year={1998}, month={Apr}, pages={443–448} }
 @article{muddiman_smith_1998, title={Sequencing and Characterization of Larger Oligonucleotides by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry}, volume={17}, ISSN={2191-0189 0793-0135}, url={http://dx.doi.org/10.1515/revac.1998.17.1.1}, DOI={10.1515/revac.1998.17.1.1}, abstractNote={2}, number={1}, journal={Reviews in Analytical Chemistry}, publisher={Walter de Gruyter GmbH}, author={Muddiman, David C. and Smith, Richard D.}, year={1998}, month={Jan}, pages={1–68} }
 @article{muddiman_huang_anderson_rockwood_hofstadler_weir-lipton_proctor_wu_smith_1997, title={Application of sequential paired covariance to liquid chromatography-mass spectrometry data enhancements in both the signal-to-noise ratio and the resolution of analyte peaks in the chromatogram}, volume={771}, ISSN={0021-9673}, url={http://dx.doi.org/10.1016/s0021-9673(97)00069-1}, DOI={10.1016/s0021-9673(97)00069-1}, abstractNote={The algorithm of sequential paired covariance (SPC) has been previously reported to dramatically enhance the signal-to-noise (S/N) ratio for on-line separations combined with mass spectrometry. That initial study focused on a limited number of data sets derived from the combination of capillary electrophoresis (CE) with time-of-flight mass spectrometry using an electrospray interface. Results from the initial study clearly demonstrated that a significant enhancement (almost two orders of magnitude) in the S/N ratio of the eluting peaks in the electropherogram could be obtained, facilitating identification of the analytes. In this report, the algorithm has been applied to liquid chromatography-mass spectrometry data obtained on a triple quadrupole instrument and we have evaluated the general applicability of the SPC approach to several types of microcolumn separations with mass spectrometric detection, including CE coupled with Fourier transform ion cyclotron resonance mass spectrometry. In all the cases we tested, we found the algorithm enhanced the S/N ratios of the resulting chromatograms or electropherograms to a similar extent. This report further demonstrates the SPC approach to enhance the resolution as well as the S/N ratio of the eluting peaks of a complex peptide mixture. While many variations of the algorithm are possible, we have also found higher order covariance (e.g., 3rd order) is useful for eliminating coincidental noise in sequential mass spectra, giving the potential to extract broad, low intensity analyte peaks. We also demonstrate the sequential covariance approach for enhancing the S/N ratio of mass spectra.}, number={1-2}, journal={Journal of Chromatography A}, publisher={Elsevier BV}, author={Muddiman, David C. and Huang, Baoming M. and Anderson, Gordon A. and Rockwood, Alan and Hofstadler, Steven A. and Weir-Lipton, Mary S. and Proctor, Andrew and Wu, Qinyuan and Smith, Richard D.}, year={1997}, month={May}, pages={1–7} }
 @article{liu_muddiman_tang_smith_1997, title={Improving the Microdialysis Procedure for Electrospray Ionization Mass Spectrometry of Biological Samples}, volume={32}, ISSN={1076-5174 1096-9888}, url={http://dx.doi.org/10.1002/(sici)1096-9888(199704)32:4<425::aid-jms493>3.0.co;2-e}, DOI={10.1002/(sici)1096-9888(199704)32:4<425::aid-jms493>3.0.co;2-e}, abstractNote={Significant advances in the area of microdialysis which allowed more effective handling of small volumes (microliters) of samples, more efficient desalting and enhanced mass spectrometric detection sensitivity are described. The previously reported on-line coupling of microdialysis with electrospray ionization (ESI) mass spectrometry has been found to be highly effective; however, direct coupling requires relatively high sample flow rates (∽2 μl min-1) to obtain a stable ESI current compared with the flow rates of newer ESI sources (e.g. ‘microspray,’ 10–100 nl min-1). To circumvent this major limitation imposed by the dimensions of currently available materials, the microdialysis procedure was modified to an off-line mode in order to avoid excessive sample consumption. A more than tenfold decrease in sample consumption was achieved using the off-line modevsthe on-line mode, which resulted in a similar quality spectrum. In addition, several other aspects of the microdialysis approach were altered to improve its performance further: (i) an increase in dialysis temperature was found to increase the desalting efficiency greatly and therefore improve the spectrum quality; (ii) the addition of piperidine and imidazole to the dialysis buffer solution resulted in a reduction of charge states and a further increase in detection sensitivity for DNA and (iii) use of low concentrations (0–2.5 mM NH4OAc) of dialysis buffer shifted the DNA negative ions to higher charge states and produced a nearly tenfold increase in detection sensitivity and a slightly decreased desalting efficiency. Protocols for desalting different samples using microdialysis are discussed. © 1997 by John Wiley & Sons, Ltd.