@article{gentry_collins_panitchpakdi_belda-ferre_stewart_terrazas_lu_zuffa_yan_avila-pacheco_et al._2024, title={Reverse metabolomics for the discovery of chemical structures from humans}, volume={626}, ISSN={["1476-4687"]}, DOI={10.1038/s41586-023-06906-8}, abstractNote={Abstract}, number={7998}, journal={NATURE}, author={Gentry, Emily C. and Collins, Stephanie L. and Panitchpakdi, Morgan and Belda-Ferre, Pedro and Stewart, Allison K. and Terrazas, Marvic Carrillo and Lu, Hsueh-han and Zuffa, Simone and Yan, Tingting and Avila-Pacheco, Julian and et al.}, year={2024}, month={Feb} }
 @article{chappel_king_fleming_eberlin_reif_baker_2023, title={Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics}, volume={8}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.3c02389}, abstractNote={Mass spectrometry imaging (MSI) has gained increasing popularity for tissue-based diagnostics due to its ability to identify and visualize molecular characteristics unique to different phenotypes within heterogeneous samples. Data from MSI experiments are often assessed and visualized using various supervised and unsupervised statistical approaches. However, these approaches tend to fall short in identifying and concisely visualizing subtle, phenotype-relevant molecular changes. To address these shortcomings, we developed aggregated molecular phenotype (AMP) scores. AMP scores are generated using an ensemble machine learning approach to first select features differentiating phenotypes, weight the features using logistic regression, and combine the weights and feature abundances. AMP scores are then scaled between 0 and 1, with lower values generally corresponding to class 1 phenotypes (typically control) and higher scores relating to class 2 phenotypes. AMP scores, therefore, allow the evaluation of multiple features simultaneously and showcase the degree to which these features correlate with various phenotypes. Due to the ensembled approach, AMP scores are able to overcome limitations associated with individual models, leading to high diagnostic accuracy and interpretability. Here, AMP score performance was evaluated using metabolomic data collected from desorption electrospray ionization MSI. Initial comparisons of cancerous human tissues to their normal or benign counterparts illustrated that AMP scores distinguished phenotypes with high accuracy, sensitivity, and specificity. Furthermore, when combined with spatial coordinates, AMP scores allow visualization of tissue sections in one map with distinguished phenotypic borders, highlighting their diagnostic utility.}, journal={ANALYTICAL CHEMISTRY}, author={Chappel, Jessie R. and King, Mary E. and Fleming, Jonathon and Eberlin, Livia S. and Reif, David M. and Baker, Erin S.}, year={2023}, month={Aug} }
 @article{foley_walker_stewart_o'flaherty_gentry_patel_beaty_allen_pan_simpson_et al._2023, title={Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut}, volume={3}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-023-01337-7}, abstractNote={Abstract}, journal={NATURE MICROBIOLOGY}, author={Foley, Matthew H. and Walker, Morgan E. and Stewart, Allison K. and O'Flaherty, Sarah and Gentry, Emily C. and Patel, Shakshi and Beaty, Violet V. and Allen, Garrison and Pan, Meichen and Simpson, Joshua B. and et al.}, year={2023}, month={Mar} }
 @article{ryan_kostelic_hsieh_powers_aspinwall_dodds_schiel_marty_baker_2023, title={Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods}, volume={34}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.3c00321}, abstractNote={Adeno-associated virus (AAV) capsids are among the leading gene delivery platforms used to treat a vast array of human diseases and conditions. AAVs exist in a variety of serotypes due to differences in viral protein (VP) sequences with distinct serotypes targeting specific cells and tissues. As the utility of AAVs in gene therapy increases, ensuring their specific composition is imperative for the correct targeting and gene delivery. From a quality control perspective, current analytical tools are limited in their selectivity for viral protein (VP) subunits due to their sequence similarities, instrumental difficulties in assessing the large molecular weights of intact capsids, and the uncertainty in distinguishing empty and filled capsids. To address these challenges, we combined two distinct analytical workflows that assess the intact capsids and VP subunits separately. First, a selective temporal overview of resonant ion (STORI)-based charge detection-mass spectrometry (CD-MS) was applied for characterization of the intact capsids. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations were then used for the capsid denaturing measurements. This multimethod combination was applied to three AAV serotypes (AAV2, AAV6, and AAV8) to evaluate their intact empty and filled capsid ratios and then examine the distinct VP sequences and modifications present.}, number={12}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Ryan, Jack P. and Kostelic, Marius M. and Hsieh, Chih-Chieh and Powers, Joshua and Aspinwall, Craig and Dodds, James N. and Schiel, John E. and Marty, Michael T. and Baker, Erin S.}, year={2023}, month={Nov}, pages={2811–2821} }
 @article{cordova_klaren_ford_grimm_baker_zhou_wright_rusyn_2023, title={Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams}, volume={11}, ISSN={["2305-6304"]}, url={https://www.mdpi.com/2305-6304/11/7/586}, DOI={10.3390/toxics11070586}, abstractNote={Human cell-based test methods can be used to evaluate potential hazards of mixtures and products of petroleum refining (“unknown or variable composition, complex reaction products, or biological materials” substances, UVCBs). Analyses of bioactivity and detailed chemical characterization of petroleum UVCBs were used separately for grouping these substances; a combination of the approaches has not been undertaken. Therefore, we used a case example of representative high production volume categories of petroleum UVCBs, 25 lower olefin substances from low benzene naphtha and resin oils categories, to determine whether existing manufacturing-based category grouping can be supported. We collected two types of data: nontarget ion mobility spectrometry-mass spectrometry of both neat substances and their organic extracts and in vitro bioactivity of the organic extracts in five human cell types: umbilical vein endothelial cells and induced pluripotent stem cell-derived hepatocytes, endothelial cells, neurons, and cardiomyocytes. We found that while similarity in composition and bioactivity can be observed for some substances, existing categories are largely heterogeneous. Strong relationships between composition and bioactivity were observed, and individual constituents that determine these associations were identified. Overall, this study showed a promising approach that combines chemical composition and bioactivity data to better characterize the variability within manufacturing categories of petroleum UVCBs.}, number={7}, journal={TOXICS}, author={Cordova, Alexandra C. and Klaren, William D. and Ford, Lucie C. and Grimm, Fabian A. and Baker, Erin S. and Zhou, Yi-Hui and Wright, Fred A. and Rusyn, Ivan}, year={2023}, month={Jul} }
 @article{stewart_foley_dougherty_mcgill_gulati_gentry_hagey_dorrestein_theriot_dodds_et al._2023, title={Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems}, volume={95}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.3c03057}, abstractNote={Bile acids play key roles in nutrient uptake, inflammation, signaling, and microbiome composition. While previous bile acid analyses have primarily focused on profiling 5 canonical primary and secondary bile acids and their glycine and taurine amino acid-bile acid (AA-BA) conjugates, recent studies suggest that many other microbial conjugated bile acids (or MCBAs) exist. MCBAs are produced by the gut microbiota and serve as biomarkers, providing information about early disease onset and gut health. Here we analyzed 8 core bile acids synthetically conjugated with 22 proteinogenic and nonproteogenic amino acids totaling 176 MCBAs. Since many of the conjugates were isomeric and only 42 different m/z values resulted from the 176 MCBAs, a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) was used for their separation. Their molecular characteristics were then used to create an in-house extended bile acid library for a combined total of 182 unique compounds. Additionally, ∼250 rare bile acid extracts were also assessed to provide additional resources for bile acid profiling and identification. This library was then applied to healthy mice dosed with antibiotics and humans having fecal microbiota transplantation (FMT) to assess the MCBA presence and changes in the gut before and after each perturbation.}, number={41}, journal={ANALYTICAL CHEMISTRY}, author={Stewart, Allison K. and Foley, Matthew H. and Dougherty, Michael K. and Mcgill, Sarah K. and Gulati, Ajay S. and Gentry, Emily C. and Hagey, Lee R. and Dorrestein, Pieter C. and Theriot, Casey M. and Dodds, James N. and et al.}, year={2023}, month={Oct}, pages={15357–15366} }
 @article{butler_baker_2022, title={A High-Throughput Ion Mobility Spectrometry-Mass Spectrometry Screening Method for Opioid Profiling}, volume={9}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.2c00186}, abstractNote={In 2017, the United States Department of Health and Human Services declared the widespread misuse and abuse of prescription and illicit opioids an epidemic. However, this epidemic dates back to the 1990s when opioids were extensively prescribed for pain management. Currently, opioids are still recommended for pain management, and given their abuse potential, rapid screening is imperative for patient treatment. Of particular importance is assessing pain management patient compliance, where evaluating drug use is crucial for preventing opioid abuse and potential overdoses. In this work, we utilized drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) to develop a rapid screening method for 33 target opioids and opioid urinary metabolites. Collision cross section values were determined for all target molecules using a flow-injection DTIMS-MS method, and clear differentiation of 27 out of the 33 opioids without prior chromatographic separation was observed when utilizing a high resolution demultiplexing screening approach. An automated solid phase extraction (SPE) platform was then coupled to DTIMS-MS for 10 s sample-to-sample analyses. This SPE-IMS-MS approach enabled the rapid screening of urine samples for opioids and presents a major improvement in sample throughput compared to traditional chromatographic analyses coupled with MS, which routinely take several minutes per sample. Overall, this vast reduction in analysis time facilitates a faster turn-around for patient samples, providing great benefits to clinical applications.}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Butler, Karen E. and Baker, Erin S.}, year={2022}, month={Sep} }
 @article{bilbao_gibbons_stow_kyle_bloodsworth_payne_smith_ibrahim_baker_fjeldsted_2022, title={A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows}, volume={21}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00425}, abstractNote={The ability to improve the data quality of ion mobility-mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Bilbao, Aivett and Gibbons, Bryson C. and Stow, Sarah M. and Kyle, Jennifer E. and Bloodsworth, Kent J. and Payne, Samuel H. and Smith, Richard D. and Ibrahim, Yehia M. and Baker, Erin S. and Fjeldsted, John C.}, year={2022}, month={Mar}, pages={798–807} }
 @article{valdiviezo_aly_luo_cordova_casillas_foster_baker_rusyn_2022, title={Analysis of per- and polyfluoroalkyl substances in Houston Ship Channel and Galveston Bay following a large-scale industrial fire using ion-mobility-spectrometry-mass spectrometry}, volume={115}, ISSN={["1878-7320"]}, DOI={10.1016/j.jes.2021.08.004}, abstractNote={Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants of concern because of their ubiquitous presence in surface and ground water; analytical methods that can be used for rapid comprehensive exposure assessment and fingerprinting of PFAS are needed. Following the fires at the Intercontinental Terminals Company (ITC) in Deer Park, TX in 2019, large quantities of PFAS-containing firefighting foams were deployed. The release of these substances into the Houston Ship Channel/Galveston Bay (HSC/GB) prompted concerns over the extent and level of PFAS contamination. A targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based study of temporal and spatial patterns of PFAS associated with this incident revealed presence of 7 species; their levels gradually decreased over a 6-month period. Because the targeted LC-MS/MS analysis was focused on about 30 PFAS molecules, it may have missed other PFAS compounds present in firefighting foams. Therefore, we utilized untargeted LC-ion mobility spectrometry-mass spectrometry (LC-IMS-MS)-based analytical approach for a more comprehensive characterization of PFAS in these water samples. We analyzed 31 samples from 9 sites in the HSC/GB that were collected over 5 months after the incident. Our data showed that additional 19 PFAS were detected in surface water of HSC/GB, most of them decreased gradually after the incident. PFAS features detected by LC-MS/MS correlated well in abundance with LC-IMS-MS data; however, LC-IMS-MS identified a number of additional PFAS, many known to be components of firefighting foams. These findings therefore illustrate that untargeted LC-IMS-MS improved our understanding of PFAS presence in complex environmental samples.}, journal={JOURNAL OF ENVIRONMENTAL SCIENCES}, author={Valdiviezo, Alan and Aly, Noor A. and Luo, Yu-Syuan and Cordova, Alexandra and Casillas, Gaston and Foster, MaKayla and Baker, Erin S. and Rusyn, Ivan}, year={2022}, month={May}, pages={350–362} }
 @article{doyle_odenkirk_stewart_nelson_baker_cruz_2022, title={Assessing the Fate of Dissolved Organic Compounds in Landfill Leachate and Wastewater Treatment Systems}, volume={11}, ISSN={["2690-0637"]}, url={https://doi.org/10.1021/acsestwater.2c00320}, DOI={10.1021/acsestwater.2c00320}, abstractNote={Landfill leachate and municipal wastewater are major sources of chemical pollutants that contaminate our drinking water sources. Evaluating the dissolved organic chemical composition in wastewater treatment plants is therefore essential to understand how the discharge impacts the environment, wildlife, and human health. In this study, we utilized a nontargeted analysis method coupling liquid chromatography and tandem mass spectrometry (LC-MS/MS) to analyze chemical features at different points along two landfill leachate treatment plants (LLTPs) and two municipal wastewater treatment plants (WWTPs) in the Southeastern United States. Significant feature differences were observed for the WWTPs where activated sludge clarification was employed versus the LLTPs utilizing reverse osmosis. Specifically, even though both LLTPs had the largest number of features in their influent water, their effluent following reverse osmosis yielded a lower number of features than the WWTPs. Additionally, the clarification processes of each WWTP exhibited different efficiencies as chemical disinfection removed more features than UV disinfection. Feature identification was then made using the LC, MS, and MS/MS information. Analysis of the identified molecules showed that lipids were the most effectively removed from all plants, while alkaloid and organic nitrogen compounds were the most recalcitrant.}, journal={ACS ES&T WATER}, author={Doyle, Michael G. and Odenkirk, Melanie T. and Stewart, Allison K. and Nelson, Jacob P. and Baker, Erin S. and Cruz, Florentino}, year={2022}, month={Nov} }
 @article{rainey_watson_asef_foster_baker_fernandez_2022, title={CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics}, volume={12}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.2c03491}, abstractNote={Metabolite annotation continues to be the widely accepted bottleneck in nontargeted metabolomics workflows. Annotation of metabolites typically relies on a combination of high-resolution mass spectrometry (MS) with parent and tandem measurements, isotope cluster evaluations, and Kendrick mass defect (KMD) analysis. Chromatographic retention time matching with standards is often used at the later stages of the process, which can also be followed by metabolite isolation and structure confirmation utilizing nuclear magnetic resonance (NMR) spectroscopy. The measurement of gas-phase collision cross-section (CCS) values by ion mobility (IM) spectrometry also adds an important dimension to this workflow by generating an additional molecular parameter that can be used for filtering unlikely structures. The millisecond timescale of IM spectrometry allows the rapid measurement of CCS values and allows easy pairing with existing MS workflows. Here, we report on a highly accurate machine learning algorithm (CCSP 2.0) in an open-source Jupyter Notebook format to predict CCS values based on linear support vector regression models. This tool allows customization of the training set to the needs of the user, enabling the production of models for new adducts or previously unexplored molecular classes. CCSP produces predictions with accuracy equal to or greater than existing machine learning approaches such as CCSbase, DeepCCS, and AllCCS, while being better aligned with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Another unique aspect of CCSP 2.0 is its inclusion of a large library of 1613 molecular descriptors via the Mordred Python package, further encoding the fine aspects of isomeric molecular structures. CCS prediction accuracy was tested using CCS values in the McLean CCS Compendium with median relative errors of 1.25, 1.73, and 1.87% for the 170 [M - H]-, 155 [M + H]+, and 138 [M + Na]+ adducts tested. For superclass-matched data sets, CCS predictions via CCSP allowed filtering of 36.1% of incorrect structures while retaining a total of 100% of the correct annotations using a ΔCCS threshold of 2.8% and a mass error of 10 ppm.}, journal={ANALYTICAL CHEMISTRY}, author={Rainey, Markace A. and Watson, Chandler A. and Asef, Carter K. and Foster, Makayla R. and Baker, Erin S. and Fernandez, Facundo M.}, year={2022}, month={Dec} }
 @article{roman-hubers_cordova_rohde_chiu_mcdonald_wright_dodds_baker_rusyn_2022, title={Characterization of compositional variability in petroleum substances}, volume={317}, ISSN={["1873-7153"]}, DOI={10.1016/j.fuel.2022.123547}, abstractNote={In the process of registration of substances of Unknown or Variable Composition, Complex Reaction Products or Biological Materials (UVCBs), information sufficient to enable substance identification must be provided. Substance identification for UVCBs formed through petroleum refining is particularly challenging due to their chemical complexity, as well as variability in refining process conditions and composition of the feedstocks. This study aimed to characterize compositional variability of petroleum UVCBs both within and across product categories. We utilized ion mobility spectrometry (IMS)-MS as a technique to evaluate detailed chemical composition of independent production cycle-derived samples of 6 petroleum products from 3 manufacturing categories (heavy aromatic, hydrotreated light paraffinic, and hydrotreated heavy paraffinic). Atmospheric pressure photoionization and drift tube IMS-MS were used to identify structurally related compounds and quantified between- and within-product variability. In addition, we determined both individual molecules and hydrocarbon blocks that were most variable in samples from different production cycles. We found that detailed chemical compositional data on petroleum UVCBs obtained from IMS-MS can provide the information necessary for hazard and risk characterization in terms of quantifying the variability of the products in a manufacturing category, as well as in subsequent production cycles of the same product.}, journal={FUEL}, author={Roman-Hubers, Alina T. and Cordova, Alexandra C. and Rohde, Arlean M. and Chiu, Weihsueh A. and McDonald, Thomas J. and Wright, Fred A. and Dodds, James N. and Baker, Erin S. and Rusyn, Ivan}, year={2022}, month={Jun} }
 @article{dodds_wang_patti_baker_2022, title={Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses}, volume={1}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.1c04430}, abstractNote={While the combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments, ensuring these prioritized features originate from endogenous metabolism remains challenging. Isotopologue workflows, such as isotopic ratio outlier analysis (IROA), mass isotopomer ratio analysis of U-13C labeled extracts (MIRACLE), and credentialing incorporate isotopic labels directly into metabolic precursors, guaranteeing that all features of interest are unequivocal byproducts of cellular metabolism. Furthermore, comprehensive separation and annotation of small molecules continue to challenge the metabolomics field, particularly for isomeric systems. In this paper, we evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) as an additional separation mechanism into standard LC-MS/MS isotopologue workflows. Since isotopically labeled molecules codrift in the IMS dimension with their 12C versions, LC-IMS-CID-MS provides four dimensions (LC, IMS, MS, and MS/MS) to directly investigate the metabolic activity of prioritized untargeted features. Here, we demonstrate this additional selectivity by showcasing how a preliminary data set of 30 endogeneous metabolites are putatively annotated from isotopically labeled Escherichia coli cultures when analyzed by LC-IMS-CID-MS. Metabolite annotations were based on several molecular descriptors, including accurate mass measurement, carbon number, annotated fragmentation spectra, and collision cross section (CCS), collectively illustrating the importance of incorporating IMS into isotopologue workflows. Overall, our results highlight the enhanced separation space and increased annotation confidence afforded by IMS for metabolic characterization and provide a unique perspective for future developments in isotopically labeled MS experiments.}, journal={ANALYTICAL CHEMISTRY}, author={Dodds, James N. and Wang, Lingjue and Patti, Gary J. and Baker, Erin S.}, year={2022}, month={Jan} }
 @article{zhu_schrecke_tang_odenkirk_walker_stover_lyu_zhang_russell_baker_et al._2022, title={Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions}, volume={144}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.2c00612}, abstractNote={TRAAK and TREK2 are two-pore domain K+ (K2P) channels and are modulated by diverse factors including temperature, membrane stretching, and lipids, such as phosphatidic acid. In addition, copper and zinc, both of which are essential for life, are known to regulate TREK2 and a number of other ion channels. However, the role of ions in the association of lipids with integral membrane proteins is poorly understood. Here, we discover cupric ions selectively modulate the binding of phosphatidylserine (PS) to TRAAK but not TREK2. Other divalent cations (Ca2+, Mg2+, and Zn2+) bind both channels but have no impact on binding PS and other lipids. Additionally, TRAAK binds more avidly to Cu2+ and Zn2+ than TREK2. In the presence of Cu2+, TRAAK binds similarly to PS with different acyl chains, indicating a crucial role of the serine headgroup in coordinating Cu2+. High-resolution native mass spectrometry (MS) enables the determination of equilibrium binding constants for distinct Cu2+-bound stoichiometries and uncovered the highest coupling factor corresponds to a 1:1 PS-to-Cu2+ ratio. Interestingly, the next three highest coupling factors had a ∼1.5:1 PS-to-Cu2+ ratio. Our findings bring forth the role of cupric ions as an essential cofactor in selective TRAAK-PS interactions.}, number={16}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Zhu, Yun and Schrecke, Samantha and Tang, Shuli and Odenkirk, Melanie T. and Walker, Thomas and Stover, Lauren and Lyu, Jixing and Zhang, Tianqi and Russell, David and Baker, Erin S. and et al.}, year={2022}, month={Apr}, pages={7048–7053} }
 @article{rampler_baker_kirkwood_schwaiger-haber_tam_jones_sherman_2022, title={Empowering women and addressing underrepresentation in the field of mass spectrometry}, volume={2}, ISSN={["1744-8387"]}, DOI={10.1080/14789450.2022.2039631}, abstractNote={Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; Department of Chemistry, North Carolina State University, Raleigh, NC, USA; Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA; Science and Engineering Directorate, Canada Border Services Agency, Ottawa, ON, Canada; Biocrates Life Sciences Ag, Innsbruck, Austria; MOBILion Systems, Inc, Chadds Ford, PA, USA}, journal={EXPERT REVIEW OF PROTEOMICS}, author={Rampler, Evelyn and Baker, Erin S. and Kirkwood, Kaylie I and Schwaiger-Haber, Michaela and Tam, Maggie and Jones, Marissa A. and Sherman, Melissa}, year={2022}, month={Feb} }
 @article{valdiviezo_kato_baker_chiu_rusyn_2022, title={Evaluation of Metabolism of a Defined Pesticide Mixture through Multiple In Vitro Liver Models}, volume={10}, ISSN={["2305-6304"]}, url={https://www.mdpi.com/2305-6304/10/10/566}, DOI={10.3390/toxics10100566}, abstractNote={The evaluation of exposure to multiple contaminants in a mixture presents a number of challenges. For example, the characterization of chemical metabolism in a mixture setting remains a research area with critical knowledge gaps. Studies of chemical metabolism typically utilize suspension cultures of primary human hepatocytes; however, this model is not suitable for studies of more extended exposures and donor-to-donor variability in a metabolic capacity is unavoidable. To address this issue, we utilized several in vitro models based on human-induced pluripotent stem cell (iPSC)-derived hepatocytes (iHep) to characterize the metabolism of an equimolar (1 or 5 µM) mixture of 20 pesticides. We used iHep suspensions and 2D sandwich cultures, and a microphysiological system OrganoPlate® 2-lane 96 (MimetasTM) that also included endothelial cells and THP-1 cell-derived macrophages. When cell culture media were evaluated using gas and liquid chromatography coupled to tandem mass spectrometry methods, we found that the parent molecule concentrations diminished, consistent with metabolic activity. This effect was most pronounced in iHep suspensions with a 1 µM mixture, and was lowest in OrganoPlate® 2-lane 96 for both mixtures. Additionally, we used ion mobility spectrometry–mass spectrometry (IMS-MS) to screen for metabolite formation in these cultures. These analyses revealed the presence of five primary metabolites that allowed for a more comprehensive evaluation of chemical metabolism in vitro. These findings suggest that iHep-based suspension assays maintain higher metabolic activity compared to 2D sandwich and OrganoPlate® 2-lane 96 model. Moreover, this study illustrates that IMS-MS can characterize in vitro metabolite formation following exposure to mixtures of environmental contaminants.}, number={10}, journal={TOXICS}, author={Valdiviezo, Alan and Kato, Yuki and Baker, Erin S. and Chiu, Weihsueh A. and Rusyn, Ivan}, year={2022}, month={Oct} }
 @article{butler_dodds_flick_campuzano_baker_2022, title={High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening}, volume={94}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.1c05533}, abstractNote={Isomeric peptide analyses are an analytical challenge of great importance to therapeutic monoclonal antibody and other biotherapeutic product development workflows. Aspartic acid (Asp, D) to isoaspartic acid (isoAsp, isoD) isomerization is a critical quality attribute (CQA) that requires careful control, monitoring, and quantitation during the drug discovery and production processes. While the formation of isoAsp has been implicated in a variety of disease states such as autoimmune diseases and several types of cancer, it is also understood that the formation of isoAsp results in a structural change impacting efficacy, potency, and immunogenic properties, all of which are undesirable. Currently, lengthy ultrahigh-performance liquid chromatography (UPLC) separations are coupled with MS for CQA analyses; however, these measurements often take over an hour and drastically limit analysis throughput. In this manuscript, drift tube ion mobility spectrometry-mass spectrometry (DTIMS-MS) and both a standard and high-resolution demultiplexing approach were utilized to study eight isomeric Asp and isoAsp peptide pairs. While the limited resolving power associated with the standard DTIMS analysis only separated three of the eight pairs, the application of HRdm distinguished seven of the eight and was only unable to separate DL and isoDL. The rapid high-throughput HRdm DTIMS-MS method was also interfaced with both flow injection and an automated solid phase extraction system to present the first application of HRdm for isoAsp and Asp assessment and demonstrate screening capabilities for isomeric peptides in complex samples, resulting in a workflow highly suitable for biopharmaceutical research needs.}, number={16}, journal={ANALYTICAL CHEMISTRY}, author={Butler, Karen E. and Dodds, James N. and Flick, Tawnya and Campuzano, Iain D. G. and Baker, Erin S.}, year={2022}, month={Apr}, pages={6191–6199} }
 @article{witchey_doyle_fredenburg_st armour_horman_odenkirk_aylor_baker_patisaul_2022, title={Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters}, volume={9}, ISSN={["1423-0194"]}, DOI={10.1159/000526959}, abstractNote={<b><i>Introduction:</i></b> Flame retardants (FRs) are common bodily and environmental pollutants, creating concern about their potential toxicity. We and others have found that the commercial mixture FireMaster® 550 (FM 550) or its individual brominated (BFR) and organophosphate ester (OPFR) components are potential developmental neurotoxicants. Using Wistar rats, we previously reported that developmental exposure to FM 550 or its component classes produced sex- and compound-specific effects on adult socioemotional behaviors. The underlying mechanisms driving the behavioral phenotypes are unknown. <b><i>Methods:</i></b> To further mechanistic understanding, here we conducted transcriptomics in parallel with a novel lipidomics approach using cortical tissues from newborn siblings of the rats in the published behavioral study. Inclusion of lipid composition is significant because it is rarely examined in developmental neurotoxicity studies. Pups were gestationally exposed via oral dosing to the dam to FM 550 or the BFR or OPFR components at environmentally relevant doses. <b><i>Results:</i></b> The neonatal cortex was highly sexually dimorphic in lipid and transcriptome composition, and males were more significantly impacted by FR exposure. Multiple adverse modes of action for the BFRs and OPFRs on neurodevelopment were identified, with the OPFRs being more disruptive than the BFRs via multiple mechanisms including dysregulation of mitochondrial function and disruption of cholinergic and glutamatergic systems. Disrupted mitochondrial function by environmental factors has been linked to a higher risk of autism spectrum disorders and neurodegenerative disorders. Impacted lipid classes included ceramides, sphingomyelins, and triacylglycerides. Robust ceramide upregulation in the OPFR females could suggest a heightened risk of brain metabolic disease. <b><i>Conclusions:</i></b> This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern. }, journal={NEUROENDOCRINOLOGY}, author={Witchey, S. K. and Doyle, M. G. and Fredenburg, J. D. and St Armour, G. and Horman, B. and Odenkirk, M. T. and Aylor, D. L. and Baker, E. S. and Patisaul, H. B.}, year={2022}, month={Sep} }
 @article{mcdonald_ejsing_kopczynski_holcapek_aoki_arita_arita_baker_bertrand-michel_bowden_et al._2022, title={Introducing the Lipidomics Minimal Reporting Checklist}, volume={8}, ISSN={["2522-5812"]}, DOI={10.1038/s42255-022-00628-3}, abstractNote={The rapid increase in lipidomic data has triggered a community-based movement to develop guidelines and minimum requirements for generating, reporting and publishing lipidomic data. The creation of a dynamic checklist summarizing key details of lipidomic analyses using a common language has the potential to harmonize the field by improving both traceability and reproducibility.}, journal={NATURE METABOLISM}, author={McDonald, Jeffrey G. and Ejsing, Christer S. and Kopczynski, Dominik and Holcapek, Michal and Aoki, Junken and Arita, Makoto and Arita, Masanori and Baker, Erin S. and Bertrand-Michel, Justine and Bowden, John A. and et al.}, year={2022}, month={Aug} }
 @article{kostelic_ryan_brown_jackson_hsieh_zak_sanders_liu_chen_byrne_et al._2022, title={Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry}, volume={8}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.2c02378}, abstractNote={Adeno-associated viral (AAV) vectors have emerged as gene therapy and vaccine delivery systems. Differential scanning fluorimetry or differential scanning calorimetry is commonly used to measure the thermal stability of AAVs, but these global methods are unable to distinguish the stabilities of different AAV subpopulations in the same sample. To address this challenge, we combined charge detection-mass spectrometry (CD-MS) with a variable temperature (VT) electrospray source that controls the temperature of the solution prior to electrospray. Using VT-CD-MS, we measured the thermal stabilities of empty and filled capsids. We found that filled AAVs ejected their cargo first and formed intermediate empty capsids before completely dissociating. Finally, we observed that pH stress caused a major decrease in thermal stability. This new approach better characterizes the thermal dissociation of AAVs, providing the simultaneous measurement of the stabilities and dissociation pathways of different subpopulations.}, journal={ANALYTICAL CHEMISTRY}, author={Kostelic, Marius M. and Ryan, Jack P. and Brown, Levi S. and Jackson, Tyler W. and Hsieh, Chih-Chieh and Zak, Ciara K. and Sanders, Henry M. and Liu, Yang and Chen, Victor Shugui and Byrne, Michael and et al.}, year={2022}, month={Aug} }
 @article{kostelic_hsieh_sanders_zak_ryan_baker_aspinwall_marty_2022, title={Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry}, volume={33}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.2c00087}, abstractNote={Native mass spectrometry (MS) and charge detection-mass spectrometry (CD-MS) have become versatile tools for characterizing a wide range of proteins and macromolecular complexes. Both commonly use nanoelectrospray ionization (nESI) from pulled borosilicate needles, but some analytes are known to nonspecifically adsorb to the glass, which may lower sensitivity and limit the quality of the data. To improve the sensitivity of native MS and CD-MS, we modified the surface of nESI needles with inert surface modifiers, including polyethylene-glycol. We found that the surface modification improved the signal intensity for native MS of proteins and for CD-MS of adeno-associated viral capsids. Based on mechanistic comparisons, we hypothesize that the improvement is more likely due to an increased flow rate with coated ESI needles rather than less nonspecific adsorption. In any case, these surface-modified needles provide a simple and inexpensive method for improving the sensitivity of challenging analytes.}, number={6}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Kostelic, Marius M. and Hsieh, Chih-Chieh and Sanders, Henry M. and Zak, Ciara K. and Ryan, Jack P. and Baker, Erin S. and Aspinwall, Craig A. and Marty, Michael T.}, year={2022}, month={Jun}, pages={1031–1037} }
 @article{roman-hubers_aeppli_dodds_baker_mcfarlin_letinski_zhao_mitchell_parkerton_prince_et al._2022, title={Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight}, volume={185}, ISSN={["1879-3363"]}, DOI={10.1016/j.marpolbul.2022.114360}, abstractNote={Photooxidation can alter the environmental fate and effects of spilled oil. To better understand this process, oil slicks were generated on seawater mesocosms and exposed to sunlight for 8 days. The molecular composition of seawater under irradiated and non-irradiated oil slicks was characterized using ion mobility spectrometry-mass spectrometry and polyaromatic hydrocarbons analyses. Biomimetic extraction was performed to quantify neutral and ionized constituents. Results show that seawater underneath irradiated oil showed significantly higher amounts of hydrocarbons with oxygen- and sulfur-containing by-products peaking by day 4-6; however, concentrations of dissolved organic carbon were similar. Biomimetic extraction indicated toxic units in irradiated mesocosms increased, mainly due to ionized components, but remained <1, suggesting limited potential for ecotoxicity. Because the experimental design mimicked important aspects of natural conditions (freshly collected seawater, natural sunlight, and relevant oil thickness and concentrations), this study improves our understanding of the effects of photooxidation during a marine oil spill.}, journal={MARINE POLLUTION BULLETIN}, author={Roman-Hubers, Alina T. and Aeppli, Christoph and Dodds, James N. and Baker, Erin S. and McFarlin, Kelly M. and Letinski, Daniel J. and Zhao, Lin and Mitchell, Douglas A. and Parkerton, Thomas F. and Prince, Roger C. and et al.}, year={2022}, month={Dec} }
 @article{foster_rainey_watson_dodds_kirkwood_fernandez_baker_2022, title={Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning}, volume={56}, ISSN={["1520-5851"]}, DOI={10.1021/acs.est.2c00201}, abstractNote={The identification of xenobiotics in nontargeted metabolomic analyses is a vital step in understanding human exposure. Xenobiotic metabolism, transformation, excretion, and coexistence with other endogenous molecules, however, greatly complicate the interpretation of features detected in nontargeted studies. While mass spectrometry (MS)-based platforms are commonly used in metabolomic measurements, deconvoluting endogenous metabolites from xenobiotics is also often challenged by the lack of xenobiotic parent and metabolite standards as well as the numerous isomers possible for each small molecule m/z feature. Here, we evaluate a xenobiotic structural annotation workflow using ion mobility spectrometry coupled with MS (IMS-MS), mass defect filtering, and machine learning to uncover potential xenobiotic classes and species in large metabolomic feature lists. Xenobiotic classes examined included those of known high toxicities, including per- and polyfluoroalkyl substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and pesticides. Specifically, when the workflow was applied to identify PFAS in the NIST SRM 1957 and 909c human serum samples, it greatly reduced the hundreds of detected liquid chromatography (LC)-IMS-MS features by utilizing both mass defect filtering and m/z versus IMS collision cross sections relationships. These potential PFAS features were then compared to the EPA CompTox entries, and while some matched within specific m/z tolerances, there were still many unknowns illustrating the importance of nontargeted studies for detecting new molecules with known chemical characteristics. Additionally, this workflow can also be utilized to evaluate other xenobiotics and enable more confident annotations from nontargeted studies.}, number={12}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Foster, MaKayla and Rainey, Markace and Watson, Chandler and Dodds, James N. and Kirkwood, Kaylie I and Fernandez, Facundo M. and Baker, Erin S.}, year={2022}, month={Jun}, pages={9133–9143} }
 @article{kirkwood_fleming_nguyen_reif_baker_belcher_2022, title={Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS)}, volume={56}, ISSN={["1520-5851"]}, url={https://doi.org/10.1021/acs.est.1c06483}, DOI={10.1021/acs.est.1c06483}, abstractNote={As concerns over exposure to per- and polyfluoroalkyl substances (PFAS) are continually increasing, novel methods to monitor their presence and modifications are greatly needed, as some have known toxic and bioaccumulative characteristics while most have unknown effects. This task however is not simple, as the Environmental Protection Agency (EPA) CompTox PFAS list contains more than 9000 substances as of September 2020 with additional substances added continually. Nontargeted analyses are therefore crucial to investigating the presence of this immense list of possible PFAS. Here, we utilized archived and field-sampled pine needles as widely available passive samplers and a novel nontargeted, multidimensional analytical method coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) to evaluate the temporal and spatial presence of numerous PFAS. Over 70 PFAS were detected in the pine needles from this study, including both traditionally monitored legacy perfluoroalkyl acids (PFAAs) and their emerging replacements such as chlorinated derivatives, ultrashort chain PFAAs, perfluoroalkyl ether acids including hexafluoropropylene oxide dimer acid (HFPO-DA, "GenX") and Nafion byproduct 2, and a cyclic perfluorooctanesulfonic acid (PFOS) analog. Results from this study provide critical insight related to PFAS transport, contamination, and reduction efforts over the past six decades.}, number={6}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, publisher={American Chemical Society (ACS)}, author={Kirkwood, Kaylie I and Fleming, Jonathon and Nguyen, Helen and Reif, David M. and Baker, Erin S. and Belcher, Scott M.}, year={2022}, month={Mar}, pages={3441–3451} }
 @article{kirkwood_pratt_shulman_tamura_maccoss_maclean_baker_2022, title={Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions}, volume={7}, ISSN={["1750-2799"]}, DOI={10.1038/s41596-022-00714-6}, abstractNote={Lipidomics studies suffer from analytical and annotation challenges because of the great structural similarity of many of the lipid species. To improve lipid characterization and annotation capabilities beyond those afforded by traditional mass spectrometry (MS)-based methods, multidimensional separation methods such as those integrating liquid chromatography, ion mobility spectrometry, collision-induced dissociation and MS (LC-IMS-CID-MS) may be used. Although LC-IMS-CID-MS and other multidimensional methods offer valuable hydrophobicity, structural and mass information, the files are also complex and difficult to assess. Thus, the development of software tools to rapidly process and facilitate confident lipid annotations is essential. In this Protocol Extension, we use the freely available, vendor-neutral and open-source software Skyline to process and annotate multidimensional lipidomic data. Although Skyline ( https://skyline.ms/skyline.url ) was established for targeted processing of LC-MS-based proteomics data, it has since been extended such that it can be used to analyze small-molecule data as well as data containing the IMS dimension. This protocol uses Skyline's recently expanded capabilities, including small-molecule spectral libraries, indexed retention time and ion mobility filtering, and provides a step-by-step description for importing data, predicting retention times, validating lipid annotations, exporting results and editing our manually validated 500+ lipid library. Although the time required to complete the steps outlined here varies on the basis of multiple factors such as dataset size and familiarity with Skyline, this protocol takes ~5.5 h to complete when annotations are rigorously verified for maximum confidence.}, journal={NATURE PROTOCOLS}, author={Kirkwood, Kaylie I and Pratt, Brian S. and Shulman, Nicholas and Tamura, Kaipo and MacCoss, Michael J. and MacLean, Brendan X. and Baker, Erin S.}, year={2022}, month={Jul} }
 @article{roman-hubers_mcdonald_baker_chiu_rusyn_2021, title={A Comparative Analysis of Analytical Techniques for Rapid Oil Spill Identification}, volume={40}, ISSN={["1552-8618"]}, DOI={10.1002/etc.4961}, abstractNote={Abstract}, number={4}, journal={ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY}, author={Roman-Hubers, Alina T. and McDonald, Thomas J. and Baker, Erin S. and Chiu, Weihsueh A. and Rusyn, Ivan}, year={2021}, month={Apr}, pages={1034–1049} }
 @article{roman-hubers_cordova_aly_mcdonald_lloyd_wright_baker_chiu_rusyn_2021, title={Data Processing Workflow to Identify Structurally Related Compounds in Petroleum Substances Using Ion Mobility Spectrometry-Mass Spectrometry}, volume={35}, ISSN={["1520-5029"]}, DOI={10.1021/acs.energyfuels.1c00892}, abstractNote={Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) is a post-ionization separation technique that can be used for rapid multidimensional analyses of complex samples. IMS-MS offers untargeted analysis, including ion-specific conformational data derived as collisional cross section (CCS) values. Here, we combine nitrogen gas drift tube CCS (DTCCSN2) and Kendrick mass defect (KMD) analyses based on CH2 and H functional units to enable compositional analyses of petroleum substances. First, polycyclic aromatic compound standards were analyzed by IMS-MS to demonstrate how CCS assists the identification of isomeric species in homologous series. Next, we used case studies of a gasoline standard previously characterized for paraffin, isoparaffin, aromatic, naphthene, and olefinic (PIANO) compounds, and a crude oil sample to demonstrate the application of the KMD analyses and CCS filtering. Finally, we propose a workflow that enables confident molecular formula assignment to the IMS-MS-derived features in petroleum samples. Collectively, this work demonstrates how rapid untargeted IMS-MS analysis and the proposed data processing workflow can be used to provide confident compositional characterization of hydrocarbon-containing substances.}, number={13}, journal={ENERGY & FUELS}, author={Roman-Hubers, Alina T. and Cordova, Alexandra C. and Aly, Noor A. and McDonald, Thomas J. and Lloyd, Dillon T. and Wright, Fred A. and Baker, Erin S. and Chiu, Weihsueh A. and Rusyn, Ivan}, year={2021}, month={Jul}, pages={10529–10539} }
 @article{kirkwood_christopher_burgess_littau_foster_richey_pratt_shulman_tamura_maccoss_et al._2021, title={Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity}, volume={12}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00820}, abstractNote={The implication of lipid dysregulation in diseases, toxic exposure outcomes, and inflammation has brought great interest to lipidomic studies. However, lipids have proven to be analytically challenging due to their highly isomeric nature and vast concentration ranges in biological matrices. Therefore, multidimensional techniques such as those integrating liquid chromatography, ion mobility spectrometry, collision-induced dissociation, and mass spectrometry (LC-IMS-CID-MS) have been implemented to separate lipid isomers as well as provide structural information and increased identification confidence. These data sets are however extremely large and complex, resulting in challenges for data processing and annotation. Here, we have overcome these challenges by developing sample-specific multidimensional lipid libraries using the freely available software Skyline. Specifically, the human plasma library developed for this work contains over 500 unique lipids and is combined with adapted Skyline functions such as indexed retention time (iRT) for retention time prediction and IMS drift time filtering for enhanced selectivity. For comparison with other studies, this database was used to annotate LC-IMS-CID-MS data from a NIST SRM 1950 extract. The same workflow was then utilized to assess plasma and bronchoalveolar lavage fluid (BALF) samples from patients with varying degrees of smoke inhalation injury to identify lipid-based patient prognostic and diagnostic markers.}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Kirkwood, Kaylie I and Christopher, Michael W. and Burgess, Jefferey L. and Littau, Sally R. and Foster, Kevin and Richey, Karen and Pratt, Brian S. and Shulman, Nicholas and Tamura, Kaipo and MacCoss, Michael J. and et al.}, year={2021}, month={Dec} }
 @misc{dodds_alexander_kirkwood_foster_hopkins_knappe_baker_2021, title={From Pesticides to Per- and Polyfluoroalkyl Substances: An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics}, volume={93}, ISSN={["1520-6882"]}, url={https://doi.org/10.1021/acs.analchem.0c04359}, DOI={10.1021/acs.analchem.0c04359}, abstractNote={Environmental analysis of xenobiotics is a challenging yet necessary undertaking to characterize pollution levels, assess the effectiveness of remediation interventions, and prevent adverse environmental and health outcomes. Xenobiotics are concerning from an environmental perspective due to their chemical persistence, toxicity to humans and wildlife, and prolific use in agricultural and industrial applications.1 Many xenobiotics are persistent organic pollutants (POPs), and the number of POPs listed in the Stockholm Convention is}, number={1}, journal={ANALYTICAL CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Dodds, James N. and Alexander, Nancy Lee M. and Kirkwood, Kaylie I and Foster, MaKayla R. and Hopkins, Zachary R. and Knappe, Detlef R. U. and Baker, Erin S.}, year={2021}, month={Jan}, pages={641–656} }