}, number={4}, journal={Journal of Mass Spectrometry}, publisher={Wiley}, author={Liu, Chuanliang and Muddiman, David C. and Tang, Keqi and Smith, Richard D.}, year={1997}, month={Apr}, pages={425–431} }
 @article{muddiman_anderson_hofstadler_smith_1997, title={Length and Base Composition of PCR-Amplified Nucleic Acids Using Mass Measurements from Electrospray Ionization Mass Spectrometry}, volume={69}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac961134r}, DOI={10.1021/ac961134r}, abstractNote={A generally applicable algorithm has been developed to allow base composition of polymerase chain reaction (PCR) products to be determined from mass spectrometrically measured molecular weights and the complementary nature of DNA. Mass measurements of arbitrary precision for single-stranded DNA species are compatible with an increasingly large number of possible base compositions as molecular weight increases. For example, the number of base compositions that are consistent with a molecular weight of 35,000 is approximately 6000, based on a mass measurement precision of 0.01%. However, given the low misincorporation rate of standard DNA polymerases, mass measurement of both of the complementary single strands produced in the PCR reduces the number of possibilities to less than 100 at 0.01% mass precision, and base composition is uniquely defined at 0.001% mass precision. Taking into account the low misincorporation rate of standard DNA polymerases and the fact that the final PCR product also contains primers of known sequence (generally 15-20-mer in size, which flank the targeted region), this reduces the number of possible base combinations to only approximately 3 at MW = 35,000. In addition, the number of base pairs (i.e., length of the DNA molecule) is uniquely defined. We show that the use of modified bases in PCR or post-PCR modification chemistry allows unique solutions for the base composition of the PCR product with only modest mass measurement precision.}, number={8}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Anderson, Gordon A. and Hofstadler, Steven A. and Smith, Richard D.}, year={1997}, month={Apr}, pages={1543–1549} }
 @article{muddiman_bakhtiar_hofstadler_smith_1997, title={Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Instrumentation and Applications}, volume={74}, ISSN={0021-9584 1938-1328}, url={http://dx.doi.org/10.1021/ed074p1288}, DOI={10.1021/ed074p1288}, abstractNote={This article introduces educators and researchers to the theory, principles, instrumentation, and some applications of MALDI-MS. Reflectron time-of-flight (TOF) mass analyzers are described in detail, since TOF is the most common mass analyzer for ions produced by MALDI. Several excellent reviews give a more detailed account of MALDI-MS.}, number={11}, journal={Journal of Chemical Education}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Bakhtiar, Ray and Hofstadler, Steven A. and Smith, Richard D.}, year={1997}, month={Nov}, pages={1288} }
 @article{stang_cao_chen_gray_muddiman_smith_1997, title={Molecular Architecture via Coordination:  Marriage of Crown Ethers and Calixarenes with Molecular Squares, Unique Tetranuclear Metallamacrocycles from Metallacrown Ether and Metallacalixarene Complexes via Self-Assembly}, volume={119}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja9642267}, DOI={10.1021/ja9642267}, abstractNote={Reaction of metallacrown and metallacalixarene platinum bistriflates with bipyridine as well as other bidentate connector ligands results in the formation of tetranuclear macrocycles via self-assembly that combine crown ether and calixarene chemistry with molecular squares. Multinuclear NMR spectroscopy and electrospray mass spectrometry are employed to characterize these unique supramolecular species. The calixarene metallamacrocycles are used in simple transport experiments to carry sulfonate salts from one aqueous phase into another through chloroform.}, number={22}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Stang, Peter J. and Cao, Danh H. and Chen, Kuanchiang and Gray, Gary M. and Muddiman, David C. and Smith, Richard D.}, year={1997}, month={Jun}, pages={5163–5168} }
 @article{manna_kuehl_whiteford_stang_muddiman_hofstadler_smith_1997, title={Nanoscale Tectonics:  Self-Assembly, Characterization, and Chemistry of a Novel Class of Organoplatinum Square Macrocycles}, volume={119}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja972668s}, DOI={10.1021/ja972668s}, abstractNote={Six nanoscale molecular squares are reported. They are prepared in essentially quantitative yields via spontaneous self-assembly of preprogrammed 90° angular units with diverse bimetallic linear linkers. Characterization was accomplished with multinuclear NMR and, in two cases, via ESI-FTICR mass spectral data. The size of these novel metallomacrocycles range from 3.6 nm (diagonal) and 2.6 nm (side) for the smallest to 4.7 nm (diagonal) and 3.4 nm (side) for the largest as estimated by extensible systematic force field calculations. The molecular squares incorporating alkynyl units as corners are able to complex four Ag+ ions via the π-tweezer effect.}, number={48}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Manna, Joseph and Kuehl, Christopher J. and Whiteford, Jeffery A. and Stang, Peter J. and Muddiman, David C. and Hofstadler, Steven A. and Smith, Richard D.}, year={1997}, month={Dec}, pages={11611–11619} }
 @article{stang_olenyuk_muddiman_smith_1997, title={Transition-Metal-Mediated Rational Design and Self-Assembly of Chiral, Nanoscale Supramolecular Polyhedra with UniqueTSymmetry†}, volume={16}, ISSN={0276-7333 1520-6041}, url={http://dx.doi.org/10.1021/om9702993}, DOI={10.1021/om9702993}, abstractNote={A novel family of chiral, discrete, nanoscale-sized supramolecular cages are prepared, via self-assembly and noncovalent interactions from the tridentate ligand 1,3,5-tris[(4-pyridyl)ethynyl]benzene and [(R)-(+)-BINAP]PdII and -PtII bis(triflates). The cationic parts of these highly symmetrical species possess large three-dimensional cavities and are rare examples of molecules with T symmetry.}, number={14}, journal={Organometallics}, publisher={American Chemical Society (ACS)}, author={Stang, Peter J. and Olenyuk, Bogdan and Muddiman, David C. and Smith, Richard D.}, year={1997}, month={Jul}, pages={3094–3096} }
 @article{gusev_muddiman_proctor_sharkey_tata_venkataramanan_hercules_1996, title={A Quantitative Study ofin vitroHepatic Metabolism of Tacrolimus (FK506) Using Secondary Ion and Matrix-assisted Laser Desorption/Ionization Mass Spectrometry}, volume={10}, ISSN={0951-4198 1097-0231}, url={http://dx.doi.org/10.1002/(sici)1097-0231(19960731)10:10<1215::aid-rcm647>3.0.co;2-k}, DOI={10.1002/(sici)1097-0231(19960731)10:10<1215::aid-rcm647>3.0.co;2-k}, abstractNote={The identification and simultaneous quantification of Tacrolimus and its hepatic metabolites in baboons has been achieved using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry and static secondary-ion mass spectrometry (TOF-SIMS). Little fragmentation, high sensitivity and tolerance to contamination are the major advantages of these methods, allowing facile identification and quantification of metabolites produced in vitro with minor analyte isolation. Based on the MALDI and TOF-SIMS results, seven metabolites have been identified: de-methylated, di de-methylated, hydroxylated, di hydroxylated, de-methylated hydroxylated, dihydrodiol, and di de-methylated hydroxylated. The concentrations of the parent drug and its major metabolites (e.g. de-methylated, di de-methylated) were measured using Rapamycin as an internal standard. The time course of Tacrolimus and its major metabolites as a function of incubation time was calculated. Good correlation between SIMS and MALDI results was obtained.}, number={10}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Gusev, Arkady I. and Muddiman, David C. and Proctor, Andrew and Sharkey, Andrew G. and Tata, Prasad N. V. and Venkataramanan, Raman and Hercules, David M.}, year={1996}, month={Jul}, pages={1215–1218} }
 @article{wunschel_fox_fox_bruce_muddiman_smith_1996, title={Analysis of Double-stranded Polymerase Chain Reaction Products from the Bacillus cereus Group by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry}, volume={10}, number={1}, journal={Rapid Communications in Mass Spectrometry}, author={Wunschel, D.S. and Fox, K.F. and Fox, A. and Bruce, J.E. and Muddiman, D.C. and Smith, R.D.}, year={1996}, pages={29–35} }