 @article{khadempour_kyle_webb-robertson_nicora_smith_smith_lipton_currie_baker_burnum-johnson_2021, title={From Plants to Ants: Fungal Modification of Leaf Lipids for Nutrition and Communication in the Leaf-Cutter Ant Fungal Garden Ecosystem}, volume={6}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/mSystems.01307-20}, DOI={10.1128/msystems.01307-20}, abstractNote={In this work, we examined the role of lipids in the mutualism between leaf-cutter ants and fungus. These ants cut fresh leaf material, which they provide to their fungal cultivar, that converts energy and nutrients from the plants and provides it to the ants in specialized hyphal swellings called gongylidia.}, number={2}, journal={MSYSTEMS}, author={Khadempour, Lily and Kyle, Jennifer E. and Webb-Robertson, Bobbie-Jo M. and Nicora, Carrie D. and Smith, Francesca B. and Smith, Richard D. and Lipton, Mary S. and Currie, Cameron R. and Baker, Erin S. and Burnum-Johnson, Kristin E.}, year={2021}, month={Apr} }
 @article{odenkirk_stratton_bramer_webb-robertson_bloodsworth_monroe_burnum-johnson_baker_2021, title={From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions}, volume={11}, ISSN={["2218-273X"]}, url={https://www.mdpi.com/2218-273X/11/1/40}, DOI={10.3390/biom11010040}, abstractNote={While a molecular assessment of the perturbations and injury arising from diseases is essential in their diagnosis and treatment, understanding changes due to preventative strategies is also imperative. Currently, complex diseases such as cardiovascular disease (CVD), the leading cause of death worldwide, suffer from a limited understanding of how the molecular mechanisms taking place following preventive measures (e.g., exercise) differ from changes occurring due to the injuries caused from the disease (e.g., myocardial infarction (MI)). Therefore, this manuscript assesses lipidomic changes before and one hour after exercise treadmill testing (ETT) and before and one hour after a planned myocardial infarction (PMI) in two separate patient cohorts. Strikingly, unique lipidomic perturbations were observed for these events, as could be expected from their vastly different stresses on the body. The lipidomic results were then combined with previously published metabolomic characterizations of the same patients. This integration provides complementary insights into the exercise and PMI events, thereby giving a more holistic understanding of the molecular changes associated with each.}, number={1}, journal={BIOMOLECULES}, author={Odenkirk, Melanie T. and Stratton, Kelly G. and Bramer, Lisa M. and Webb-Robertson, Bobbie-Jo M. and Bloodsworth, Kent J. and Monroe, Matthew E. and Burnum-Johnson, Kristin E. and Baker, Erin S.}, year={2021}, month={Jan} }
 @article{dodds_baker_2021, title={Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry-Mass Spectrometry}, volume={93}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.1c04267}, abstractNote={Detection and diagnosis of congenital disorders is the principal aim of newborn screening (NBS) programs worldwide. Mass spectrometry (MS) has become the preferred primary testing method for high-throughput NBS sampling because of its speed and selectivity. However, the ever-increasing list of NBS biomarkers included in expanding panels creates unique analytical challenges for multiplexed MS assays due to isobaric/isomeric overlap and chimeric fragmentation spectra. Since isobaric and isomeric systems limit the diagnostic power of current methods and require costly follow-up exams due to many false-positive results, here, we explore the utility of ion mobility spectrometry (IMS) to enhance the accuracy of MS assays for primary (tier 1) screening. Our results suggest that ∼400 IMS resolving power would be required to confidently assess most NBS biomarkers of interest in dried blood spots (DBSs) that currently require follow-up testing. While this level of selectivity is unobtainable with most commercially available platforms, the separations detailed here for a commercially available drift tube IMS (Agilent 6560 with high-resolution demultiplexing, HRdm) illustrate the unique capabilities of IMS to separate many diagnostic NBS biomarkers from interferences. Furthermore, to address the need for increased speed of NBS analyses, we utilized an automated solid-phase extraction (SPE) system for ∼10 s sampling of simulated NBS samples prior to IMS-MS. This proof-of-concept work demonstrates the unique capabilities of SPE-IMS-MS for high-throughput sample introduction and enhanced separation capacity conducive for increasing speed and accuracy for NBS.}, number={51}, journal={ANALYTICAL CHEMISTRY}, author={Dodds, James N. and Baker, Erin S.}, year={2021}, month={Dec}, pages={17094–17102} }
 @article{duncan_sun_baker_dey_lanekoff_2021, title={In situ imaging reveals disparity between prostaglandin localization and abundance of prostaglandin synthases}, volume={4}, ISSN={["2399-3642"]}, DOI={10.1038/s42003-021-02488-1}, abstractNote={Abstract}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Duncan, Kyle D. and Sun, Xiaofei and Baker, Erin S. and Dey, Sudhansu K. and Lanekoff, Ingela}, year={2021}, month={Aug} }
 @article{ligare_morrison_hewitt_reveles_govind_hernandez_baker_clowers_laskin_johnson_2021, title={Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au-7(PPh3)(7)H-5(2+)}, volume={12}, ISSN={["1948-7185"]}, DOI={10.1021/acs.jpclett.0c03664}, abstractNote={We employ ion mobility spectrometry and density functional theory to determine the structure of Au7(PPh3)7H52+ (PPh3 = triphenylphosphine), which was recently identified by high mass resolution mass spectrometry. Experimental ion-neutral collision cross sections represent the momentum transfer between the ionic clusters and gas molecules averaged over the relative thermal velocities of the colliding pair, thereby providing structural insights. Theoretical calculations indicate the geometry of Au7(PPh3)7H52+ is similar to Au7(PPh3)7+, with three hydrogen atoms bridging two gold atoms and two hydrogen atoms forming single Au-H bonds. Collision-induced dissociation products observed during IMS experiments reveal that smaller hydrogen-containing clusters may be produced through fragmentation of Au7(PPh3)7H52+. Our findings indicate that hydrogen-containing species like Au7(PPh3)7H52+ act as intermediates in the formation of larger phosphine ligated gold clusters. These results advance the understanding and ability to control the mechanisms of size-selective cluster formation, which is necessary for scalable synthesis of clusters with tailored properties.}, number={10}, journal={JOURNAL OF PHYSICAL CHEMISTRY LETTERS}, author={Ligare, Marshall R. and Morrison, Kelsey A. and Hewitt, Michael A. and Reveles, J. Ulises and Govind, Niranjan and Hernandez, Heriberto and Baker, Erin S. and Clowers, Brian H. and Laskin, Julia and Johnson, Grant E.}, year={2021}, month={Mar}, pages={2502–2508} }
 @article{odenkirk_reif_baker_2021, title={Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments}, volume={93}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.0c04850}, abstractNote={The need for holistic molecular measurements to better understand disease initiation, development, diagnosis, and therapy has led to an increasing number of multiomic analyses. The wealth of information available from multiomic assessments, however, requires both the evaluation and interpretation of extremely large data sets, limiting analysis throughput and ease of adoption. Computational methods utilizing artificial intelligence (AI) provide the most promising way to address these challenges, yet despite the conceptual benefits of AI and its successful application in singular omic studies, the widespread use of AI in multiomic studies remains limited. Here, we discuss present and future capabilities of AI techniques in multiomic studies while introducing analytical checks and balances to validate the computational conclusions.}, number={22}, journal={ANALYTICAL CHEMISTRY}, author={Odenkirk, Melanie T. and Reif, David M. and Baker, Erin S.}, year={2021}, month={Jun}, pages={7763–7773} }
 @article{baker_knappe_2021, title={Per- and polyfluoroalkyl substances (PFAS)-contaminants of emerging concern}, volume={12}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-021-03811-9}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Baker, Erin S. and Knappe, Detlef R. U.}, year={2021}, month={Dec} }
 @misc{koefeler_ahrends_baker_ekroos_han_hoffmann_holcapek_wenk_liebisch_2021, title={Recommendations for good practice in MS-based lipidomics}, volume={62}, ISSN={["1539-7262"]}, DOI={10.1016/j.jlr.2021.100138}, abstractNote={In the last 2 decades, lipidomics has become one of the fastest expanding scientific disciplines in biomedical research. With an increasing number of new research groups to the field, it is even more important to design guidelines for assuring high standards of data quality. The Lipidomics Standards Initiative is a community-based endeavor for the coordination of development of these best practice guidelines in lipidomics and is embedded within the International Lipidomics Society. It is the intention of this review to highlight the most quality-relevant aspects of the lipidomics workflow, including preanalytics, sample preparation, MS, and lipid species identification and quantitation. Furthermore, this review just does not only highlights examples of best practice but also sheds light on strengths, drawbacks, and pitfalls in the lipidomic analysis workflow. While this review is neither designed to be a step-by-step protocol by itself nor dedicated to a specific application of lipidomics, it should nevertheless provide the interested reader with links and original publications to obtain a comprehensive overview concerning the state-of-the-art practices in the field.}, journal={JOURNAL OF LIPID RESEARCH}, author={Koefeler, Harald C. and Ahrends, Robert and Baker, Erin S. and Ekroos, Kim and Han, Xianlin and Hoffmann, Nils and Holcapek, Michal and Wenk, Markus R. and Liebisch, Gerhard}, year={2021} }
 @article{luo_chen_blanchette_zhou_wright_baker_chiu_rusyn_2021, title={Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes}, volume={149}, ISSN={["1873-6351"]}, url={https://doi.org/10.1016/j.fct.2021.111979}, DOI={10.1016/j.fct.2021.111979}, abstractNote={Consumption of energy drinks has been associated with adverse cardiovascular effects; however, little is known about the ingredients that may contribute to these effects. We therefore characterized the chemical profiles and in vitro effects of energy drinks and their ingredients on human induced pluripotent stem cell (iPSC)-derived cardiomyocytes, and identified the putative active ingredients using a multivariate prediction model. Energy drinks from 17 widely-available over-the-counter brands were evaluated in this study. The concentrations of six common ingredients (caffeine, taurine, riboflavin, pantothenic acid, adenine, and L-methionine) were quantified by coupling liquid chromatography with a triple quadrupole mass spectrometer for the acquisition of LC-MS/MS spectra. In addition, untargeted analyses for each beverage were performed with a platform combining LC, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) measurements. Approximately 300 features were observed across samples in the untargeted studies, and of these ~100 were identified. In vitro effects of energy drinks and some of their ingredients were then tested in iPSC-derived cardiomyocytes. Data on the beat rate (positive and negative chronotropy), ion channel function (QT prolongation), and cytotoxicity were collected in a dilution series. We found that some of the energy drinks elicited adverse effects on the cardiomyocytes with the most common being an increase in the beat rate, while QT prolongation was also observed at the lowest concentrations. Finally, concentration addition modeling using quantitative data from the 6 common ingredients and multivariate prediction modeling was used to determine potential ingredients responsible for the adverse effects on the cardiomyocytes. These analyses suggested theophylline, adenine, and azelate as possibly contributing to the in vitro effects of energy drinks on QT prolongation in cardiomyocytes.}, journal={FOOD AND CHEMICAL TOXICOLOGY}, author={Luo, Yu-Syuan and Chen, Zunwei and Blanchette, Alexander D. and Zhou, Yi-Hui and Wright, Fred A. and Baker, Erin S. and Chiu, Weihsueh A. and Rusyn, Ivan}, year={2021}, month={Mar} }
 @article{spatial distribution of polycyclic aromatic hydrocarbon contaminants after hurricane harvey in a houston neighborhood._2021, url={https://europepmc.org/articles/PMC8009646}, DOI={10.5696/2156-9614-11.29.210308}, abstractNote={Background. Hurricane Harvey made landfall along the Texas Gulf Coast as a Category 4 hurricane on August 25, 2017, producing unprecedented precipitation that devastated coastal areas. Catastrophic flooding in the City of Houston inundated industrial and residential properties resulting in the displacement and transfer of soil, sediment, and debris and heightening existing environmental justice (EJ) concerns. Objectives. The primary aim of this study was to evaluate the presence, distribution, and potential human health implications of polycyclic aromatic hydrocarbons (PAHs) in a residential neighborhood of Houston, Texas following a major hurricane. Methods. Concentrations of PAHs in 40 soil samples collected from a residential neighborhood in Houston, Texas were measured. Spatial interpolation was applied to determine the distribution of PAHs. Potential human health risks were evaluated by calculating toxicity equivalency quotients (TEQs) and incremental excess lifetime cancer risk (IELCR). Results. Total priority PAH concentrations varied across samples (range: 9.7 × 101 ng/g-1.6 × 104 ng/g; mean: 3.0 × 103 ng/g ± 3.6 × 103 standard deviation). Spatial analysis indicated a variable distribution of PAH constituents and concentrations. The IELCR analysis indicated that nine of the 40 samples were above minimum standards. Conclusions. Findings from this study highlight the need for fine scale soil testing in residential areas as well as the importance of site-specific risk assessment. Competing Interests. The authors declare no competing financial interests.}, journal={Journal of health & pollution}, year={2021}, month={Mar} }
 @article{butler_takinami_rainczuk_baker_roberts_2021, title={Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase}, volume={9}, ISSN={["2296-2646"]}, DOI={10.3389/fchem.2021.614595}, abstractNote={Native mass spectrometry has emerged as a powerful tool for structural biology as it enables the evaluation of molecules as they occur in their physiological conditions. Ion mobility spectrometry-mass spectrometry (IMS-MS) has shown essential in these analyses as it allows the measurement of the shape of a molecule, denoted as its collision cross section (CCS), and mass. The structural information garnered from native IMS-MS provides insight into the tertiary and quaternary structure of proteins and can be used to validate NMR or crystallographic X-ray structures. Additionally, due to the rapid nature (millisecond measurements) and ability of IMS-MS to analyze heterogeneous solutions, it can be used to address structural questions not possible with traditional structural approaches. Herein, we applied multiple solution conditions to systematically denature bovine Cu/Zn-superoxide dismutase (SOD1) and assess its unfolding pathway from the holo-dimer to the holo-monomer, single-metal monomer, and apo-monomer. Additionally, we compared and noted 1–2% agreement between CCS values from both drift tube IMS and trapped IMS for the SOD1 holo-monomer and holo-dimer. The observed CCS values were in excellent agreement with computational CCS values predicted from the homo-dimer crystal structure, showcasing the ability to use both IMS-MS platforms to provide valuable structural information for molecular modeling of protein interactions and structural assessments.}, journal={FRONTIERS IN CHEMISTRY}, author={Butler, Karen E. and Takinami, Yoshihiko and Rainczuk, Adam and Baker, Erin S. and Roberts, Blaine R.}, year={2021}, month={Feb} }
 @article{aly_dodds_luo_grimm_foster_rusyn_baker_2021, title={Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites}, volume={10}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-021-03686-w}, abstractNote={Persistent organic pollutants (POPs) are xenobiotic chemicals of global concern due to their long-range transport capabilities, persistence, ability to bioaccumulate, and potential to have negative effects on human health and the environment. Identifying POPs in both the environment and human body is therefore essential for assessing potential health risks, but their diverse range of chemical classes challenge analytical techniques. Currently, platforms coupling chromatography approaches with mass spectrometry (MS) are the most common analytical methods employed to evaluate both parent POPs and their respective metabolites and/or degradants in samples ranging from d rinking water to biofluids. Unfortunately, different types of analyses are commonly needed to assess both the parent and metabolite/degradant POPs from the various chemical classes. The multiple time-consuming analyses necessary thus present a number of technical and logistical challenges when rapid evaluations are needed and sample volumes are limited. To address these challenges, we characterized 64 compounds including parent per- and polyfluoroalkyl substances (PFAS), pesticides, polychlorinated biphenyls (PCBs), industrial chemicals, and pharmaceuticals and personal care products (PPCPs), in addition to their metabolites and/or degradants, using ion mobility spectrometry coupled with MS (IMS-MS) as a potential rapid screening technique. Different ionization sources including electrospray ionization (ESI) and atmospheric pressure photoionization (APPI) were employed to determine optimal ionization for each chemical. Collectively, this study advances the field of exposure assessment by structurally characterizing the 64 important environmental pollutants, assessing their best ionization sources, and evaluating their rapid screening potential with IMS-MS.}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Aly, Noor A. and Dodds, James N. and Luo, Yu-Syuan and Grimm, Fabian A. and Foster, MaKayla and Rusyn, Ivan and Baker, Erin S.}, year={2021}, month={Oct} }
 @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{ekelof_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={Mass Spectrom}, author={Ekelof, M. and Dodds, J.N. and Khodjaniyazova, S. and Garrard, Kenneth P. and Baker, E.S. and Muddiman, D.C.}, year={2020}, month={Jan}, pages={642–650} }
 @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{soper-hopper_vandegrift_baker_fernandez_2020, title={Metabolite collision cross section prediction without energy-minimized structures}, volume={145}, ISSN={["1364-5528"]}, DOI={10.1039/d0an00198h}, abstractNote={Matching experimental ion mobility-mass spectrometry data to computationally-generated collision cross section (CCS) values enables more confident metabolite identifications.}, number={16}, journal={The Analyst}, author={Soper-Hopper, M.T. and Vandegrift, J. and Baker, E.S. and Fernandez, F.M.}, year={2020}, pages={5414–5418} }
 @article{orwoll_wiedrick_nielson_jacobs_baker_piehowski_petyuk_gao_shi_smith_et al._2020, title={Proteomic assessment of serum biomarkers of longevity in older men}, volume={19}, ISSN={["1474-9726"]}, DOI={10.1111/acel.13253}, abstractNote={Abstract}, number={11}, journal={AGING CELL}, author={Orwoll, Eric S. and Wiedrick, Jack and Nielson, Carrie M. and Jacobs, Jon and Baker, Erin S. and Piehowski, Paul and Petyuk, Vladislav and Gao, Yuqian and Shi, Tujin and Smith, Richard D. and et al.}, year={2020}, month={Nov} }
 @article{luo_aly_mccord_strynar_chiu_dodds_baker_rusyn_2020, title={Rapid Characterization of Emerging Per- and Polyfluoroalkyl Substances in Aqueous Film-Forming Foams Using Ion Mobility Spectrometry-Mass Spectrometry}, volume={54}, ISSN={["1520-5851"]}, DOI={10.1021/acs.est.0c04798}, abstractNote={Aqueous film-forming foams (AFFF) are mixtures formulated with numerous hydrocarbon- and fluoro-containing surfactants. AFFF use leads to environmental releases of unknown per- and polyfluoroalkyl substances (PFAS). AFFF composition is seldom disclosed, and their use elicits concerns from both regulatory agencies and the public because PFAS are persistent in the environment and potentially associated with adverse health effects. In this study, we demonstrate the use of coupled liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) to rapidly characterize both known and unknown PFAS in AFFF. Ten AFFF formulations from seven brands were analyzed using LC-IMS-MS in both negative and positive ion modes. Untargeted analysis of the formulations was followed by feature identification of PFAS-like features utilizing database matching, mass defect and homologous series evaluation, and MS/MS fragmentation experiments. Across the tested AFFF formulations, we identified 33 homologous series; only ten of these homologous series have been previously reported. Among tested AFFF, the FireStopper (n = 85) contained the greatest number of PFAS-like features and Phos-Check contained zero. This work demonstrates that LC-IMS-MS-enabled untargeted analysis of complex formulations, followed by feature identification using data-processing algorithms, can be used for rapid exposure characterization of known and putative PFAS during fire suppression-related contamination events.}, number={23}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Luo, Yu-Syuan and Aly, Noor A. and McCord, James and Strynar, Mark J. and Chiu, Weihsueh A. and Dodds, James N. and Baker, Erin S. and Rusyn, Ivan}, year={2020}, month={Dec}, pages={15024–15034} }
 @article{dodds_hopkins_knappe_baker_2020, title={Rapid Characterization of Per- and Polyfluoroalkyl Substances (PFAS) by Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)}, volume={92}, url={https://doi.org/10.1021/acs.analchem.9b05364}, DOI={10.1021/acs.analchem.9b05364}, abstractNote={Per- and polyfluoroalkyl substances (PFAS) are an ensemble of persistent organic pollutants of global interest because of their associations with adverse health outcomes. Currently, environmental PFAS pollution is prolific as a result of the widespread manufacturing of these compounds and their chemical persistence. In this work, we demonstrate the advantages of adding ion mobility spectrometry (IMS) separation to existing LC-MS workflows for PFAS analysis. Using a commercially available drift tube IMS-MS, we characterized PFAS species and isomeric content both in analytical standards and wastewater samples. Molecular trendlines based on intrinsic mass and structural relationships were also explored for the PFAS subclasses (e.g. PFSA, PFCA, etc.). Results from rapid IMS-MS analyses provided a link between mass and collision cross sections (CCS) for specific PFAS families and are linked to compositional differences in molecular structure. In addition, CCS values provide additional confidence of annotating prioritized features in untargeted screening studies for potential environmental pollutants. Results from this study show that the IMS separation provides novel information to support traditional LC-MS PFAS analyses and will greatly benefit the evaluation of unknown pollutants in future environmental studies.}, number={6}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Dodds, J.N. and Hopkins, Z.R. and Knappe, D.R.U. and Baker, E.S.}, year={2020}, month={Feb}, pages={4427–4435} }
 @article{odenkirk_zin_ash_reif_fourches_baker_2020, title={Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems}, volume={145}, ISSN={["1364-5528"]}, DOI={10.1039/d0an01638a}, abstractNote={SCOPE is a toolbox for expanding upon lipid data interpretation capabilities. Herein we utilize SCOPE to explore how lipid structure, biological connections and metadata linkages contribute to the results observed from lipidomic experiments.}, number={22}, journal={ANALYST}, author={Odenkirk, Melanie T. and Zin, Phyo Phyo K. and Ash, Jeremy R. and Reif, David M. and Fourches, Denis and Baker, Erin S.}, year={2020}, month={Nov}, pages={7197–7209} }
 @article{aly_luo_liu_casillas_mcdonald_kaihatu_jun_ellis_gossett_dodds_et al._2020, title={Temporal and spatial analysis of per and polyfluoroalkyl substances in surface waters of Houston ship channel following a large-scale industrial fire incident}, volume={265}, ISSN={["1873-6424"]}, DOI={10.1016/j.envpol.2020.115009}, abstractNote={Firefighting foams contain per- and polyfluoroalkyl substances (PFAS) – a class of compounds widely used as surfactants. PFAS are persistent organic pollutants that have been reported in waterways and drinking water systems across the United States. These substances are of interest to both regulatory agencies and the general public because of their persistence in the environment and association with adverse health effects. PFAS can be released in large quantities during industrial incidents because they are present in most firefighting foams used to suppress chemical fires; however, little is known about persistence of PFAS in public waterways after such events. In response to large-scale fires at Intercontinental Terminal Company (ITC) in Houston, Texas in March 2019, almost 5 million liters of class B firefighting foams were used. Much of this material flowed into the Houston Ship Channel and Galveston Bay (HSC/GB) and concerns were raised about the levels of PFAS in these water bodies that have commercial and recreational uses. To evaluate the impact of the ITC incident response on PFAS levels in HSC/GB, we collected 52 surface water samples from 12 locations over a 6-month period after the incident. Samples were analyzed using liquid chromatography–mass spectrometry to evaluate 27 PFAS, including perfluorocarboxylic acids, perfluorosulfonates and fluorotelomers. Among PFAS that were evaluated, 6:2 FTS and PFOS were detected at highest concentrations. Temporal and spatial profiles of PFAS were established; we found a major peak in the level of many PFAS in the days and weeks after the incident and a gradual decline over several months with patterns consistent with the tide- and wave-associated water movements. This work documents the impact of a large-scale industrial fire, on the environmental levels of PFAS, establishes a baseline concentration of PFAS in HSC/GB, and highlights the critical need for development of PFAS water quality standards.}, number={B}, journal={Environmental Pollution}, author={Aly, N.A. and Luo, Y.-S. and Liu, Y. and Casillas, G. and McDonald, T. and Kaihatu, J. and Jun, M. and Ellis, N. and Gossett, S. and Dodds, J.N. and et al.}, year={2020}, month={Oct}, pages={115009} }
 @article{odenkirk_stratton_gritsenko_bramer_webb-robertson_bloodsworth_weitz_lipton_monroe_ash_et al._2020, title={Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools}, volume={16}, ISSN={["2515-4184"]}, DOI={10.1039/d0mo00074d}, abstractNote={Specific lipid and protein changes characterized term preeclampsia (PRE) and gestational diabetes mellitus (GDM) and novel visualization tools were created to aid in the process.}, number={6}, journal={MOLECULAR OMICS}, author={Odenkirk, Melanie T. and Stratton, Kelly G. and Gritsenko, Marina A. and Bramer, Lisa M. and Webb-Robertson, Bobbie-Jo M. and Bloodsworth, Kent J. and Weitz, Karl K. and Lipton, Anna K. and Monroe, Matthew E. and Ash, Jeremy R. and et al.}, year={2020}, month={Dec} }
 @article{odenkirk_baker_2020, title={Utilizing Drift Tube Ion Mobility Spectrometry for the Evaluation of Metabolites and Xenobiotics}, volume={2084}, ISBN={["978-1-0716-0029-0"]}, ISSN={["1940-6029"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85075114871&partnerID=MN8TOARS}, DOI={10.1007/978-1-0716-0030-6_2}, abstractNote={Metabolites and xenobiotics are small molecules with a molecular weight that often falls below 600 Da. Over the last few decades, multiple small molecule databases have been curated listing structures, masses, and fragmentation spectra possible in metabolomic and exposomic measurements. To date only a small portion of the spectra in these databases are experimentally derived due to the high expense of obtaining, synthesizing, and analyzing standards. A vast majority of spectra have thus been created using theoretical programs to fit the available experimental data. The errors associated with theoretical data have however caused problems with current small molecule identifications, and accurate quantitation as searching the databases using just one or two analysis dimensions (i.e., chromatography retention times and mass spectrometry (MS) m/z values) results in numerous annotations for each experimental feature. Additional analysis dimensions are therefore needed to better annotate and identify small molecules. Drift tube ion mobility spectrometry coupled with MS (DTIMS-MS) is a promising technique to address this challenge as it is able to perform rapid structural evaluations of small molecules in complex matrices by assessing the collision cross section values for each in addition to their m/z values. The use of IMS in conjunction with other separation techniques such as gas or liquid chromatography and MS has therefore enabled more accurate identifications for the small molecules present in complex biological and environmental samples. Here, we present a review of relevant parameter considerations for DTIMS application with emphasis on xenobiotics and metabolomics isomer separations.}, journal={ION MOBILITY-MASS SPECTROMETRY: METHODS AND PROTOCOLS}, author={Odenkirk, Melanie T. and Baker, Erin S.}, year={2020}, pages={35–54} }
 @article{eugenia monge_dodds_baker_edison_fernandez_2019, title={Challenges in Identifying the Dark Molecules of Life}, volume={12}, ISSN={["1936-1327"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85067284122&partnerID=MN8TOARS}, DOI={10.1146/annurev-anchem-061318-114959}, abstractNote={ Metabolomics is the study of the metabolome, the collection of small molecules in living organisms, cells, tissues, and biofluids. Technological advances in mass spectrometry, liquid- and gas-phase separations, nuclear magnetic resonance spectroscopy, and big data analytics have now made it possible to study metabolism at an omics or systems level. The significance of this burgeoning scientific field cannot be overstated: It impacts disciplines ranging from biomedicine to plant science. Despite these advances, the central bottleneck in metabolomics remains the identification of key metabolites that play a class-discriminant role. Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate. In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task. }, journal={ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 12}, author={Eugenia Monge, Maria and Dodds, James N. and Baker, Erin S. and Edison, Arthur S. and Fernandez, Facundo M.}, year={2019}, pages={177–199} }
 @article{zheng_smith_aly_cai_smith_patterson_baker_2019, title={Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry}, volume={411}, ISSN={["1618-2650"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85066032454&partnerID=MN8TOARS}, DOI={10.1007/s00216-019-01869-0}, abstractNote={Bile acids (BAs) play an integral role in digestion through the absorption of nutrients, emulsification of fats and fat-soluble vitamins, and maintenance of cholesterol levels. Metabolic disruption, diabetes, colorectal cancer, and numerous other diseases have been linked with BA disruption, making improved BA analyses essential. To date, most BA measurements are performed using liquid chromatography separations in conjunction with mass spectrometry measurements (LC-MS). However, 10–40 min LC gradients are often used for BA analyses and these may not even be sufficient for distinguishing all the important isomers present in the human body. Ion mobility spectrometry (IMS) is a promising tool for BA evaluations due to its ability to quickly separate isomeric molecules with subtle structural differences. In this study, we utilized drift tube IMS (DTIMS) coupled with MS to characterize 56 different unlabeled BA standards and 16 deuterated versions. In the DTIMS-MS analyses of 12 isomer groups, BAs with smaller m/z values were easily separated in either their deprotonated or sodiated forms (or both). However, as the BAs grew in m/z value, they became more difficult to separate with two isomer groups being inseparable. Metal ions such as copper and zinc were then added to the overlapping BAs, and due to different binding sites, the resulting complexes were separable. Thus, the rapid structural measurements possible with DTIMS-MS show great potential for BAs measurements with and without prior LC separations.}, number={19}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Zheng, Xueyun and Smith, Francesca B. and Aly, Noor A. and Cai, Jingwei and Smith, Richard D. and Patterson, Andrew D. and Baker, Erin S.}, year={2019}, month={Jul}, pages={4673–4682} }
 @article{zhang_zhong_connor_miller_cao_shen_song_baker_tang_pulavarti_et al._2019, title={Folding and Assembly of Short α, β, Î-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures}, volume={141}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072057414&partnerID=MN8TOARS}, DOI={10.1021/jacs.9b06094}, abstractNote={Multilevel protein structures typically involve polypeptides of sufficient lengths. Here we report the folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues. These are two sets of hybrid peptides, with three members in one set and four in the other, having complementary hydrogen-bonding sequences that were hypothesized to pair into linear H-bonded duplexes. However, instead of undergoing the anticipated pairing, the initially examined three oligomers, 1 and 2a or 2b, differing only in their central αβ hybrid dipeptide sequence, do not associate with each other and exhibit distinctly different folding behavior. Experiments based on NMR and mass spectrometry, along with computational studies and systematic inference, reveal that oligomer 1 folds into an expanded β-turn containing an unusual hybrid α/β-amino acid sequence composed of glycine and β-alanine, two α- and β-amino acid residues that are conformationally most flexible; and peptides 2a and 2b adopt a non-canonical, extended helical conformation and dimerize into double helices undergoing rapid conformational exchange or helix inversion. The different central dipeptide sequences, αβ vs βα, result in drastically different intramolecular H-bonding patterns that are responsible for the observed folding behavior of 1 and 2. The revealed turn and double helix have few natural or synthetic counterparts, and provide novel and unique folding prototypes based on which chiral α- and β-amino acids are incorporated. The resultant derivatives 1a, 1b, 2c, and 2d follow the same folding and assembling behavior and demonstrate the generality of this system with the formation of expanded β-turns and double helices with enhanced folding stabilities, hampered helix inversion, as well as defined and dominant helical sense. This work has demonstrated the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. The revealed systems offer ample opportunity for further structural optimization and applications.}, number={36}, journal={Journal of the American Chemical Society}, author={Zhang, Y. and Zhong, Y. and Connor, A.L. and Miller, D.P. and Cao, R. and Shen, J. and Song, B. and Baker, E.S. and Tang, Q. and Pulavarti, S.V.S.R.K. and et al.}, year={2019}, pages={14239–14248} }
 @article{dodds_baker_2019, title={Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead}, volume={30}, ISSN={["1879-1123"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85073982332&partnerID=MN8TOARS}, DOI={10.1007/s13361-019-02288-2}, abstractNote={Ion mobility spectrometry (IMS) is a rapid separation technique that has experienced exponential growth as a field of study. Interfacing IMS with mass spectrometry (IMS-MS) provides additional analytical power as complementary separations from each technique enable multidimensional characterization of detected analytes. IMS separations occur on a millisecond timescale, and therefore can be readily nested into traditional GC and LC/MS workflows. However, the continual development of novel IMS methods has generated some level of confusion regarding the advantages and disadvantages of each. In this critical insight, we aim to clarify some common misconceptions for new users in the community pertaining to the fundamental concepts of the various IMS instrumental platforms (i.e., DTIMS, TWIMS, TIMS, FAIMS, and DMA), while addressing the strengths and shortcomings associated with each. Common IMS-MS applications are also discussed in this review, such as separating isomeric species, performing signal filtering for MS, and incorporating collision cross-section (CCS) values into both targeted and untargeted omics-based workflows as additional ion descriptors for chemical annotation. Although many challenges must be addressed by the IMS community before mobility information is collected in a routine fashion, the future is bright with possibilities.}, number={11}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Dodds, James N. and Baker, Erin S.}, year={2019}, month={Nov}, pages={2185–2195} }
 @book{chouinard_nagy_smith_baker_2019, title={Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses}, volume={83}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85058397105&partnerID=MN8TOARS}, DOI={10.1016/bs.coac.2018.11.001}, abstractNote={Ion mobility-mass spectrometry (IMS-MS) is rapidly gaining attention for improving metabolomic, lipidomic and proteomic analyses. Through the simultaneous measurement of molecular structures and mass, IMS-MS enables more complete analysis of mixtures, more confident molecular assignments, the construction of multicharacteristic molecular libraries, and the evaluation of unknown features in complex samples. Studies over the last decade have utilized IMS-MS to distinguish and study structurally similar small molecules, such as glycan anomers, polycyclic aromatic hydrocarbons, and lipid double bond isomers, leading to the discovery of new compounds with potentially high biological importance. Furthermore, IMS-MS has become an advanced proteomics tool not only for bottom-up peptide identification and quantitation but also for the study of native/intact proteins and their role in structural biology and disease progression. Additionally, recent advances in higher resolution IMS separations and its successful coupling with other preseparation, fragmentation, and characterization illustrate how IMS-MS will allow a more in-depth look into complex systems and further advance omics measurements.}, journal={Comprehensive Analytical Chemistry}, author={Chouinard, C.D. and Nagy, G. and Smith, R.D. and Baker, E.S.}, year={2019}, pages={123–159} }
 @misc{burnum-johnson_zheng_dodds_ash_fourches_nicora_wendler_metz_waters_jansson_et al._2019, title={Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples}, volume={116}, ISSN={["1879-3142"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85065908529&partnerID=MN8TOARS}, DOI={10.1016/j.trac.2019.04.022}, abstractNote={Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), lowering the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.}, journal={TRAC-TRENDS IN ANALYTICAL CHEMISTRY}, author={Burnum-Johnson, Kristin E. and Zheng, Xueyun and Dodds, James N. and Ash, Jeremy and Fourches, Denis and Nicora, Carrie D. and Wendler, Jason P. and Metz, Thomas O. and Waters, Katrina M. and Jansson, Janet K. and et al.}, year={2019}, month={Jul}, pages={292–299} }
 @article{baker_patti_2019, title={Perspectives on Data Analysis in Metabolomics: Points of Agreement and Disagreement from the 2018 ASMS Fall Workshop}, volume={30}, ISSN={["1879-1123"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85071321181&partnerID=MN8TOARS}, DOI={10.1007/s13361-019-02295-3}, abstractNote={In November 2018, the American Society for Mass Spectrometry hosted the Annual Fall Workshop on informatic methods in metabolomics. The Workshop included sixteen lectures presented by twelve invited speakers. The focus of the talks was untargeted metabolomics performed with liquid chromatography/mass spectrometry. In this review, we highlight five recurring topics that were covered by multiple presenters: (i) data sharing, (ii) artifacts and contaminants, (iii) feature degeneracy, (iv) database organization, and (v) requirements for metabolite identification. Our objective here is to present viewpoints that were widely shared among participants, as well as those in which varying opinions were articulated. We note that most of the presenting speakers employed different data processing software, which underscores the diversity of informatic programs currently being used in metabolomics. We conclude with our thoughts on the potential role of reference datasets as a step towards standardizing data processing methods in metabolomics.}, number={10}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Baker, Erin S. and Patti, Gary J.}, year={2019}, month={Oct}, pages={2031–2036} }
 @article{plante_francovic-fontaine_may_mclean_baker_laviolette_marchand_corbeil_2019, title={Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS}, volume={91}, ISSN={["1520-6882"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85064178745&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.8b05821}, abstractNote={Untargeted metabolomic measurements using mass spectrometry are a powerful tool for uncovering new small molecules with environmental and biological importance. The small molecule identification step, however, still remains an enormous challenge due to fragmentation difficulties or unspecific fragment ion information. Current methods to address this challenge are often dependent on databases or require the use of nuclear magnetic resonance (NMR), which have their own difficulties. The use of the gas-phase collision cross section (CCS) values obtained from ion mobility spectrometry (IMS) measurements were recently demonstrated to reduce the number of false positive metabolite identifications. While promising, the amount of empirical CCS information currently available is limited, thus predictive CCS methods need to be developed. In this article, we expand upon current experimental IMS capabilities by predicting the CCS values using a deep learning algorithm. We successfully developed and trained a prediction model for CCS values requiring only information about a compound's SMILES notation and ion type. The use of data from five different laboratories using different instruments allowed the algorithm to be trained and tested on more than 2400 molecules. The resulting CCS predictions were found to achieve a coefficient of determination of 0.97 and median relative error of 2.7% for a wide range of molecules. Furthermore, the method requires only a small amount of processing power to predict CCS values. Considering the performance, time, and resources necessary, as well as its applicability to a variety of molecules, this model was able to outperform all currently available CCS prediction algorithms.}, number={8}, journal={ANALYTICAL CHEMISTRY}, author={Plante, Pier-Luc and Francovic-Fontaine, Elina and May, Jody C. and McLean, John A. and Baker, Erin S. and Laviolette, Francois and Marchand, Mario and Corbeil, Jacques}, year={2019}, month={Apr}, pages={5191–5199} }
 @article{orton_tfaily_moore_lamarche_zheng_fillmore_chu_weitz_monroe_kelly_et al._2018, title={A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements}, volume={90}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85040192500&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.7b02986}, abstractNote={To better understand disease conditions and environmental perturbations, multiomic studies combining proteomic, lipidomic, and metabolomic analyses are vastly increasing in popularity. In a multiomic study, a single sample is typically extracted in multiple ways, and various analyses are performed using different instruments, most often based upon mass spectrometry (MS). Thus, one sample becomes many measurements, making high throughput and reproducible evaluations a necessity. One way to address the numerous samples and varying instrumental conditions is to utilize a flow injection analysis (FIA) system for rapid sample injections. While some FIA systems have been created to address these challenges, many have limitations such as costly consumables, low pressure capabilities, limited pressure monitoring, and fixed flow rates. To address these limitations, we created an automated, customizable FIA system capable of operating at a range of flow rates (∼50 nL/min to 500 μL/min) to accommodate both low- and high-flow MS ionization sources. This system also functions at varying analytical throughputs from 24 to 1200 samples per day to enable different MS analysis approaches. Applications ranging from native protein analyses to molecular library construction were performed using the FIA system, and results showed a highly robust and reproducible platform capable of providing consistent performance over many days without carryover, as long as washing buffers specific to each molecular analysis were utilized.}, number={1}, journal={Analytical Chemistry}, author={Orton, D.J. and Tfaily, M.M. and Moore, R.J. and Lamarche, B.L. and Zheng, X. and Fillmore, T.L. and Chu, R.K. and Weitz, K.K. and Monroe, M.E. and Kelly, R.T. and et al.}, year={2018}, pages={737–744} }
 @article{bilbao_gibbons_slysz_crowell_monroe_ibrahim_smith_payne_baker_2018, title={An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies}, volume={427}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85034616829&partnerID=MN8TOARS}, DOI={10.1016/j.ijms.2017.11.003}, abstractNote={The mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can yield erroneous results if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flight MS. In this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases for highly saturated species and dynamic range increased by 1-2 orders of magnitude for peptides in a blood serum sample.}, journal={International Journal of Mass Spectrometry}, author={Bilbao, A. and Gibbons, B.C. and Slysz, G.W. and Crowell, K.L. and Monroe, M.E. and Ibrahim, Y.M. and Smith, R.D. and Payne, S.H. and Baker, E.S.}, year={2018}, pages={91–99} }
 @article{kedia_wendler_baker_burnum-johnson_jarsberg_stratton_wright_piehowski_gritsenko_lewinsohn_et al._2018, title={Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis}, volume={112}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85050666053&partnerID=MN8TOARS}, DOI={10.1016/j.tube.2018.07.005}, abstractNote={The monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment. We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy. Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points. A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status. A comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care.}, journal={Tuberculosis}, author={Kedia, K. and Wendler, J.P. and Baker, E.S. and Burnum-Johnson, K.E. and Jarsberg, L.G. and Stratton, K.G. and Wright, A.T. and Piehowski, P.D. and Gritsenko, M.A. and Lewinsohn, D.M. and et al.}, year={2018}, pages={52–61} }
 @article{kyle_clair_bandyopadhyay_misra_zink_bloodsworth_shukla_du_lillis_myers_et al._2018, title={Cell type-resolved human lung lipidome reveals cellular cooperation in lung function}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85053010617&partnerID=MN8TOARS}, DOI={10.1038/s41598-018-31640-x}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, author={Kyle, J.E. and Clair, G. and Bandyopadhyay, G. and Misra, R.S. and Zink, E.M. and Bloodsworth, K.J. and Shukla, A.K. and Du, Y. and Lillis, J. and Myers, J.R. and et al.}, year={2018} }
 @article{horney_casillas_baker_stone_kirsch_camargo_wade_mcdonald_2018, title={Comparing residential contamination in a Houston environmental justice neighborhood before and after Hurricane Harvey}, volume={13}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85041735845&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0192660}, abstractNote={Introduction Polycyclic aromatic hydrocarbons (PAHs) are complex environmental toxicants. Exposure to them has been linked to adverse health outcomes including cancer, as well as diseases of the skin, liver, and immune system. Based on an ongoing community engagement partnership with stakeholder groups and residents, we conducted a small longitudinal study to assess domestic exposure to PAHs among residents of Manchester, an environmental justice neighborhood located in the East End of Houston, TX. Methods In December, 2016, we used fiber wipes to collect samples of household dust from 25 homes in Manchester. Following Hurricane Harvey, in September 2017, we revisited 24 of the 25 homes to collect soil samples from the front yards of the same homes. Wipes and soil were analyzed for the presence of PAHs using gas chromatography–mass spectrometry (GC-MS) methods. Principal component analysis plots, heatmaps, and PAH ratios were used to compare pre- and post-Hurricane Harvey samples. Results While direct comparison is not possible, we present three methods for comparing PAHs found in pre-hurricane fiber wipes and post-hurricane soil samples. The methods demonstrate that the PAHs found before and after Hurricane Harvey are likely from similar sources and that those sources are most likely to be associated with combustion. We also found evidence of redistribution of PAHs due to extreme flooding associated with Hurricane Harvey. Discussion Residents of the Manchester neighborhood of Houston, TX, are exposed to a range of PAHs in household dust and outdoor soil. While it was not possible to compare directly, we were able to use several methods to assess detected concentrations, changes in site-specific PAH allocations, and PAH origination. Additional research is needed to identify specific sources of domestic PAH exposure in these communities and continued work involving community members and policy makers should aim to develop interventions to reduce domestic exposure to and prevent negative health outcomes from PAHs.}, number={2}, journal={PLoS ONE}, author={Horney, J.A. and Casillas, G.A. and Baker, E. and Stone, K.W. and Kirsch, K.R. and Camargo, K. and Wade, T.L. and McDonald, T.J.}, year={2018} }