 @article{muddiman_wunschel_liu_paša-tolić_fox_fox_anderson_smith_1996, title={Characterization of PCR Products from Bacilli Using Electrospray Ionization FTICR Mass Spectrometry}, volume={68}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac960689j}, DOI={10.1021/ac960689j}, abstractNote={A procedure for rapid purification of polymerase chain reaction (PCR) products allowing precise molecular weight determination using electrospray ionization-Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry is described. PCR amplification utilized the DNA polymerase from Pyrococcus furiosus (Pfu) which, unlike Taq, does not incorporate a nontemplated terminal deoxyadenosine phosphate. An 89-base pair nucleotide portion of the spacer region between the 16S and 23S ribosomal rRNA genes was amplified from the genome of three members of Bacillus cereus group and a 114 nucleotide region from the Bacillus subtilis. PCR involves polymerization of nucleotide precursors using two oligonucleotide primers and an amplification enzyme, as well as the presence of metal ions. Mass spectrometric analysis greatly benefits from removal of the oligonucleotide primers (15- and 17-mers in this instance) and nucleotide precursors since they adversely affect sensitivity and metal ion adduction results in an inaccurate molecular weight determination. In the presence of guanidinium hydrochloride the PCR products bind preferentially to a silica resin, allowing removal of other components (i.e., dNTP's primers, and salts). Further removal of metal ions was accomplished using a microdialysis device, allowing samples to be pumped through a hollow cellulose fiber with external countercurrent flow of 2.5 mM ammonium acetate. Prior to injection into the mass spectrometer, the sample buffer was adjusted to 50 vol % acetronitrile, 25 mM piperidine, and 25 mM imidazole, which enhanced signal intensity. The molecular weights of the PCR products determined by nucleotide sequence and MS analysis were in excellent agreement, and several PCR products were analyzed where mass differences corresponding to single base substitutions could be accurately assigned. These assignments were possible due to the high mass precision, accuracy, and resolution FTICR inherently affords. This constitutes the first report demonstrating the ionization and detection of PCR products by mass spectrometry with mass precision and accuracy for assignment of such modifications or substitutions.}, number={21}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Wunschel, David S. and Liu, Chuanliang and Paša-Tolić, Ljiljana and Fox, Karen F. and Fox, Alvin and Anderson, Gordon A. and Smith, Richard D.}, year={1996}, month={Jan}, pages={3705–3712} }
 @article{muddiman_cheng_udseth_smith_1996, title={Charge-state reduction with improved signal intensity of oligonucleotides in electrospray ionization mass spectrometry}, volume={7}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/1044-0305(96)80516-2}, DOI={10.1016/1044-0305(96)80516-2}, abstractNote={The shift of charge states of oligonucleotide negative ions formed in electrospray ionization mass spectrometry to higher mass-to-charge ratio has been accomplished by addition of organic acids and bases to the solution to be electrosprayed. The use of acetic acid or formic acid combined with piperidine and imidazole effectively reduced charge states. Signal intensity and stability were enhanced greatly when the infused solution contained a high percentage of acetonitrile. In addition, the cocktail that contained imidazole, piperidine, and acetic acid in 80% acetonitrile not only reduced charge states, but also substantially suppressed Na adduction. Several oligonucleotides that varied in base composition and length were investigated, and studies of mixtures showed a significant reduction in spectral complexity.}, number={8}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Cheng, Xueheng and Udseth, Harold R. and Smith, Richard D.}, year={1996}, month={Aug}, pages={697–706} }
 @article{manna_whiteford_stang_muddiman_smith_1996, title={Design and Self-Assembly of Nanoscale Organoplatinum Macrocycles}, volume={118}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja962041u}, DOI={10.1021/ja962041u}, abstractNote={Herein we describe the synthesis and characterization of two novel organometallic nanodimensional macrocycles. In contrast to our previously reported macrocycles, these new complexes display two trans-platinum linear linkages along the sides of the square, as well as platinum or iodonium centers with roughly 90{degree} geometries at the corners of the macrocycle. We propose that these new organometallic macrocycles, and other similar complexes currently under investigation, will be potentially useful devices, particularly in the area of organic synthesis and organometallic catalysis. Furthermore, complex 7 is of significant interest in regard to its potential nonlinear optical and electronic properties, given the presence of metal-alkynyl units and possible {pi}-conjugation within the macrocycle frame. 18 refs.}, number={36}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Manna, Joseph and Whiteford, Jeffery A. and Stang, Peter J. and Muddiman, David C. and Smith, Richard D.}, year={1996}, month={Jan}, pages={8731–8732} }
 @article{muddiman_gusev_martin_hercules_1996, title={Direct quantification of cocaine in urine by time-of-flight mass spectrometry}, volume={354}, ISSN={0937-0633 1432-1130}, url={http://dx.doi.org/10.1007/s002169600017}, DOI={10.1007/s002169600017}, number={1}, journal={Fresenius' Journal of Analytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Muddiman, David C. and Gusev, Arkady I. and Martin, Lee B. and Hercules, David M.}, year={1996}, month={Jan}, pages={103–110} }
 @article{nicola_muddiman_hercules_1996, title={Enhancement of ion intensity in time-of-flight secondary-ionization mass spectrometry}, volume={7}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1016/1044-0305(96)00006-2}, DOI={10.1016/1044-0305(96)00006-2}, abstractNote={Enhancement of ion intensity in static secondary-ionization mass spectrometry (SIMS) has been achieved by using a matrix-assisted sample preparation technique. Previous investigations of polymers and biomolecules by SIMS indicated that secondary-ion (SI) yield is dependent on substrate coverage. Recently we discovered a sample preparation technique that enhanced the SI yield of cyclosporin A (CsA) in an allograft patient sample and neat samples of CsA (1202 u) and polystyrene (M w=2650 u). The preparation technique involves deposition of a submonolayer of cocaine hydrochloride (5 µL of a 20-µg/mL MeOH solution) on an etched silver substrate, solvent evaporation, and subsequent deposition of the analyte. This preparation method resulted in ∼300% increase in the SI yield of CsA and polystyrene when deposited from neat solutions. The original discovery was observed when a blood extract that contained CsA was deposited on an etched Ag substrate that had been soaking in a dilute cocaine solution for ∼2 months. In these initial experiments, the SI yield of CsA was enhanced by over 1 order of magnitude.}, number={5}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Nicola, Anthony J. and Muddiman, David C. and Hercules, David M.}, year={1996}, month={May}, pages={467–472} }
 @article{muddiman_nicola_proctor_hercules_1996, title={Important Aspects concerning the Quantification of Biomolecules by Time-of-Flight Secondary-Ion Mass Spectrometry}, volume={50}, ISSN={0003-7028 1943-3530}, url={http://dx.doi.org/10.1366/0003702963906410}, DOI={10.1366/0003702963906410}, abstractNote={Fundamental aspects regarding the use of time-of-flight secondary-ion mass spectrometry (TOF-SIMS) as a quantitative tool for the analysis of organic compounds are reported. The following factors are discussed: (1) the use of Poisson's law to correct for dead-time in single-ion data collection; (2) practical considerations concerning the analysis of “real world” samples; and (3) the effect of the etching process on the reproducibility of the intensity ratio (analyte/internal standard) of Ag-cationized species. To evaluate the importance of these factors, we used cocaine and cyclosporin A (CsA) as analytes because they show protonated and Ag-cationized species, respectively, in their SIMS spectra. Correction for detector dead-time using Poisson's law of single-ion counting expanded the dynamic range for cocaine by ∼2 orders of magnitude. For analyses requiring only a small dynamic range (i.e., CsA), the correction improved the % RSD of the slope from 2.43 to 0.87%. The maximum secondary-ion (SI) yield of CsA (Ag-cationized species) occurs at a CsA concentration ∼3 orders of magnitude higher than the therapeutic levels in blood (25–2000 ng/mL). It is discussed how this problem should be addressed. Analysis of variance (ANOVA) indicates that Ag substrates must be etched under identical conditions to obtain quantitative results when species requiring cationization are being analyzed.}, number={2}, journal={Applied Spectroscopy}, publisher={SAGE Publications}, author={Muddiman, David C. and Nicola, Anthony J. and Proctor, Andrew and Hercules, David M.}, year={1996}, month={Feb}, pages={161–166} }