 @article{nagy_chouinard_attah_webb_garimella_ibrahim_baker_smith_2018, title={Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations}, volume={39}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85053448912&partnerID=MN8TOARS}, DOI={10.1002/elps.201800294}, abstractNote={Abstract}, number={24}, journal={Electrophoresis}, author={Nagy, G. and Chouinard, C.D. and Attah, I.K. and Webb, I.K. and Garimella, S.V.B. and Ibrahim, Y.M. and Baker, E.S. and Smith, R.D.}, year={2018}, pages={3148–3155} }
 @article{barran_baker_2018, title={Editorial overview: Omics}, volume={42}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042395623&partnerID=MN8TOARS}, DOI={10.1016/j.cbpa.2018.02.007}, journal={Current Opinion in Chemical Biology}, author={Barran, P. and Baker, E.}, year={2018}, pages={A1–A2} }
 @article{kyle_aly_zheng_burnum-johnson_smith_baker_2018, title={Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85043975901&partnerID=MN8TOARS}, DOI={10.4155/bio-2017-0245}, abstractNote={ Aim: Lipid mediators (LMs) are broadly defined as a class of bioactive lipophilic molecules that regulate cell-to-cell communication events with many having a strong correlation with various human diseases and conditions. LMs are usually analyzed with  LC–MS, but their numerous isomers greatly complicate the measurements with essentially identical fragmentation spectra and LC separations are not always sufficient for distinguishing the features. Results/methodology: In this work, we characterized LMs using ion mobility spectrometry (IMS) coupled with MS (IMS–MS). The collision cross-sections and m/z values from the IMS and MS analyses displayed distinct trend lines. Specifically, the structural trend lines for sodiated LMs originating from docosahexaenoic acid had the smallest collision cross-section values in relation to m/z, while those from linoleic acid had the largest. LC–IMS–MS analyses were also performed on LMs in flu infected mouse tissue samples. These multidimensional studies were able to assess known LMs while also detecting new species. Conclusion: Adding IMS separations to conventional LC–MS analyses show great utility for enabling better identification and characterization of LMs in complex biological samples. }, number={5}, journal={Bioanalysis}, author={Kyle, J.E. and Aly, N. and Zheng, X. and Burnum-Johnson, K.E. and Smith, R.D. and Baker, E.S.}, year={2018}, pages={279–289} }
 @article{baker_ogorzalek loo_2018, title={Guest editor's personal foreward}, volume={427}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85044001941&partnerID=MN8TOARS}, DOI={10.1016/j.ijms.2018.03.002}, journal={International Journal of Mass Spectrometry}, author={Baker, E.S. and Ogorzalek Loo, R.}, year={2018}, pages={1–3} }
 @article{orwoll_wiedrick_jacobs_baker_piehowski_petyuk_gao_shi_smith_bauer_et al._2018, title={High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men}, volume={17}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85041307766&partnerID=MN8TOARS}, DOI={10.1111/acel.12717}, abstractNote={Summary}, number={2}, journal={Aging Cell}, author={Orwoll, E.S. and Wiedrick, J. and Jacobs, J. and Baker, E.S. and Piehowski, P. and Petyuk, V. and Gao, Y. and Shi, T. and Smith, R.D. and Bauer, D.C. and et al.}, year={2018} }
 @article{chouinard_nagy_webb_shi_baker_prost_liu_ibrahim_smith_2018, title={Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry}, volume={90}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85052897753&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.8b02397}, abstractNote={Phosphoproteomics greatly augments proteomics and holds tremendous potential for insights into the modulation of biological systems for various disease states. However, numerous challenges hinder conventional methods in terms of measurement sensitivity, throughput, quantification, and capabilities for confident phosphopeptide and phosphosite identification. In this work, we report the first example of integrating structures for lossless ion manipulations ion mobility-mass spectrometry (SLIM IM-MS) with online reversed-phase liquid chromatography (LC) to evaluate its potential for addressing the aforementioned challenges. A mixture of 51 heavy-labeled phosphopeptides was analyzed with a SLIM IM module having integrated ion accumulation and long-path separation regions. The SLIM IM-MS provided limits of detection as low as 50-100 pM (50-100 amol/μL) for several phosphopeptides, with the potential for significant further improvements. In addition, conventionally problematic phosphopeptide isomers could be resolved following an 18 m SLIM IM separation. The 2-D LC-IM peak capacity was estimated as ∼9000 for a 90 min LC separation coupled to an 18 m SLIM IM separation, considerably higher than LC alone and providing a basis for both improved identification and quantification, with additional gains projected with the future use of longer path SLIM IM separations. Thus, LC-SLIM IM-MS offers great potential for improving the sensitivity, separation, and throughput of phosphoproteomics analyses.}, number={18}, journal={Analytical Chemistry}, author={Chouinard, C.D. and Nagy, G. and Webb, I.K. and Shi, T. and Baker, E.S. and Prost, S.A. and Liu, T. and Ibrahim, Y.M. and Smith, R.D.}, year={2018}, pages={10889–10896} }
 @misc{dautel_khan_brandvold_brislawn_hutchison_weitz_heyman_song_ilhan_hill_et al._2018, title={Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism}, url={http://dx.doi.org/10.1101/296020}, DOI={10.1101/296020}, abstractNote={ABSTRACT}, publisher={Cold Spring Harbor Laboratory}, author={Dautel, Sydney and Khan, Nymul and Brandvold, Kristoffer R. and Brislawn, Colin J. and Hutchison, Janine and Weitz, Karl K. and Heyman, Heino M. and Song, Hyun-Seob and Ilhan, Zehra Esra and Hill, Eric A. and et al.}, year={2018}, month={Apr} }
 @article{poad_zheng_mitchell_smith_baker_blanksby_2018, title={Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses}, volume={90}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85040692961&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.7b04091}, abstractNote={One of the most significant challenges in contemporary lipidomics lies in the separation and identification of lipid isomers that differ only in site(s) of unsaturation or geometric configuration of the carbon-carbon double bonds. While analytical separation techniques including ion mobility spectrometry (IMS) and liquid chromatography (LC) can separate isomeric lipids under appropriate conditions, conventional tandem mass spectrometry cannot provide unequivocal identification. To address this challenge, we have implemented ozone-induced dissociation (OzID) in-line with LC, IMS, and high resolution mass spectrometry. Modification of an IMS-capable quadrupole time-of-flight mass spectrometer was undertaken to allow the introduction of ozone into the high-pressure trapping ion funnel region preceding the IMS cell. This enabled the novel LC-OzID-IMS-MS configuration where ozonolysis of ionized lipids occurred rapidly (10 ms) without prior mass-selection. LC-elution time alignment combined with accurate mass and arrival time extraction of ozonolysis products facilitated correlation of precursor and product ions without mass-selection (and associated reductions in duty cycle). Unsaturated lipids across 11 classes were examined using this workflow in both positive and negative ion modalities, and in all cases, the positions of carbon-carbon double bonds were unequivocally assigned based on predictable OzID transitions. Under these conditions, geometric isomers exhibited different IMS arrival time distributions and distinct OzID product ion ratios providing a means for discrimination of cis/trans double bonds in complex lipids. The combination of OzID with multidimensional separations shows significant promise for facile profiling of unsaturation patterns within complex lipidomes including human plasma.}, number={2}, journal={Analytical Chemistry}, author={Poad, B.L.J. and Zheng, X. and Mitchell, T.W. and Smith, R.D. and Baker, E.S. and Blanksby, S.J.}, year={2018}, pages={1292–1300} }
 @article{chouinard_nagy_webb_garimella_baker_ibrahim_smith_2018, title={Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations}, volume={90}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85052280105&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.8b02990}, abstractNote={Bile acids (BAs) constitute an important class of steroid metabolites often displaying changes associated with disease states and other health conditions. Current analyses for these structurally similar compounds are limited by a lack of sensitivity and long separation times with often poor isomeric resolution. To overcome these challenges and provide rapid analyses for the BA isomers, we utilized cyclodextrin adducts in conjunction with novel ion mobility (IM) separation capabilities provided by structures for lossless ion manipulations (SLIM). Cyclodextrin was found to interact with both the tauro- and glyco-conjugated BA isomers studied, forming rigid noncovalent host-guest inclusion complexes. Without the use of cyclodextrin adducts, the BA isomers were found to be nearly identical in their respective mobilities and thus unable to be baseline resolved. Each separation of the cyclodextrin-bile acid host-guest inclusion complex was performed in less than 1 s, providing a much more rapid alternative to current liquid chromatography-based separations. SLIM provided capabilities for the accumulation of larger ion populations and IM peak compression that resulted in much higher resolution separations and increased signal intensities for the BA isomers studied.}, number={18}, journal={Analytical Chemistry}, author={Chouinard, C.D. and Nagy, G. and Webb, I.K. and Garimella, S.V.B. and Baker, E.S. and Ibrahim, Y.M. and Smith, R.D.}, year={2018}, pages={11086–11091} }
 @article{zheng_smith_baker_2018, title={Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches}, volume={42}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85037379449&partnerID=MN8TOARS}, DOI={10.1016/j.cbpa.2017.11.009}, abstractNote={Lipids are a vital class of molecules that play important and varied roles in biological processes, however, fully understanding these roles is extremely difficult due to the immense number and diversity of possible lipid species. While recent advances in chromatography and high resolution mass spectrometry have greatly progressed knowledge about distinct lipid species and functions, effectively separating many lipids still remains problematic. Isomeric lipids have made lipid characterization especially difficult and occur due to subclasses having the same chemical composition, or species having multiple acyl chain connectivities (sn-1, sn-2, or sn-3), double bond positions and orientations (cis or trans), and functional group stereochemistries (R versus S). To aid in isomer characterization, ion mobility spectrometry separations, ion-molecule reactions and fragmentation techniques have increasingly been added to lipid analysis workflows. In this manuscript, we review the current state of these approaches and their capabilities for improving the identification of lipid species.}, journal={Current Opinion in Chemical Biology}, author={Zheng, X. and Smith, R.D. and Baker, E.S.}, year={2018}, pages={111–118} }
 @article{nicora_burnum-johnson_nakayasu_casey_white_chowdhury_kyle_kim_smith_metz_et al._2018, title={The MPLEx protocol for multi-omic analyses of soil samples}, volume={2018}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85048523229&partnerID=MN8TOARS}, DOI={10.3791/57343}, abstractNote={Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges, since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for the simultaneous extraction of metabolites, proteins, and lipids (MPLEx) from the same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be both simple and robust for many sample types, even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.}, number={135}, journal={Journal of Visualized Experiments}, author={Nicora, C.D. and Burnum-Johnson, K.E. and Nakayasu, E.S. and Casey, C.P. and White, R.A. and Chowdhury, T.R. and Kyle, J.E. and Kim, Y.-M. and Smith, R.D. and Metz, T.O. and et al.}, year={2018} }
 @article{garabedian_benigni_ramirez_baker_liu_smith_fernandez-lima_2018, title={Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS}, volume={29}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042265514&partnerID=MN8TOARS}, DOI={10.1007/s13361-017-1787-8}, abstractNote={In the present work, the potential of trapped ion mobility spectrometry coupled to TOF mass spectrometry (TIMS-TOF MS) for discovery and targeted monitoring of peptide biomarkers from human-in-mouse xenograft tumor tissue was evaluated. In particular, a TIMS-MS workflow was developed for the detection and quantification of peptide biomarkers using internal heavy analogs, taking advantage of the high mobility resolution (R = 150-250) prior to mass analysis. Five peptide biomarkers were separated, identified, and quantified using offline nanoESI-TIMS-CID-TOF MS; the results were in good agreement with measurements using a traditional LC-ESI-MS/MS proteomics workflow. The TIMS-TOF MS analysis permitted peptide biomarker detection based on accurate mobility, mass measurements, and high sequence coverage for concentrations in the 10-200 nM range, while simultaneously achieving discovery measurements of not initially targeted peptides as markers from the same proteins and, eventually, other proteins. Graphical Abstract ᅟ.}, number={5}, journal={Journal of the American Society for Mass Spectrometry}, author={Garabedian, A. and Benigni, P. and Ramirez, C.E. and Baker, E.S. and Liu, T. and Smith, R.D. and Fernandez-Lima, F.}, year={2018}, pages={817–826} }
 @article{nagy_attah_garimella_tang_ibrahim_baker_smith_2018, title={Unraveling the isomeric heterogeneity of glycans: Ion mobility separations in structures for lossless ion manipulations}, volume={54}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85054888122&partnerID=MN8TOARS}, DOI={10.1039/c8cc06966b}, abstractNote={A new ultrahigh resolution ion mobility platform enables the fast separation and characterization of isomeric glycoforms.}, number={83}, journal={Chemical Communications}, author={Nagy, G. and Attah, I.K. and Garimella, S.V.B. and Tang, K. and Ibrahim, Y.M. and Baker, E.S. and Smith, R.D.}, year={2018}, pages={11701–11704} }
 @article{maclean_pratt_egertson_maccoss_smith_baker_2018, title={Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions}, volume={29}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85054891413&partnerID=MN8TOARS}, DOI={10.1007/s13361-018-2028-5}, abstractNote={Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations, and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline's ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly. Graphical Abstract ᅟ.}, number={11}, journal={Journal of the American Society for Mass Spectrometry}, author={MacLean, B.X. and Pratt, B.S. and Egertson, J.D. and MacCoss, M.J. and Smith, R.D. and Baker, E.S.}, year={2018}, pages={2182–2188} }
 @article{zheng_dupuis_aly_zhou_smith_tang_smith_baker_2018, title={Utilizing Ion Mobility Spectrometry and Mass Spectrometry for the Analysis of Polycyclic Aromatic Hydrocarbons, Polychlorinated Biphenyls, Polybrominated Diphenyl Ethers and Their Metabolites}, volume={1037}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85043992934&partnerID=MN8TOARS}, DOI={10.1016/j.aca.2018.02.054}, abstractNote={Polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are persistent environmental pollutants originating from incomplete combustion of organic materials and synthetic sources. PAHs, PCBs, and PBDEs have all been shown to have a significant effect on human health with correlations to cancer and other diseases. Therefore, measuring the presence of these xenobiotics in the environment and human body is imperative for assessing their health risks. To date, their analyses require both gas chromatography and liquid chromatography separations in conjunction with mass spectrometry measurements for detection of both the parent molecules and their hydroxylated metabolites, making their studies extremely time consuming. In this work, we characterized PAHs, PCBs, PBDEs and their hydroxylated metabolites using ion mobility spectrometry coupled with mass spectrometry (IMS-MS) and in combination with different ionization methods including electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI). The collision cross section and m/z trend lines derived from the IMS-MS analyses displayed distinct trends for each molecule type. Additionally, the rapid isomeric and molecular separations possible with IMS-MS showed great promise for quickly distinguishing the parent and metabolized PAH, PCB, and PDBE molecules in complex environmental and biological samples.}, journal={Analytica Chimica Acta}, author={Zheng, X. and Dupuis, K.T. and Aly, N.A. and Zhou, Y. and Smith, F.B. and Tang, K. and Smith, R.D. and Baker, E.S.}, year={2018}, month={Dec}, pages={265–273} }
 @article{zheng_aly_zhou_dupuis_bilbao_paurus_orton_wilson_payne_smith_et al._2017, title={A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85032012649&partnerID=MN8TOARS}, DOI={10.1039/c7sc03464d}, abstractNote={DTIMS collision cross section database for metabolites and xenobiotics.}, number={11}, journal={Chemical Science}, author={Zheng, X. and Aly, N.A. and Zhou, Y. and Dupuis, K.T. and Bilbao, A. and Paurus, V.L. and Orton, D.J. and Wilson, R. and Payne, S.H. and Smith, R.D. and et al.}, year={2017}, pages={7724–7736} }
 @article{stow_causon_zheng_kurulugama_mairinger_may_rennie_baker_smith_mclean_et al._2017, title={An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements}, volume={89}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85028930122&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.7b01729}, abstractNote={Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these DTCCSN2 values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field DTCCSN2 values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.}, number={17}, journal={Analytical Chemistry}, author={Stow, S.M. and Causon, T.J. and Zheng, X. and Kurulugama, R.T. and Mairinger, T. and May, J.C. and Rennie, E.E. and Baker, E.S. and Smith, R.D. and McLean, J.A. and et al.}, year={2017}, pages={9048–9055} }
 @article{burnum-johnson_baker_metz_2017, title={Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging}, volume={60}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85017158447&partnerID=MN8TOARS}, DOI={10.1016/j.placenta.2017.03.016}, abstractNote={Successful pregnancy is dependent upon discrete biological events, which include embryo implantation, decidualization, and placentation. Problems associated with each of these events can cause infertility or conditions such as preeclampsia. A greater understanding of the molecular changes associated with these complex processes is necessary to aid in identifying treatments for each condition. Previous nuclear magnetic resonance spectroscopy and mass spectrometry studies have been used to identify metabolites and lipids associated with pregnancy-related complications. However, due to limitations associated with conventional implementations of both techniques, novel technology developments are needed to more fully understand the initiation and development of pregnancy related problems at the molecular level. In this perspective, we describe current analytical techniques for metabolomic and lipidomic characterization of pregnancy complications and discuss the potential for new technologies such as ion mobility spectrometry-mass spectrometry and mass spectrometry imaging to contribute to a better understanding of the molecular changes that affect the placenta and pregnancy outcomes.}, journal={Placenta}, author={Burnum-Johnson, K.E. and Baker, E.S. and Metz, T.O.}, year={2017}, pages={S67–S72} }
 @article{kyle_casey_stratton_zink_kim_zheng_monroe_weitz_bloodsworth_orton_et al._2017, title={Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies}, volume={31}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000394512600006&KeyUID=WOS:000394512600006}, DOI={10.1002/rcm.7808}, abstractNote={RationaleThe use of dried blood spots (DBS) has many advantages over traditional plasma and serum samples such as the smaller blood volume required, storage at room temperature, and ability to sample in remote locations. However, understanding the robustness of different analytes in DBS samples is essential, especially in older samples collected for longitudinal studies.}, number={5}, journal={Rapid Communications in Mass Spectrometry}, author={Kyle, Jennifer E. and Casey, Cameron P. and Stratton, Kelly G. and Zink, Erika M. and Kim, Young-Mo and Zheng, Xueyun and Monroe, Matthew E. and Weitz, Karl K. and Bloodsworth, Kent J. and Orton, Daniel J. and et al.}, year={2017}, pages={447–456} }
 @article{deng_garimella_hamid_webb_attah_norheim_prost_zheng_sandoval_baker_et al._2017, title={Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)}, volume={89}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85021637956&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.7b00189}, abstractNote={We report on the implementation of a traveling wave (TW) based compression ratio ion mobility programming (CRIMP) approach within structures for lossless ion manipulations (SLIM) that enables both greatly enlarged trapped ion charge capacities and also efficient ion population compression for use in ion mobility (IM) separations. Ion accumulation is conducted in a SLIM serpentine ultralong path with extended routing (SUPER) region after which CRIMP compression allows the large ion populations to be "squeezed". The SLIM SUPER IM module has two regions, one operating with conventional traveling waves (i.e., traveling trap; TT region) and the second having an intermittently pausing or "stuttering" TW (i.e., stuttering trap; ST region). When a stationary voltage profile was used in the ST region, ions are blocked at the TT-ST interface and accumulated in the TT region and then can be released by resuming a conventional TW in the ST region. The population can also be compressed using CRIMP by the repetitive merging of ions distributed over multiple TW bins in the TT region into a single TW bin in the ST region. Ion accumulation followed by CRIMP compression provides the basis for the use of larger ion populations for IM separations. We show that over 109 ions can be accumulated with high efficiency in the present device and that the extent of subsequent compression is only limited by the space charge capacity of the trapping region. Approximately 5 × 109 charges introduced from an electrospray ionization source were trapped for a 40 s accumulation period, more than 2 orders of magnitude greater than the previously reported charge capacity of an ion funnel trap. Importantly, we show that extended ion accumulation in conjunction with CRIMP compression and multiple passes through the serpentine path provides the basis for a highly desirable combination of ultrahigh sensitivity and SLIM SUPER high-resolution IM separations.}, number={12}, journal={Analytical Chemistry}, author={Deng, L. and Garimella, S.V.B. and Hamid, A.M. and Webb, I.K. and Attah, I.K. and Norheim, R.V. and Prost, S.A. and Zheng, X. and Sandoval, J.A. and Baker, E.S. and et al.}, year={2017}, pages={6432–6439} }
 @inbook{heyman_zhang_tang_baker_metz_2017, title={Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications}, ISBN={9780128032244}, url={http://dx.doi.org/10.1016/b978-0-12-409547-2.12132-8}, DOI={10.1016/B978-0-12-409547-2.12132-8}, abstractNote={Metabolomics is the quantitative analysis of all metabolites in a given sample. Due to the chemical complexity of the metabolome, optimal separations are required for comprehensive identification and quantification of sample constituents. This article provides an overview of both conventional and advanced separation methods in practice for reducing the complexity of metabolite extracts delivered to the mass spectrometer detector, and covers gas chromatography, liquid chromatography, capillary electrophoresis, supercritical fluid chromatography, and ion mobility spectrometry separation techniques coupled with mass spectrometry as both uni- and multidimensional approaches.}, booktitle={Encyclopedia of Spectroscopy and Spectrometry}, publisher={Elsevier}, author={Heyman, H.M. and Zhang, X. and Tang, K. and Baker, E.S. and Metz, T.O.}, year={2017}, pages={376–384} }
 @book{zheng_wojcik_zhang_ibrahim_burnum-johnson_orton_monroe_moore_smith_baker_2017, title={Coupling front-end separations, ion mobility spectrometry, and mass spectrometry for enhanced multidimensional biological and environmental analyses}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85020700007&partnerID=MN8TOARS}, DOI={10.1146/annurev-anchem-061516-045212}, abstractNote={ Ion mobility spectrometry (IMS) is a widely used analytical technique for rapid molecular separations in the gas phase. Though IMS alone is useful, its coupling with mass spectrometry (MS) and front-end separations is extremely beneficial for increasing measurement sensitivity, peak capacity of complex mixtures, and the scope of molecular information available from biological and environmental sample analyses. In fact, multiple disease screening and environmental evaluations have illustrated that the IMS-based multidimensional separations extract information that cannot be acquired with each technique individually. This review highlights three-dimensional separations using IMS-MS in conjunction with a range of front-end techniques, such as gas chromatography, supercritical fluid chromatography, liquid chromatography, solid-phase extractions, capillary electrophoresis, field asymmetric ion mobility spectrometry, and microfluidic devices. The origination, current state, various applications, and future capabilities of these multidimensional approaches are described in detail to provide insight into their uses and benefits. }, journal={Annual Review of Analytical Chemistry}, author={Zheng, X. and Wojcik, R. and Zhang, X. and Ibrahim, Y.M. and Burnum-Johnson, K.E. and Orton, D.J. and Monroe, M.E. and Moore, R.J. and Smith, R.D. and Baker, E.S.}, year={2017}, pages={71–92} }
 @article{zheng_deng_baker_ibrahim_petyuk_smith_2017, title={Distinguishing D- and L-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry}, volume={53}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85023742938&partnerID=MN8TOARS}, DOI={10.1039/c7cc03321d}, abstractNote={Ion mobility spectrometry (IMS) was utilized to separate Aβ peptide variants containing isomeric asparic and isoaspartic acid residues with either al- ord-form. The abundance of each variant is of great interest in Alzheimer's disease studies and also to evaluate how often these modifications are occurring in other environmental and biological samples.}, number={56}, journal={Chemical Communications}, author={Zheng, X. and Deng, L. and Baker, E.S. and Ibrahim, Y.M. and Petyuk, V.A. and Smith, R.D.}, year={2017}, pages={7913–7916} }
 @article{zheng_zhang_schocker_renslow_orton_khamsi_ashmus_almeida_tang_costello_et al._2017, title={Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses}, volume={409}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000391364200010&KeyUID=WOS:000391364200010}, DOI={10.1007/s00216-016-9866-4}, abstractNote={Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules, such as proteins and lipids, and alter their properties and functions, so glycan characterization is essential for understanding the effects they have on cellular systems. However, the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycan standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest that specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS.}, number={2}, journal={Analytical and Bioanalytical Chemistry}, author={Zheng, Xueyun and Zhang, Xing and Schocker, Nathaniel S. and Renslow, Ryan S. and Orton, Daniel J. and Khamsi, Jamal and Ashmus, Roger A. and Almeida, Igor C. and Tang, Keqi and Costello, Catherine E. and et al.}, year={2017}, pages={467–476} }
 @article{nielson_wiedrick_shen_jacobs_baker_baraff_piehowski_lee_baratt_petyuk_et al._2017, title={Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics}, volume={32}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85017431107&partnerID=MN8TOARS}, DOI={10.1002/jbmr.3125}, abstractNote={ABSTRACT}, number={7}, journal={Journal of Bone and Mineral Research}, author={Nielson, C.M. and Wiedrick, J. and Shen, J. and Jacobs, J. and Baker, E.S. and Baraff, A. and Piehowski, P. and Lee, C.G. and Baratt, A. and Petyuk, V. and et al.}, year={2017}, pages={1559–1567} }
 @article{metz_baker_schymanski_renslow_thomas_causon_webb_hann_smith_teeguarden_2017, title={Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go?}, volume={9}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390768100008&KeyUID=WOS:000390768100008}, DOI={10.4155/bio-2016-0244}, abstractNote={ Measuring the exposome remains a challenge due to the range and number of anthropogenic molecules that are encountered in our daily lives, as well as the complex systemic responses to these exposures. One option for improving the coverage, dynamic range and throughput of measurements is to incorporate ion mobility spectrometry (IMS) into current MS-based analytical methods. The implementation of IMS in exposomics studies will lead to more frequent observations of previously undetected chemicals and metabolites. LC-IMS-MS will provide increased overall measurement dynamic range, resulting in detections of lower abundance molecules. Alternatively, the throughput of IMS-MS alone will provide the opportunity to analyze many thousands of longitudinal samples over lifetimes of exposure, capturing evidence of transitory accumulations of chemicals or metabolites. The volume of data corresponding to these new chemical observations will almost certainly outpace the generation of reference data to enable their confident identification. In this perspective, we briefly review the state-of-the-art in measuring the exposome, and discuss the potential use for IMS-MS and the physico-chemical property of collisional cross section in both exposure assessment and molecular identification. }, number={1}, journal={Bioanalysis}, author={Metz, Thomas O. and Baker, Erin S. and Schymanski, Emma L. and Renslow, Ryan S. and Thomas, Dennis G. and Causon, Tim J. and Webb, Ian K. and Hann, Stephan and Smith, Richard D. and Teeguarden, Justin G.}, year={2017}, pages={81–98} }
 @article{ligare_baker_laskin_johnson_2017, title={Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry}, volume={53}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85021671391&partnerID=MN8TOARS}, DOI={10.1039/c7cc02251d}, abstractNote={Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry.}, number={53}, journal={Chemical Communications}, author={Ligare, M.R. and Baker, E.S. and Laskin, J. and Johnson, G.E.}, year={2017}, pages={7389–7392} }
 @article{wojcik_webb_deng_garimella_prost_ibrahim_baker_smith_2017, title={Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations}, volume={18}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000393030600180&KeyUID=WOS:000393030600180}, DOI={10.3390/ijms18010183}, abstractNote={Understanding the biological roles and mechanisms of lipids and glycolipids is challenging due to the vast number of possible isomers that may exist. Mass spectrometry (MS) measurements are currently the dominant approach for studying and providing detailed information on lipid and glycolipid presence and changes. However, difficulties in distinguishing the many structural isomers, due to the distinct lipid acyl chain positions, double bond locations or specific glycan types, inhibit the delineation and assignment of their biological roles. Here we utilized ultra-high resolution ion mobility spectrometry (IMS) separations by applying traveling waves in a serpentine multi-pass Structures for Lossless Ion Manipulations (SLIM) platform to enhance the separation of selected lipid and glycolipid isomers. The multi-pass arrangement allowed the investigation of paths ranging from ~16 m (one pass) to ~60 m (four passes) for the distinction of lipids and glycolipids with extremely small structural differences. These ultra-high resolution SLIM IMS-MS analyses provide a foundation for exploring and better understanding isomer-specific biological activities and disease processes.}, number={1}, journal={International Journal of Molecular Sciences}, author={Wojcik, Roza and Webb, Ian K. and Deng, Liulin and Garimella, Sandilya V. B. and Prost, Spencer A. and Ibrahim, Yehia M. and Baker, Erin S. and Smith, Richard D.}, year={2017} }
 @article{ibrahim_hamid_deng_garimella_webb_baker_smith_2017, title={New frontiers for mass spectrometry based upon structures for lossless ion manipulations}, volume={142}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85016476731&partnerID=MN8TOARS}, DOI={10.1039/c7an00031f}, abstractNote={SLIM utilize manipulations in ion conduits created from electric fields generated by applying potentials to arrays of electrodes patterned on two planar surfaces.}, number={7}, journal={Analyst}, author={Ibrahim, Y.M. and Hamid, A.M. and Deng, L. and Garimella, S.V.B. and Webb, I.K. and Baker, E.S. and Smith, R.D.}, year={2017}, pages={1010–1021} }
 @article{ma_casey_zheng_ibrahim_wilkins_renslow_thomas_payne_monroe_smith_et al._2017, title={PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association}, volume={33}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85033490700&partnerID=MN8TOARS}, DOI={10.1093/bioinformatics/btx305}, abstractNote={Abstract}, number={17}, journal={Bioinformatics (Oxford, England)}, author={Ma, J. and Casey, C.P. and Zheng, X. and Ibrahim, Y.M. and Wilkins, C.S. and Renslow, R.S. and Thomas, D.G. and Payne, S.H. and Monroe, M.E. and Smith, R.D. and et al.}, year={2017}, pages={2715–2722} }
 @article{rosnow_anderson_nair_baker_wright_2017, title={Profiling microbial lignocellulose degradation and utilization by emergent omics technologies}, volume={37}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000402018600006&KeyUID=WOS:000402018600006}, DOI={10.1080/07388551.2016.1209158}, abstractNote={Abstract The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emerging technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production.}, number={5}, journal={Critical Reviews in Biotechnology}, author={Rosnow, J. and Anderson, L.N. and Nair, R.N. and Baker, E.S. and Wright, A.T.}, year={2017}, pages={626–640} }
 @article{deng_webb_garimella_hamid_zheng_norheim_prost_anderson_sandoval_baker_et al._2017, title={Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations}, volume={89}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000399858800046&KeyUID=WOS:000399858800046}, DOI={10.1021/acs.analchem.7b00185}, abstractNote={Ion mobility (IM) separations have a broad range of analytical applications, but insufficient resolution often limits their utility. Here, we report on ion mobility separations in a structures for lossless ion manipulations (SLIM) serpentine ultralong path with extended routing (SUPER) traveling wave (TW) ion mobility (IM) module in conjunction with mass spectrometry (MS). Ions were confined in the SLIM by rf fields in conjunction with a DC guard bias, enabling essentially lossless TW transmission over greatly extended paths. The extended routing utilized multiple passes (e.g., ∼1094 m over 81 passes through the 13.5 m serpentine path) and was facilitated by the introduction of a lossless ion switch that allowed ions to be directed to either the MS detector or for another pass through the serpentine separation region, allowing theoretically unlimited IM path lengths. The multipass SUPER IM-MS provided resolution approximately proportional to the square root of the number of passes (or total path length). More than 30-fold higher IM resolution (∼340 vs ∼10) for Agilent tuning mix m/z 622 and 922 ions was achieved for 40 passes compared to commercially available drift tube IM and other TWIM-based platforms. An initial evaluation of the isomeric sugars lacto-N-hexaose and lacto-N-neohexaose showed the isomeric structures to be baseline resolved, and a new conformational feature for lacto-N-neohexaose was revealed after 9 passes. The new SLIM SUPER high resolution TWIM platform has broad utility in conjunction with MS and is expected to enable a broad range of previously challenging or intractable separations.}, number={8}, journal={Analytical Chemistry}, author={Deng, Liulin and Webb, Ian K. and Garimella, Sandilya V. B. and Hamid, Ahmed M. and Zheng, Xueyun and Norheim, Randolph V. and Prost, Spencer A. and Anderson, Gordon A. and Sandoval, Jeremy A. and Baker, Erin S. and et al.}, year={2017}, pages={4628–4634} }
 @article{zheng_renslow_makola_webb_deng_thomas_govind_ibrahim_kabanda_dubery_et al._2017, title={Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry}, volume={8}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000398884800010&KeyUID=WOS:000398884800010}, DOI={10.1021/acs.jpclett.6b03015}, abstractNote={Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.}, number={7}, journal={Journal of Physical Chemistry Letters}, author={Zheng, Xueyun and Renslow, Ryan S. and Makola, Mpho M. and Webb, Ian K. and Deng, Liulin and Thomas, Dennis G. and Govind, Niranjan and Ibrahim, Yehia M. and Kabanda, Mwadham M. and Dubery, Ian A. and et al.}, year={2017}, pages={1381–1388} }
 @article{webb_garimella_norheim_baker_ibrahim_smith_2016, title={A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation}, volume={27}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000377416200017&KeyUID=WOS:000377416200017}, DOI={10.1007/s13361-016-1397-x}, abstractNote={A collision induced dissociation (CID) structure for lossless ion manipulations (SLIM) module is introduced and coupled to a quadrupole time-of-flight (QTOF) mass spectrometer. The SLIM CID module was mounted after an ion mobility (IM) drift tube to enable IM/CID/MS studies. The efficiency of CID was studied by using the model peptide leucine enkephalin. CID efficiencies (62%) compared favorably with other beam-type CID methods. Additionally, the SLIM CID module was used to fragment a mixture of nine peptides after IM separation. This work also represents the first application of SLIM in the 0.3 to 0.5 Torr pressure regime, an order of magnitude lower in pressure than previously studied.}, number={7}, journal={Journal of the American Society For Mass Spectrometry}, author={Webb, Ian K. and Garimella, Sandilya V. B. and Norheim, Randolph V. and Baker, Erin S. and Ibrahim, Yehia M. and Smith, Richard D.}, year={2016}, pages={1285–1288} }
 @article{jansson_baker_2016, title={A multi-omic future for microbiome studies}, volume={1}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000383605200010&KeyUID=WOS:000383605200010}, DOI={10.1038/NMICROBIOL.2016.49}, abstractNote={Integration of multiple ‘omics’ technologies will allow researchers to gain a more complete picture of the constituents and functions of microbial communities and provide far richer information for predictive modelling of community phenotypes.}, number={5}, journal={Nature Microbiology}, author={Jansson, Janet K. and Baker, Erin S.}, year={2016} }
 @article{hamid_garimella_ibrahim_deng_zheng_webb_anderson_prost_norheim_tolmachev_et al._2016, title={Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations}, volume={88}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384038400006&KeyUID=WOS:000384038400006}, DOI={10.1021/acs.analchem.6b01914}, abstractNote={We report on ion mobility (IM) separations achievable using traveling waves (TW) in a Structures for Lossless Ion Manipulations (SLIM) module having a 44 cm path length and 16 90° turns. The performance of the TW-SLIM module was evaluated for ion transmission and IM separations with different RF, TW parameters, and SLIM surface gaps in conjunction with mass spectrometry. In this work, TWs were created by the transient and dynamic application of DC potentials. The module demonstrated highly robust performance and, even with 16 closely spaced turns, achieving IM resolution performance and ion transmission comparable to a similar straight path module. We found an IM peak capacity of ∼31 and peak generation rate of 780 s(-1) for TW speeds of ∼80 m/s using the current multi-turn TW-SLIM module. The separations achieved for isomers of peptides and tetrasaccharides were found to be comparable to those from a ∼0.9-m drift tube-based IM-MS platform operated at the same pressure (4 Torr). The combined attributes of flexible design, low voltage requirements and lossless ion transmission through multiple turns for the present TW-SLIM module provides a basis for SLIM devices capable of achieving much greater IM resolution via greatly extended ion path lengths and using compact serpentine designs.}, number={18}, journal={Analytical Chemistry}, author={Hamid, Ahmed M. and Garimella, Sandilya V. B. and Ibrahim, Yehia M. and Deng, Liulin and Zheng, Xueyun and Webb, Ian K. and Anderson, Gordon A. and Prost, Spencer A. and Norheim, Randolph V. and Tolmachev, Aleksey V. and et al.}, year={2016}, pages={8949–8956} }
 @article{ibrahim_garimella_prost_wojcik_norheim_baker_rusyn_smith_2016, title={Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform}, volume={88}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390621000027&KeyUID=WOS:000390621000027}, DOI={10.1021/acs.analchem.6b03027}, abstractNote={Complex samples benefit from multidimensional measurements where higher resolution enables more complete characterization of biological and environmental systems. To address this challenge, we developed a drift tube-based ion mobility spectrometry-Orbitrap mass spectrometer (IMS-Orbitrap MS) platform. To circumvent the time scale disparity between the fast IMS separation and the much slower Orbitrap MS acquisition, we utilized a dual gate and pseudorandom sequences to multiplex the injection of ions and allow operation in signal averaging (SA), single multiplexing (SM), and double multiplexing (DM) IMS modes to optimize the signal-to-noise ratio of the measurements. For the SM measurements, a previously developed algorithm was used to reconstruct the IMS data. A new algorithm was developed for the DM analyses involving a two-step process that first recovers the SM data and then decodes the SM data. The algorithm also performs multiple refining procedures to minimize demultiplexing artifacts. The new IMS-Orbitrap MS platform was demonstrated by the analysis of proteomic and petroleum samples, where the integration of IMS and high mass resolution proved essential for accurate assignment of molecular formulas.}, number={24}, journal={Analytical Chemistry}, author={Ibrahim, Yehia M. and Garimella, Sandilya V. B. and Prost, Spencer A. and Wojcik, Roza and Norheim, Randolph V. and Baker, Erin S. and Rusyn, Ivan and Smith, Richard D.}, year={2016}, pages={12152–12160} }
 @article{deng_ibrahim_garimella_webb_hamid_norheim_prost_sandoval_baker_smith_2016, title={Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations}, volume={88}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000385907400038&KeyUID=WOS:000385907400038}, DOI={10.1021/acs.analchem.6b02678}, abstractNote={The initial use of traveling waves (TW) for ion mobility (IM) separations using structures for lossless ion manipulations (SLIM) employed an ion funnel trap (IFT) to accumulate ions from a continuous electrospray ionization source and was limited to injected ion populations of ∼106 charges due to the onset of space charge effects in the trapping region. Additional limitations arise due to the loss of resolution for the injection of ions over longer periods, such as in extended pulses. In this work a new SLIM "flat funnel" (FF) module has been developed and demonstrated to enable the accumulation of much larger ion populations and their injection for IM separations. Ion current measurements indicate a capacity of ∼3.2 × 108 charges for the extended trapping volume, over an order of magnitude greater than that of the IFT. The orthogonal ion injection into a funnel shaped separation region can greatly reduce space charge effects during the initial IM separation stage, and the gradually reduced width of the path allows the ion packet to be increasingly compressed in the lateral dimension as the separation progresses, allowing efficient transmission through conductance limits or compatibility with subsequent ion manipulations. This work examined the TW, rf, and dc confining field SLIM parameters involved in ion accumulation, injection, transmission, and IM separation in the FF module using both direct ion current and MS measurements. Wide m/z range ion transmission is demonstrated, along with significant increases in the signal-to-noise ratios (S/N) due to the larger ion populations injected. Additionally, we observed a reduction in the chemical background, which was attributed to more efficient desolvation of solvent related clusters over the extended ion accumulation periods. The TW SLIM FF IM module is anticipated to be especially effective as a front end for long path SLIM IM separation modules.}, number={20}, journal={Analytical Chemistry}, author={Deng, Liulin and Ibrahim, Yehia M. and Garimella, Sandilya V. B. and Webb, Ian K. and Hamid, Ahmed M. and Norheim, Randolph V. and Prost, Spencer A. and Sandoval, Jeremy A. and Baker, Erin S. and Smith, Richard D.}, year={2016}, pages={10143–10150} }
 @article{deng_ibrahim_baker_aly_hamid_zhang_zheng_garimella_webb_prost_et al._2016, title={Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry}, volume={1}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000395417800045&KeyUID=WOS:000395417800045}, DOI={10.1002/slct.201600460}, abstractNote={Abstract}, number={10}, journal={Chemistryselect}, author={Deng, Liulin and Ibrahim, Yehia M. and Baker, Erin S. and Aly, Noor A. and Hamid, Ahmed M. and Zhang, Xing and Zheng, Xueyun and Garimella, Sandilya V. B. and Webb, Ian K. and Prost, Spencer A. and et al.}, year={2016}, pages={2396–2399} }
 @article{cong_katipamula_trader_orton_geng_baker_kelly_2016, title={Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform}, volume={16}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000375569500001&KeyUID=WOS:000375569500001}, DOI={10.1039/c6lc00183a}, abstractNote={We present a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and an integrated electrospray ionization source for mass spectrometry-based monitoring of protein–ligand binding dynamics.}, number={9}, journal={Lab on a Chip}, author={Cong, Yongzheng and Katipamula, Shanta and Trader, Cameron D. and Orton, Daniel J. and Geng, Tao and Baker, Erin S. and Kelly, Ryan T.}, year={2016}, pages={1544–1548} }
 @article{chen_ibrahim_webb_garimella_zhang_hamid_deng_karnesky_prost_sandoval_et al._2016, title={Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations}, volume={88}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000369471100036&KeyUID=WOS:000369471100036}, DOI={10.1021/acs.analchem.5b03910}, abstractNote={The integration of ion mobility spectrometry (IMS) with mass spectrometry (MS) and the ability to trap ions in IMS-MS measurements is of great importance for performing reactions, accumulating ions, and increasing analytical measurement sensitivity. The development of Structures for Lossless Ion Manipulations (SLIM) offers the potential for ion manipulations in an extended and more effective manner, while opening opportunities for many more complex sequences of manipulations. Here, we demonstrate an ion separation and trapping module and a method based upon SLIM that consists of a linear mobility ion drift region, a switch/tee and a trapping region that allows the isolation and accumulation of mobility-separated species. The operation and optimization of the SLIM switch/tee and trap are described and demonstrated for the enrichment of the low abundance ions. A linear improvement in ion intensity was observed with the number of trapping/accumulation events using the SLIM trap, illustrating its potential for enhancing the sensitivity of low abundance or targeted species.}, number={3}, journal={Analytical Chemistry}, author={Chen, Tsung-Chi and Ibrahim, Yehia M. and Webb, Ian K. and Garimella, Sandilya V. B. and Zhang, Xing and Hamid, Ahmed M. and Deng, Liulin and Karnesky, William E. and Prost, Spencer A. and Sandoval, Jeremy A. and et al.}, year={2016}, pages={1728–1733} }