 @article{muddiman_rockwood_gao_severs_udseth_smith_proctor_1995, title={Application of Sequential Paired Covariance to Capillary Electrophoresis Electrospray Ionization Time-of-Flight Mass Spectrometry: Unraveling the Signal from the Noise in the Electropherogram}, volume={67}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac00119a027}, DOI={10.1021/ac00119a027}, abstractNote={The combination of capillary electrophoresis (CE) with electrospray ionization (ESI) time-of-flight mass spectrometry (TOF-MS) has recently been demonstrated. When CE is combined with TOF-MS using an electrospray interface, the method provides fast, high-resolution separations with rapid mass analysis and the potential for very high sensitivity. In analyzing the data, one first reconstructs an electropherogram from the data set and then identifies peaks in the mass spectra. The mass spectra corresponding to the peaks in the electropherogram are then inspected to enable solute identification. However, background noise often prevents detection of peaks in the reconstructed electropherogram, thus interfering with the analysis. In this work we demonstrate alternative electropherogram reconstruction techniques that enhance its signal-to-noise ratio, allowing more immediate identification of the number of components in a mixture and their corresponding retention times. The techniques described here should also be adaptable for on-line analysis of CE-ESI-TOF data and the combination with other separation techniques coupled to mass spectrometry (e.g., LC/MS), as well as any multichannel detection scheme. 21 refs., 4 figs., 1 tab.}, number={23}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Rockwood, Alan L. and Gao, Quanyin. and Severs, Joanne C. and Udseth, Harold R. and Smith, Richard D. and Proctor, Andrew.}, year={1995}, month={Dec}, pages={4371–4375} }
 @article{muddiman_gusev_hercules_1995, title={Application of secondary ion and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for the quantitative analysis of biological molecules}, volume={14}, ISSN={0277-7037 1098-2787}, url={http://dx.doi.org/10.1002/mas.1280140603}, DOI={10.1002/mas.1280140603}, abstractNote={AbstractThis review primarily focuses on the current status of two solid‐state mass spectrometric (MS) techniques, namely, static secondary‐ion (SIMS) and matrix‐assisted laser desorption‐ionization (MALDI) time‐of‐fight (TOF) maSs spectrometry, as applied to the quantification of biological materials. Although a number of articles have appeared in the literature for both SIMS and MALDI quantitative analysis, neither field has been extensively researched nor currently used in general practice. However, several results are very exciting and offer advantages over conventional methods. The abilities and limitations of MALDI and SIMS for quantitative analysis of biological molecules will be discussed at the fundamental and applied level. Use of an internal standard approach, development of instrumental protocols, and sample preparation will be examined in detail. Various examples demonstrating the feasibility of quantitative analysis by MALDI and SIMS, including quantification of in vivo and in vitro metabolism of drugs in real biological matrices, will be reviewed. © 1996 John Wiley & Sons, Inc.}, number={6}, journal={Mass Spectrometry Reviews}, publisher={Wiley}, author={Muddiman, David C. and Gusev, Arkady I. and Hercules, David M.}, year={1995}, month={Nov}, pages={383–429} }