 @article{zhang_romm_zheng_zink_kim_burnum-johnson_orton_apffel_ibrahim_monroe_et al._2016, title={SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids}, volume={2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85020543103&partnerID=MN8TOARS}, DOI={10.1016/j.clinms.2016.11.002}, abstractNote={Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV ⩽ 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.}, journal={Clinical Mass Spectrometry}, author={Zhang, X. and Romm, M. and Zheng, X. and Zink, E.M. and Kim, Y.-M. and Burnum-Johnson, K.E. and Orton, D.J. and Apffel, A. and Ibrahim, Y.M. and Monroe, M.E. and et al.}, year={2016}, pages={1–10} }
 @article{burnum-johnson_nie_casey_monroe_orton_ibrahim_gritsenko_clauss_shukla_moore_et al._2016, title={Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry}, volume={15}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000390346600012&KeyUID=WOS:000390346600012}, DOI={10.1074/mcp.M116.061143}, abstractNote={Current proteomic approaches include both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g. candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, whereas targeted measurements are significantly more sensitive but only sample a limited portion of the proteome. Herein, we describe a new approach that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled target peptides are spiked into tryptic digests and both the labeled and unlabeled peptides are detected using LC-IMS-MS instrumentation. Compared with the broad LC-MS discovery measurements, DTM yields greater peptide/protein coverage and detects lower abundance species. DTM also achieved detection limits similar to selected reaction monitoring (SRM) indicating its potential for combined high quality discovery and targeted analyses, which is a significant step toward the convergence of discovery and targeted approaches.}, number={12}, journal={Molecular & Cellular Proteomics}, author={Burnum-Johnson, Kristin E. and Nie, Song and Casey, Cameron P. and Monroe, Matthew E. and Orton, Daniel J. and Ibrahim, Yehia M. and Gritsenko, Marina A. and Clauss, Therese R. W. and Shukla, Anil K. and Moore, Ronald J. and et al.}, year={2016}, pages={3694–3705} }
 @article{garimella_ibrahim_tang_webb_baker_tolmachev_chen_anderson_smith_2016, title={Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry}, volume={27}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000376103700020&KeyUID=WOS:000376103700020}, DOI={10.1007/s13361-016-1371-7}, abstractNote={A novel concept for ion spatial peak compression is described, and discussed primarily in the context of ion mobility spectrometry (IMS). Using theoretical and numerical methods, the effects of using non-constant (e.g., linearly varying) electric fields on ion distributions (e.g., an ion mobility peak) is evaluated both in the physical and temporal domains. The application of a linearly decreasing electric field in conjunction with conventional drift field arrangements is shown to lead to a reduction in IMS physical peak width. When multiple ion packets (i.e., peaks) in a selected mobility window are simultaneously subjected to such fields, there is ion packet compression (i.e., a reduction in peak widths for all species). This peak compression occurs with only a modest reduction of resolution, which can be quickly recovered as ions drift in a constant field after the compression event. Compression also yields a significant increase in peak intensities. Ion mobility peak compression can be particularly useful for mitigating diffusion-driven peak broadening over very long path length separations (e.g., in cyclic multi-pass arrangements), and for achieving higher S/N and IMS resolution over a selected mobility range. Graphical Abstract ᅟ.}, number={6}, journal={Journal of the American Society For Mass Spectrometry}, author={Garimella, Sandilya V. B. and Ibrahim, Yehia M. and Tang, Keqi and Webb, Ian K. and Baker, Erin S. and Tolmachev, Aleksey V. and Chen, Tsung-Chi and Anderson, Gordon A. and Smith, Richard D.}, year={2016}, pages={1128–1135} }
 @article{garimella_hamid_deng_ibrahim_webb_baker_prost_norheim_anderson_smith_2016, title={Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming}, volume={88}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000389556900086&KeyUID=WOS:000389556900086}, DOI={10.1021/acs.analchem.6b03660}, abstractNote={In this work we report an approach for spatial and temporal gas-phase ion population manipulation, wherein we collapse ion distributions in ion mobility (IM) separations into tighter packets providing higher sensitivity measurements in conjunction with mass spectrometry (MS). We do this for ions moving from a conventional traveling wave (TW)-driven region to a region where the TW is intermittently halted or "stuttered". This approach causes the ion packets spanning a number of TW-created traveling traps (TT) to be redistributed into fewer TT, resulting in spatial compression. The degree of spatial compression is controllable and determined by the ratio of stationary time of the TW in the second region to its moving time. This compression ratio ion mobility programming (CRIMP) approach has been implemented using "structures for lossless ion manipulations" (SLIM) in conjunction with MS. CRIMP with the SLIM-MS platform is shown to provide increased peak intensities, reduced peak widths, and improved signal-to-noise (S/N) ratios with MS detection. CRIMP also provides a foundation for extremely long path length and multipass IM separations in SLIM providing greatly enhanced IM resolution by reducing the detrimental effects of diffusional peak broadening and increasing peak widths.}, number={23}, journal={Analytical Chemistry}, author={Garimella, Sandilya V. B. and Hamid, Ahmed M. and Deng, Liulin and Ibrahim, Yehia M. and Webb, Ian K. and Baker, Erin S. and Prost, Spencer A. and Norheim, Randolph V. and Anderson, Gordon A. and Smith, Richard D.}, year={2016}, pages={11877–11885} }
 @article{liu_cheng_baker_smith_zeng_gong_2016, title={Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers}, volume={52}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371477100007&KeyUID=WOS:000371477100007}, DOI={10.1039/c6cc00224b}, abstractNote={The remote end groups of aromatic foldamers are found to profoundly impact the assembling propensity of these molecules.}, number={19}, journal={Chemical Communications}, author={Liu, Rui and Cheng, Shuang and Baker, Erin S. and Smith, Richard D. and Zeng, Xiao Cheng and Gong, Bing}, year={2016}, pages={3773–3776} }
 @article{liu_chen_baker_smith_zeng_gong_2016, title={Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers (vol 52, pg 3773, 2016)}, volume={52}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000373629800030&KeyUID=WOS:000373629800030}, DOI={10.1039/c6cc90142e}, abstractNote={Correction for ‘Surprising impact of remote groups on the folding–unfolding and dimer-chain equilibria of bifunctional H-bonding unimers’ by Rui Liu et al., Chem. Commun., 2016, 52, 3773–3776.}, number={29}, journal={Chemical Communications}, author={Liu, Rui and Chen, Shuang and Baker, Erin S. and Smith, Richard D. and Zeng, Xiao Cheng and Gong, Bing}, year={2016}, pages={5205} }
 @article{khadempour_burnum-johnson_baker_nicora_webb-robertson_white_monroe_huang_smith_currie_2016, title={The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates}, volume={25}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000387659300015&KeyUID=WOS:000387659300015}, DOI={10.1111/mec.13872}, abstractNote={Abstract}, number={22}, journal={Molecular Ecology}, author={Khadempour, Lily and Burnum-Johnson, Kristin E. and Baker, Erin S. and Nicora, Carrie D. and Webb-Robertson, Bobbie-Jo M. and White, Richard A., III and Monroe, Matthew E. and Huang, Eric L. and Smith, Richard D. and Currie, Cameron R.}, year={2016}, pages={5795–5805} }
 @article{white_callister_moore_baker_jansson_2016, title={The past, present and future of microbiome analyses}, volume={11}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000384414000001&KeyUID=WOS:000384414000001}, DOI={10.1038/nprot.2016.148}, number={11}, journal={Nature Protocols}, author={White, Richard Allen, III and Callister, Stephen J. and Moore, Ronald J. and Baker, Erin S. and Jansson, Janet K.}, year={2016}, pages={4–8} }
 @article{deng_ibrahim_hamid_garimella_webb_zheng_prost_sandoval_norheim_anderson_et al._2016, title={Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module}, volume={88}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84988478571&partnerID=MN8TOARS}, DOI={10.1021/acs.analchem.6b01915}, abstractNote={We report the development and initial evaluation of a 13 m path length Structures for Lossless Manipulations (SLIM) module for achieving high resolution separations using traveling waves (TW) with ion mobility (IM) spectrometry. The TW SLIM module was fabricated using two mirror-image printed circuit boards with appropriately configured RF, DC, and TW electrodes and positioned with a 2.75 mm intersurface gap. Ions were effectively confined in field-generated conduits between the surfaces by RF-generated pseudopotential fields and moved losslessly through a serpentine path including 44 "U" turns using TWs. The ion mobility resolution was characterized at different pressures, gaps between the SLIM surfaces, and TW and RF parameters. After initial optimization, the SLIM IM-MS module provided about 5-fold higher resolution separations than present commercially available drift tube or traveling wave IM-MS platforms. Peak capacity and peak generation rates achieved were 246 and 370 s(-1), respectively, at a TW speed of 148 m/s. The high resolution achieved in the TW SLIM IM-MS enabled, e.g., isomeric sugars (lacto-N-fucopentaose I and lacto-N-fucopentaose II) to be baseline resolved, and peptides from an albumin tryptic digest were much better resolved than with existing commercial IM-MS platforms. The present work also provides a foundation for the development of much higher resolution SLIM devices based upon both considerably longer path lengths and multipass designs.}, number={18}, journal={Analytical Chemistry}, author={Deng, L. and Ibrahim, Y.M. and Hamid, A.M. and Garimella, S.V.B. and Webb, I.K. and Zheng, X. and Prost, S.A. and Sandoval, J.A. and Norheim, R.V. and Anderson, G.A. and et al.}, year={2016}, pages={8957–8964} }
 @article{kyle_zhang_weitz_monroe_ibrahim_moore_cha_sun_lovelace_wagoner_et al._2016, title={Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry}, volume={141}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000371229600010&KeyUID=WOS:000371229600010}, DOI={10.1039/c5an02062j}, abstractNote={LC-IMS-MS spectra of lipids in mouse decidua tissue.}, number={5}, journal={Analyst}, author={Kyle, Jennifer E. and Zhang, Xing and Weitz, Karl K. and Monroe, Matthew E. and Ibrahim, Yehia M. and Moore, Ronald J. and Cha, Jeeyeon and Sun, Xiaofei and Lovelace, Erica S. and Wagoner, Jessica and et al.}, year={2016}, pages={1649–1659} }
 @article{ibrahim_baker_danielson_norheim_prior_anderson_belov_smith_2015, title={Development of a new ion mobility (quadrupole) time-of-flight mass spectrometer}, volume={377}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85027921067&partnerID=MN8TOARS}, DOI={10.1016/j.ijms.2014.07.034}, abstractNote={A new ion mobility spectrometer (IMS) platform was developed to improve upon the sensitivity and reproducibility of our previous platforms, and further enhance IMS-MS utility for broad 'pan-omics' measurements. The new platform incorporated an improved electrospray ionization source and interface for enhanced sensitivity, and providing the basis for further benefits based upon implementation of multiplexed IMS. The ion optics included electrodynamic ion funnels at both the entrance and exit of the IMS, an ion funnel trap for ion injection, and a design in which nearly all ion optics (e.g. drift rings, ion funnels) were fabricated using printed circuit board technology. The IMS resolving power achieved was ~73 for singly-charged ions, very close to the predicted diffusion-limited resolving power (~75). The platform's performance evaluation (e.g. for proteomics measurements) include LC-IMS-TOF MS datasets for 30 technical replicates for a trypsin digested human serum, and included platform performance in each dimension (LC, IMS and MS) separately.}, number={1}, journal={International Journal of Mass Spectrometry}, author={Ibrahim, Y.M. and Baker, E.S. and Danielson, W.F. and Norheim, R.V. and Prior, D.C. and Anderson, G.A. and Belov, M.E. and Smith, R.D.}, year={2015}, pages={655–662} }
 @article{zhang_ibrahim_chen_kyle_norheim_monroe_smith_baker_2015, title={Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations}, volume={140}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84942612537&partnerID=MN8TOARS}, DOI={10.1039/c5an00897b}, abstractNote={Novel μFAIMS/IMS-MS three dimensional separations were optimized to enhance separation power and selectivity in biological analyses.}, number={20}, journal={Analyst}, author={Zhang, X. and Ibrahim, Y.M. and Chen, T.-C. and Kyle, J.E. and Norheim, R.V. and Monroe, M.E. and Smith, R.D. and Baker, E.S.}, year={2015}, pages={6955–6963} }
 @article{baker_burnum-johnson_ibrahim_orton_monroe_kelly_moore_zhang_théberge_costello_et al._2015, title={Enhancing bottom-up and top-down proteomic measurements with ion mobility separations}, volume={15}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938738882&partnerID=MN8TOARS}, DOI={10.1002/pmic.201500048}, abstractNote={Proteomic measurements with greater throughput, sensitivity, and structural information are essential for improving both in‐depth characterization of complex mixtures and targeted studies. While LC separation coupled with MS (LC–MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC–MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS–MS and LC–IMS–MS measurements for both bottom‐up and top‐down proteomics measurements.}, number={16}, journal={Proteomics}, author={Baker, E.S. and Burnum-Johnson, K.E. and Ibrahim, Y.M. and Orton, D.J. and Monroe, M.E. and Kelly, R.T. and Moore, R.J. and Zhang, X. and Théberge, R. and Costello, C.E. and et al.}, year={2015}, pages={2766–2776} }
 @article{zhang_garimella_prost_webb_chen_tang_tolmachev_norheim_baker_anderson_et al._2015, title={Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations}, volume={87}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356755100023&KeyUID=WOS:000356755100023}, DOI={10.1021/acs.analchem.5b00214}, abstractNote={A new Structures for Lossless Ion Manipulations (SLIM) module, having electrode arrays patterned on a pair of parallel printed circuit boards (PCB), was constructed and utilized to investigate capabilities for ion trapping at a pressure of 4 Torr. Positive ions were confined by application of RF voltages to a series of inner rung electrodes with alternating phase on adjacent electrodes, in conjunction with positive DC potentials on surrounding guard electrodes on each PCB. An axial DC field was also introduced by stepwise varying the DC potentials applied to the inner rung electrodes to control the ion transport and accumulation inside the ion trapping region. We show that ions can be trapped and accumulated with up to 100% efficiency, stored for at least 5 h with no significant losses, and then could be rapidly ejected from the SLIM trap. The present results provide a foundation for the development of much more complex SLIM devices that facilitate extended ion manipulations.}, number={12}, journal={Analytical Chemistry}, author={Zhang, X. and Garimella, S.V.B. and Prost, S.A. and Webb, I.K. and Chen, T.-C. and Tang, K. and Tolmachev, A.V. and Norheim, R.V. and Baker, E.S. and Anderson, G.A. and et al.}, year={2015}, pages={6010–6016} }
 @article{garimella_ibrahim_webb_ipsen_chen_tolmachev_baker_anderson_smith_2015, title={Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch.}, volume={140}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:26289106&KeyUID=MEDLINE:26289106}, DOI={10.1039/c5an00844a}, abstractNote={Mobility Selected Ion Manipulations into Orthogonal Channels.}, number={20}, journal={The Analyst}, author={Garimella, Sandilya V B and Ibrahim, Yehia M and Webb, Ian K and Ipsen, Andreas B and Chen, Tsung-Chi and Tolmachev, Aleksey V and Baker, Erin S and Anderson, Gordon A and Smith, Richard D}, year={2015}, pages={6845–52} }
 @inbook{wu_liu_baker_rodland_smith_2015, place={New York, NY}, title={Mass Spectrometry for Biomarker Development}, booktitle={General Methods in Biomarker Research and their Applications}, publisher={Springer}, author={Wu, C. and Liu, T. and Baker, E.S. and Rodland, K.D. and Smith, R.D.}, editor={Preedy, V.R. and Patel, V.B.Editors}, year={2015}, pages={17–48} }
 @book{wu_liu_baker_rodland_smith_2015, title={Mass spectrometry for biomarker development}, volume={1-2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84958696691&partnerID=MN8TOARS}, DOI={10.1007/978-94-007-7696-8_21}, abstractNote={Biomarkers potentially play a crucial role in early disease diagnosis, prognosis, and targeted therapy. In the past decade, mass spectrometry-based proteomics has become increasingly important in biomarker development due to large advances in technology and associated methods. This chapter mainly focuses on the application of broad (e.g., shotgun) proteomics in biomarker discovery and the utility of targeted proteomics in biomarker verification and validation. A range of mass spectrometry methodologies are discussed emphasizing their efficacy across the different stages of biomarker development, with a particular emphasis on blood-based biomarker development.}, journal={General Methods in Biomarker Research and their Applications}, author={Wu, C. and Liu, T. and Baker, E.S. and Rodland, K.D. and Smith, R.D.}, year={2015}, pages={17–48} }
 @article{cha_burnum-johnson_bartos_li_baker_tilton_webb-robertson_piehowski_monroe_jegga_et al._2015, title={Muscle Segment Homeobox Genes Direct Embryonic Diapause by Limiting Inflammation in the Uterus}, volume={290}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356177300044&KeyUID=WOS:000356177300044}, DOI={10.1074/jbc.M115.655001}, abstractNote={Background: Embryonic diapause is a reproductive strategy that confers blastocyst dormancy and uterine quiescence without implantation until conditions become favorable. Results: Mice devoid of uterine muscle segment homeobox genes (Msx) show heightened inflammatory signature with failure of diapause. Conclusion: Msx coordinates various pathways limiting inflammation in the uterus for diapause. Significance: This study identifies a previously unrecognized role of Msx in this unique phenomenon. Embryonic diapause is a reproductive strategy widespread in the animal kingdom. This phenomenon is defined by a temporary arrest in blastocyst growth and metabolic activity within a quiescent uterus without implantation until the environmental and maternal milieu become favorable for pregnancy to progress. We found that uterine Msx expression persists during diapause across species; their inactivation in the mouse uterus results in termination of diapause with the development of implantation-like responses (“pseudoimplantation”) that ultimately succumbed to resorption. To understand the cause of this failure, we compared proteome profiles between floxed and Msx-deleted uteri. In deleted uteri, several functional networks, including transcription/translation, ubiquitin-proteasome, inflammation, and endoplasmic reticulum stress, were dysregulated. Computational modeling predicted intersection of these pathways on an enhanced inflammatory signature. Further studies showed that this signature was reflected in increased phosphorylated IκB levels and nuclear NFκB in deleted uteri. This was associated with enhanced proteasome activity and endoplasmic reticulum stress. Interestingly, treatment with anti-inflammatory glucocorticoid (dexamethasone) reduced the inflammatory signature with improvement of the diapause phenotype. These findings highlight an unexpected role of uterine Msx in limiting aberrant inflammatory responses to maintain embryonic diapause.}, number={24}, journal={Journal of Biological Chemistry}, author={Cha, Jeeyeon and Burnum-Johnson, Kristin E. and Bartos, Amanda and Li, Yingju and Baker, Erin S. and Tilton, Susan C. and Webb-Robertson, Bobbie-Jo M. and Piehowski, Paul D. and Monroe, Matthew E. and Jegga, Anil G. and et al.}, year={2015}, pages={15337–15349} }
 @article{baker_burnum-johnson_jacobs_diamond_brown_ibrahim_orton_piehowski_purdy_moore_et al._2014, title={Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry*}, volume={13}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000333921700015&KeyUID=WOS:000333921700015}, DOI={10.1074/mcp.M113.034595}, abstractNote={Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is a crucial direction for the field of medicine. While MS-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new instrumental platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry separations with liquid chromatography and MS to dramatically increase measurement sensitivity and throughput, further enabling future high throughput MS-based clinical applications. An initial application of the liquid chromatography - ion mobility spectrometry-MS platform analyzing blood serum samples from 60 postliver transplant patients with recurrent fibrosis progression and 60 nontransplant patients illustrates its potential utility for disease characterization.}, number={4}, journal={Molecular & Cellular Proteomics}, author={Baker, Erin Shammel and Burnum-Johnson, Kristin E. and Jacobs, Jon M. and Diamond, Deborah L. and Brown, Roslyn N. and Ibrahim, Yehia M. and Orton, Daniel J. and Piehowski, Paul D. and Purdy, David E. and Moore, Ronald J. and et al.}, year={2014}, pages={1119–1127} }
 @article{prost_crowell_baker_ibrahim_clowers_monroe_anderson_smith_payne_2014, title={Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements}, volume={25}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344809100004&KeyUID=WOS:000344809100004}, DOI={10.1007/s13361-014-0895-y}, abstractNote={Applying Hadamard transform multiplexing to ion mobility separations (IMS) can significantly improve the signal-to-noise ratio and throughput for IMS coupled mass spectrometry (MS) measurements by increasing the ion utilization efficiency. However, it has been determined that fluctuations in ion intensity as well as spatial shifts in the multiplexed data lower the signal-to-noise ratios and appear as noise in downstream processing of the data. To address this problem, we have developed a novel algorithm that discovers and eliminates data artifacts. The algorithm employs an analytical approach to identify and remove artifacts from the data, decreasing the likelihood of false identifications in subsequent data processing. Following application of the algorithm, IMS-MS measurement sensitivity is greatly increased and artifacts that previously limited the utility of applying the Hadamard transform to IMS are avoided. Figure ᅟ}, number={12}, journal={The Journal of the American Society for Mass Spectrometry}, author={Prost, S.A. and Crowell, K.L. and Baker, E.S. and Ibrahim, Y.M. and Clowers, B.H. and Monroe, M.E. and Anderson, G.A. and Smith, R.D. and Payne, S.H.}, year={2014}, pages={2020–2027} }
 @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://doi.org/10.1007/s13361-014-1007-8Copyright © 2014 © American Society for Mass Spectrometry 2014RIGHTS & PERMISSIONSArticle Views55Altmetric-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 (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{ibrahim_garimella_tolmachev_baker_smith_2014, title={Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel Trap}, volume={86}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000336953100016&KeyUID=WOS:000336953100016}, DOI={10.1021/ac404250z}, abstractNote={Ion mobility instruments that utilize nitrogen as buffer gas are often preceded by an ion trap and accumulation region that also uses nitrogen, and for different inert gases, no significant effects upon performance are expected for ion mobility spectrometry (IMS) of larger ions. However, we have observed significantly improved performance for an ion funnel trap upon adding helium; the signal intensities for higher m/z species were improved by more than an order of magnitude compared to using pure nitrogen. The effect of helium upon IMS resolving power was also studied by introducing a He/N2 gas mixture into the drift cell, and in some cases, a slight improvement was observed compared to pure N2. The improvement in signal can be largely attributed to faster and more efficient ion ejection into the drift tube from the ion funnel trap.}, number={11}, journal={Analytical Chemistry}, author={Ibrahim, Yehia M. and Garimella, Sandilya V. B. and Tolmachev, Aleksey V. and Baker, Erin S. and Smith, Richard D.}, year={2014}, pages={5295–5299} }