 @article{muddiman_gusev_stoppek-langner_proctor_hercules_tata_venkataramanan_diven_1995, title={Simultaneous quantification of cyclosporin A and its major metabolites by time-of-flight secondary-ion mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry utilizing data analysis techniques: Comparison with high-performance liquid chromatography}, volume={30}, ISSN={1076-5174 1096-9888}, url={http://dx.doi.org/10.1002/jms.1190301013}, DOI={10.1002/jms.1190301013}, abstractNote={AbstractSimultaneous quantification of cyclosporin A (CsA) and its major metabolite (AM1) in blood has been achieved using time‐of‐flight secondary‐ion mass spectrometry (TOF‐SIMS) and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI/TOF‐MS). Previous investigations indicated that spectral interferences exist in the analysis of CsA blood samples by the above methods. In TOF‐SIMS, interference is caused by overlap of the Ag‐cationized internal standard, cyclosporin D (CsD), with the Ag‐cationized metabolite, AM1. To resolve this interference and obtain quantitative information, cross‐correlation analysis was applied to the TOF‐SIMS data. Application of damped non‐linear least squares curve‐fitting was carried out to resolve an interference in the MALDI/TOF‐MS data due to multiple cationization products (i.e. Na and K). Measurement of standard samples indicates that the minimum accuracy (95% confidence level) of the TOF‐SIMS method was better than 9% for CsA and 13% for AM1 using only one standard curve'. Similarly, the minimum accuracy of the MALDI/TOF‐MS method was determined to be 14% for CsA and better than 25% for AM1. Blood samples obtained from transplant patients receiving CsA were analyzed by polyclonal fluorescence polarization immunoassay, high‐performance liquid chromatography (HPLC), and by both TOF‐MS methods. Both TOF‐MS results for CsA and mono‐hydroxylated CsA are in good agreement with the HPLC results.}, number={10}, journal={Journal of Mass Spectrometry}, publisher={Wiley}, author={Muddiman, David C. and Gusev, Arkady I. and Stoppek-Langner, Karl and Proctor, Andrew and Hercules, David M. and Tata, Prasad and Venkataramanan, Raman and Diven, Warren}, year={1995}, month={Oct}, pages={1469–1479} }
 @article{muddiman_brockman_proctor_houalla_hercules_1994, title={Characterization of Polystyrene on Etched Silver Using Ion Scattering and X-ray Photoelectron Spectroscopy: Correlation of Secondary Ion Yield in Time-of-Flight SIMS with Surface Coverage}, volume={98}, ISSN={0022-3654 1541-5740}, url={http://dx.doi.org/10.1021/j100095a044}, DOI={10.1021/j100095a044}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of Polystyrene on Etched Silver Using Ion Scattering and X-ray Photoelectron Spectroscopy: Correlation of Secondary Ion Yield in Time-of-Flight SIMS with Surface CoverageDavid C. Muddiman, Adam H. Brockman, Andrew Proctor, Marwan Houalla, and David M. HerculesCite this: J. Phys. Chem. 1994, 98, 44, 11570–11575Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://doi.org/10.1021/j100095a044RIGHTS & PERMISSIONSArticle Views111Altmetric-Citations29LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (688 KB) Get e-Alerts}, number={44}, journal={The Journal of Physical Chemistry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Brockman, Adam H. and Proctor, Andrew and Houalla, Marwan and Hercules, David M.}, year={1994}, month={Nov}, pages={11570–11575} }
 @article{muddiman_gusev_proctor_hercules_venkataraman_diven_1994, title={Quantitative Measurement of Cyclosporin A in Blood by Time-of-Flight Mass Spectrometry}, volume={66}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac00086a023}, DOI={10.1021/ac00086a023}, abstractNote={Analytical methods have been developed for the detection and quantification of cyclosporin A (CsA) in blood using time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF-MS). Linear calibration curves were obtained for both methods in the range 25-2000 ng/mL in whole blood. The limit of detection (LOD) and limit of quantification (LOQ) were determined to be 7 and 23 ng/mL, respectively, for the TOF-SIMS method; the LOD and LOQ were 10 and 33 ng/mL, respectively, for the MALDI/TOF-MS method. Coefficients of variation ranged from 3 to 5% for the TOF-SIMS method and from 4 to 8% for the MALDI/TOF-MS method. Blood samples were also analyzed by a nonspecific method, fluorescence polarization immunoassay (FPIA), and by a specific method, high-performance liquid chromatography (HPLC). The TOF-MS results are in good agreement with the HPLC results, but not with the FPIA results. The TOF-MS methods can also provide information about CsA metabolites.}, number={14}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Muddiman, David C. and Gusev, Arkady I. and Proctor, Andrew. and Hercules, David M. and Venkataraman, Raman. and Diven, Warren.}, year={1994}, month={Jul}, pages={2362–2368} }