 @article{merkley_baker_crowell_orton_taverner_ansong_ibrahim_burnett_sanchez_cort_et al._2013, title={Combining heavy isotope labeling, chemical cross-linking, ion mobility spectrometry, and mass spectrometry to study the structure of homomultimeric protein complexes}, volume={246}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000329618401034&KeyUID=WOS:000329618401034}, journal={Abstracts of Papers of the American Chemical Society}, author={Merkley, Eric D. and Baker, Erin S. and Crowell, Kevin L. and Orton, Daniel J. and Taverner, Thomas and Ansong, Charles and Ibrahim, Yehia M. and Burnett, Meagan C. and Sanchez, Octavio and Cort, John R. and et al.}, year={2013} }
 @article{crowell_baker_payne_ibrahim_monroe_slysz_lamarche_petyuk_piehowski_danielson_et al._2013, title={Increasing confidence of LC-MS identifications by utilizing ion mobility spectrometry}, volume={354}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000327809900044&KeyUID=WOS:000327809900044}, DOI={10.1016/j.ijms.2013.06.028}, abstractNote={Ion mobility spectrometry in conjunction with liquid chromatography separations and mass spectrometry offers a range of new possibilities for analyzing complex biological samples. To fully utilize the information obtained from these three measurement dimensions, informatics tools based on the accurate mass and time tag methodology were modified to incorporate ion mobility spectrometry drift times for peptides observed in human serum. In this work a reference human serum database was created for 12,139 peptides and populated with the monoisotopic mass, liquid chromatography normalized elution time, and ion mobility spectrometry drift time(s) for each. We demonstrate that the use of three dimensions for peak matching during the peptide identification process resulted in an increased numbers of identifications and a lower false discovery rate relative to only using the mass and normalized elution time dimensions.}, journal={International Journal of Mass Spectrometry}, author={Crowell, Kevin L. and Baker, Erin S. and Payne, Samuel H. and Ibrahim, Yehia M. and Monroe, Matthew E. and Slysz, Gordon W. and LaMarche, Brian L. and Petyuk, Vladislav A. and Piehowski, Paul D. and Danielson, William F., III and et al.}, year={2013}, pages={312–317} }
 @article{crowell_slysz_baker_lamarche_monroe_ibrahim_payne_anderson_smith_2013, title={LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets}, volume={29}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000325997500024&KeyUID=WOS:000325997500024}, DOI={10.1093/bioinformatics/btt465}, abstractNote={Abstract}, number={21}, journal={Bioinformatics}, author={Crowell, Kevin L. and Slysz, Gordon W. and Baker, Erin S. and LaMarche, Brian L. and Monroe, Matthew E. and Ibrahim, Yehia M. and Payne, Samuel H. and Anderson, Gordon A. and Smith, Richard D.}, year={2013}, pages={2804–2805} }
 @article{merkley_baker_crowell_orton_taverner_ansong_ibrahim_burnet_cort_anderson_et al._2013, title={Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking}, volume={24}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000315515700016&KeyUID=WOS:000315515700016}, DOI={10.1007/s13361-012-0565-x}, abstractNote={Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.}, number={3}, journal={Journal of the American Society For Mass Spectrometry}, author={Merkley, Eric D. and Baker, Erin S. and Crowell, Kevin L. and Orton, Daniel J. and Taverner, Thomas and Ansong, Charles and Ibrahim, Yehia M. and Burnet, Meagan C. and Cort, John R. and Anderson, Gordon A. and et al.}, year={2013}, pages={444–449} }
 @article{venceslau_cort_baker_chu_robinson_dahl_saraiva_pereira_2013, title={Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction}, volume={441}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000328434800007&KeyUID=WOS:000328434800007}, DOI={10.1016/j.bbrc.2013.10.116}, abstractNote={Dissimilatory reduction of sulfite is carried out by the siroheme enzyme DsrAB, with the involvement of the protein DsrC, which has two conserved redox-active cysteines. DsrC was initially believed to be a third subunit of DsrAB. Here, we report a study of the distribution of DsrC in cell extracts to show that, in the model sulfate reducer Desulfovibrio vulgaris, the majority of DsrC is not associated with DsrAB and is thus free to interact with other proteins. In addition, we developed a cysteine-labelling gel-shift assay to monitor the DsrC redox state and behaviour, and procedures to produce the different redox forms. The oxidized state of DsrC with an intramolecular disulfide bond, which is proposed to be a key metabolic intermediate, could be successfully produced for the first time by treatment with arginine.}, number={4}, journal={Biochemical and Biophysical Research Communications}, author={Venceslau, Sofia S. and Cort, John R. and Baker, Erin S. and Chu, Rosalie K. and Robinson, Errol W. and Dahl, Christiane and Saraiva, Ligia M. and Pereira, Ines A. C.}, year={2013}, pages={732–736} }
 @article{hengel_floyd_baker_zhao_wu_pasa-tolic_2012, title={Evaluation of SDS Depletion Using an Affinity Spin Column and IMS-MS Detection}, volume={12}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000310564100003&KeyUID=WOS:000310564100003}, DOI={10.1002/pmic.201200168}, abstractNote={While the use of detergents is necessary for a variety of protein isolation preparation protocols, they are not compatible with mass spectral analysis due to ion suppression and adduct formation. This manuscript describes optimization of detergent removal, using commercially available SDS depletion spin columns containing an affinity resin, providing for both increased protein recovery and thorough SDS removal. Ion mobility spectrometry coupled with mass spectrometry (IMS‐MS) allowed for a concurrent analysis of both analyte and detergent. In the case of both proteins and peptides, higher detergent concentrations than previously reported provided an increase of sample recovery; however there was a limit as SDS was detected by IMS‐MS at higher levels of SDS indicating incomplete detergent depletion. The results also suggest that optimal conditions for SDS removal are dependent on the sample concentration. Overall, this study provides a useful guide for proteomic studies where SDS is required for efficient sample preparation.}, number={21}, journal={Proteomics}, author={Hengel, S.M. and Floyd, E. and Baker, E.S. and Zhao, R. and Wu, S. and Pasa-Tolic, L.}, year={2012}, pages={3138–3142} }
 @article{baker_liu_petyuk_burnum-johnson_ibrahim_anderson_smith_2012, title={Mass spectrometry for translational proteomics: progress and clinical implications}, volume={4}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000314575100001&KeyUID=WOS:000314575100001}, DOI={10.1186/gm364}, abstractNote={The utility of mass spectrometry (MS)-based proteomic analyses and their clinical applications have been increasingly recognized over the past decade due to their high sensitivity, specificity and throughput. MS-based proteomic measurements have been used in a wide range of biological and biomedical investigations, including analysis of cellular responses and disease-specific post-translational modifications. These studies greatly enhance our understanding of the complex and dynamic nature of the proteome in biology and disease. Some MS techniques, such as those for targeted analysis, are being successfully applied for biomarker verification, whereas others, including global quantitative analysis (for example, for biomarker discovery), are more challenging and require further development. However, recent technological improvements in sample processing, instrumental platforms, data acquisition approaches and informatics capabilities continue to advance MS-based applications. Improving the detection of significant changes in proteins through these advances shows great promise for the discovery of improved biomarker candidates that can be verified pre-clinically using targeted measurements, and ultimately used in clinical studies - for example, for early disease diagnosis or as targets for drug development and therapeutic intervention. Here, we review the current state of MS-based proteomics with regard to its advantages and current limitations, and we highlight its translational applications in studies of protein biomarkers.}, number={8}, journal={Genome Medicine}, author={Baker, Erin Shammel and Liu, Tao and Petyuk, Vladislav A. and Burnum-Johnson, Kristin E. and Ibrahim, Yehia M. and Anderson, Gordon A. and Smith, Richard D.}, year={2012} }
 @article{angel_aryal_hengel_baker_kelly_robinson_smith_2012, title={Mass spectrometry-based proteomics: existing capabilities and future directions}, volume={41}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000303320400015&KeyUID=WOS:000303320400015}, DOI={10.1039/c2cs15331a}, abstractNote={Mass spectrometry (MS)-based proteomics is emerging as a broadly effective means for identification, characterization, and quantification of proteins that are integral components of the processes essential for life. Characterization of proteins at the proteome and sub-proteome (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects of biology. Emerging technologies such as ion mobility separations coupled with MS and microchip-based-proteome measurements combined with MS instrumentation and chromatographic separation techniques, such as nanoscale reversed phase liquid chromatography and capillary electrophoresis, show great promise for both broad undirected and targeted highly sensitive measurements. MS-based proteomics increasingly contribute to our understanding of the dynamics, interactions, and roles that proteins and peptides play, advancing our understanding of biology on a systems wide level for a wide range of applications including investigations of microbial communities, bioremediation, and human health.}, number={10}, journal={Chemical Society Reviews}, author={Angel, Thomas E. and Aryal, Uma K. and Hengel, Shawna M. and Baker, Erin S. and Kelly, Ryan T. and Robinson, Errol W. and Smith, Richard D.}, year={2012}, pages={3912–3928} }
 @article{burnum_hirota_baker_yoshie_ibrahim_monroe_anderson_smith_daikoku_dey_2012, title={Uterine Deletion of Trp53 Compromises Antioxidant Responses in the Mouse Decidua}, volume={153}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000308194900044&KeyUID=WOS:000308194900044}, DOI={10.1210/en.2012-1335}, abstractNote={Preterm birth is a global health issue impacting millions of mothers and babies. However, the etiology of preterm birth is not clearly understood. Our recent finding that premature decidual senescence with terminal differentiation is a cause of preterm birth in mice with uterine Trp53 deletion, encoding p53 protein, led us to explore other potential factors that are related to preterm birth. Using proteomics approaches, here, we show that 183 candidate proteins show significant changes in deciduae with Trp53 deletion as compared with normal deciduae. Functional categorization of these proteins unveiled new pathways that are influenced by p53. In particular, down-regulation of a cluster of antioxidant enzymes in p53-deficient deciduae suggests that increased oxidative stress could be one cause of preterm birth in mice harboring uterine deletion of Trp53.}, number={9}, journal={Endocrinology}, author={Burnum, Kristin E. and Hirota, Yasushi and Baker, Erin S. and Yoshie, Mikihiro and Ibrahim, Yehia M. and Monroe, Matthew E. and Anderson, Gordon A. and Smith, Richard D. and Daikoku, Takiko and Dey, Sudhansu K.}, year={2012}, pages={4568–4579} }
 @inbook{belov_kurulugama_lopez-ferrer_ibrahim_baker_2011, title={New Developments in LC-MS and Other Hyphenated Techniques}, ISBN={9789400707580 9789400708280}, url={http://dx.doi.org/10.1007/978-94-007-0828-0_47}, DOI={10.1007/978-94-007-0828-0_47}, booktitle={Sample Preparation in Biological Mass Spectrometry}, publisher={Springer Netherlands}, author={Belov, Mikhail E. and Kurulugama, Ruwan and Lopez-Ferrer, Daniel and Ibrahim, Yehia and Baker, Erin}, year={2011}, pages={981–1030} }
 @article{buchko_niemann_baker_belov_smith_heffron_adkins_mcdermott_2010, title={A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins}, volume={6}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000283937800013&KeyUID=WOS:000283937800013}, DOI={10.1039/c0mb00097c}, abstractNote={Many pathogenic Gram-negative bacteria use a type III secretion system (T3SS) to deliver effector proteins into the host cell where they reprogram host defenses and facilitate pathogenesis. The first 20-30 N-terminal residues usually contain the 'secretion signal' that targets effector proteins for translocation, however, a consensus sequence motif has never been discerned. Recent machine-learning approaches, such as support vector machine (SVM)-based Identification and Evaluation of Virulence Effectors (SIEVE), have improved the ability to identify effector proteins from genomics sequence information. While these methods all suggest that the T3SS secretion signal has a characteristic amino acid composition bias, it is still unclear if the amino acid pattern is important and if there are any unifying structural properties that direct recognition. To address these issues a peptide corresponding to the secretion signal for Salmonella enterica serovar Typhimurium effector SseJ was synthesized (residues 1-30, SseJ) along with scrambled peptides of the same amino acid composition that produced high (SseJ-H) and low (SseJ-L) SIEVE scores. The secretion properties of these three peptides were tested using a secretion signal-CyaA fusion assay and their structural properties probed using circular dichroism, nuclear magnetic resonance, and ion mobility spectrometry-mass spectrometry. The secretion predictions from SIEVE matched signal-CyaA fusion experimental results with J774 macrophages suggesting that the SseJ secretion signal has some sequence order dependence. The structural studies showed that the SseJ, SseJ-H, and SseJ-L peptides were intrinsically disordered in aqueous solution with a small predisposition to adopt nascent helical structure only in the presence of structure stabilizing agents such as 1,1,1,3,3,3-hexafluoroisopropanol. Intrinsic disorder may be a universal feature of effector secretion signals as similar conclusions were reached following structural characterization of peptides corresponding to the N-terminal regions of the S. Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH.}, number={12}, journal={Molecular Biosystems}, author={Buchko, Garry W. and Niemann, George and Baker, Erin S. and Belov, Mikhail E. and Smith, Richard D. and Heffron, Fred and Adkins, Joshua N. and McDermott, Jason E.}, year={2010}, pages={2448–2458} }
 @article{baker_livesay_orton_moore_danielson_prior_ibrahim_lamarche_mayampurath_schepmoes_et al._2010, title={An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies}, volume={9}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000274269400036&KeyUID=WOS:000274269400036}, DOI={10.1021/pr900888b}, abstractNote={A high-throughput approach and platform using 15 min reversed-phase capillary liquid chromatography (RPLC) separations in conjunction with ion mobility spectrometry-mass spectrometry (IMS-MS) measurements was evaluated for the rapid analysis of complex proteomics samples. To test the separation quality of the short LC gradient, a sample was prepared by spiking 20 reference peptides at varying concentrations from 1 ng/mL to 10 microg/mL into a tryptic digest of mouse blood plasma and analyzed with both a LC-Linear Ion Trap Fourier Transform (FT) MS and LC-IMS-TOF MS. The LC-FT MS detected 13 out of the 20 spiked peptides that had concentrations >or=100 ng/mL. In contrast, the drift time selected mass spectra from the LC-IMS-TOF MS analyses yielded identifications for 19 of the 20 peptides with all spiking levels present. The greater dynamic range of the LC-IMS-TOF MS system could be attributed to two factors. First, the LC-IMS-TOF MS system enabled drift time separation of the low concentration spiked peptides from the high concentration mouse peptide matrix components, reducing signal interference and background, and allowing species to be resolved that would otherwise be obscured by other components. Second, the automatic gain control (AGC) in the linear ion trap of the hybrid FT MS instrument limits the number of ions that are accumulated to reduce space charge effects and achieve high measurement accuracy, but in turn limits the achievable dynamic range compared to the IMS-TOF instrument.}, number={2}, journal={Journal of Proteome Research}, author={Baker, Erin Shammel and Livesay, Eric A. and Orton, Daniel J. and Moore, Ronald J. and Danielson, William F., III and Prior, David C. and Ibrahim, Yehia M. and LaMarche, Brian L. and Mayampurath, Anoop M. and Schepmoes, Athena A. and et al.}, year={2010}, pages={997–1006} }
 @article{ibrahim_prior_baker_smith_belov_2010, title={Characterization of an ion mobility-multiplexed collision-induced dissociation-tandem time-of-flight mass spectrometry approach}, volume={293}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000278630300005&KeyUID=WOS:000278630300005}, DOI={10.1016/j.ijms.2010.03.009}, abstractNote={The confidence in peptide (and protein) identifications with ion mobility spectrometry time-of-flight mass spectrometry (IMS-TOFMS) is expected to drastically improve with the addition of information from an efficient ion dissociation step prior to MS detection. High throughput IMS-TOFMS analysis imposes a strong need for multiplexed ion dissociation approaches where multiple precursor ions yield complex sets of fragment ions that are often intermingled with each other in both the drift time and m/z domains. We have developed and evaluated an approach for collision-induced dissociation (CID) using IMS-TOFMS instrument. It has been shown that precursor ions activated inside an rf-device with an axial dc-electric field produce abundant fragment ions which are radially confined with the rf-field and collisionally cooled at an elevated pressure, resulting in high CID efficiencies comparable or higher than those measured in triple-quadrupole instruments. We have also developed an algorithm for deconvoluting these complex multiplexed tandem MS spectra by clustering both the precursor and fragment ions into matching drift time profiles and by utilizing the high mass measurement accuracy achievable with TOFMS. In a single IMS separation from direct infusion of tryptic digest of bovine serum albumin (BSA), we have reliably identified 20 unique peptides using a multiplexed CID approach downstream of the IMS separation. Peptides were identified based upon the correlation between the precursor and fragment drift time profiles and by matching the profile representative masses to those of in silico BSA tryptic peptides and their fragments. The false discovery rate (FDR) of peptide identifications from multiplexed MS/MS spectra was less than 1%.}, number={1-3}, journal={International Journal of Mass Spectrometry}, author={Ibrahim, Yehia M. and Prior, David C. and Baker, Erin S. and Smith, Richard D. and Belov, Mikhail E.}, year={2010}, pages={34–44} }
 @article{belov_baker_ibrahim_prior_danielson_kurulugama_prasad_shah_crowell_anderson_et al._2010, title={Ion mobility separations in high throughput proteomics: A novel approach to protein detection and quantitation}, volume={240}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000208164705803&KeyUID=WOS:000208164705803}, journal={Abstracts of Papers of the American Chemical Society}, author={Belov, Mikhail E. and Baker, Erin S. and Ibrahim, Yehia M. and Prior, David C. and Danielson, William F. and Kurulugama, Ruwan T. and Prasad, Satendra and Shah, Anuj R. and Crowell, Kevin L. and Anderson, Gordon A. and et al.}, year={2010} }
 @article{shah_agarwal_baker_singhal_mayampurath_ibrahim_kangas_monroe_zhao_belov_et al._2010, title={Machine learning based prediction for peptide drift times in ion mobility spectrometry}, volume={26}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000278967500004&KeyUID=WOS:000278967500004}, DOI={10.1093/bioinformatics/btq245}, abstractNote={Abstract}, number={13}, journal={Bioinformatics}, author={Shah, Anuj R. and Agarwal, Khushbu and Baker, Erin S. and Singhal, Mudita and Mayampurath, Anoop M. and Ibrahim, Yehia M. and Kangas, Lars J. and Monroe, Matthew E. and Zhao, Rui and Belov, Mikhail E. and et al.}, year={2010}, pages={1601–1607} }
 @article{baker_dupuis_bowers_2009, title={Aminoglycoside antibiotics: A-site specific binding to 16S}, volume={283}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000266808800016&KeyUID=WOS:000266808800016}, DOI={10.1016/j.ijms.2009.02.010}, abstractNote={The A-site of 16S rRNA, which is a part of the 30S ribosomal subunit involved in prokaryotic translation, is a well known aminoglycoside binding site. Full characterization of the conformational changes undergone at the A-site upon aminoglycoside binding is essential for development of future RNA/drug complexes; however, the massiveness of 16S makes this very difficult. Recently, studies have found that a 27 base RNA construct (16S27) that comprises the A-site subdomain of 16S behaves similarly to the whole A-site domain. ESI-MS, ion mobility and molecular dynamics methods were utilized in this study to analyze the A-site of 16S27 before and after the addition of ribostamycin (R), paromomycin (P) and lividomycin (L). The ESI mass spectrum for 16S27 alone illustrated both single-stranded 16S27 and double-stranded (16S27)2 complexes. Upon aminoglycoside addition, the mass spectra showed that only one aminoglycoside binds to 16S27, while either one or two bind to (16S27)2. Ion mobility measurements and molecular dynamics calculations were utilized in determining the solvent-free structures of the 16S27 and (16S27)2 complexes. These studies found 16S27 in a hairpin conformation while (16S27)2 existed as a cruciform. Only one aminoglycoside binds to the single A-site of the 16S27 hairpin and this attachment compresses the hairpin. Since two A-sites exist for the (16S27)2 cruciform, either one or two aminoglycosides may bind. The aminoglycosides compress the A-sites causing the cruciform with just one aminoglycoside bound to be larger than the cruciform with two bound. Non-specific binding was not observed in any of the aminoglycoside/16S27 complexes.}, number={1-3}, journal={International Journal of Mass Spectrometry}, author={Baker, Erin Shammel and Dupuis, Nicholas F. and Bowers, Michael T.}, year={2009}, pages={105–111} }
 @article{page_marginean_baker_kelly_tang_smith_2009, title={Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet}, volume={20}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000272628200012&KeyUID=WOS:000272628200012}, DOI={10.1016/j.jasms.2009.08.018}, abstractNote={A heated capillary inlet for an electrospray ionization mass spectrometry (ESI-MS) interface was compared with shorter versions of the inlet to determine the effects on transmission and ionization efficiencies for low-flow (nano) electrosprays. Five different inlet lengths were studied, ranging from 6.4 to 1.3 cm. As expected, the electrospray current transmission efficiency increased with decreasing capillary length due to reduced losses to the inside walls of the capillary. This increase in transmission efficiency with shorter inlets was coupled with reduced desolvation of electrosprayed droplets. Surprisingly, as the inlet length was decreased, some analytes showed little or no increase in sensitivity, while others showed as much as a 15-fold gain. The variation was shown to be at least partially correlated with analyte mobilities, with the largest gains observed for higher mobility species, but also affected by solution conductivity, flow rate, and inlet temperature. Strategies for maximizing sensitivity while minimizing biases in ion transmission through the heated capillary interface are proposed.}, number={12}, journal={Journal of the American Society For Mass Spectrometry}, author={Page, Jason S. and Marginean, Ioan and Baker, Erin S. and Kelly, Ryan T. and Tang, Keqi and Smith, Richard D.}, year={2009}, pages={2265–2272} }
 @article{baker_dupuis_bowers_2009, title={DNA Hairpin, Pseudoknot, and Cruciform Stability in a Solvent-Free Environment}, volume={113}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000263134500022&KeyUID=WOS:000263134500022}, DOI={10.1021/jp807529m}, abstractNote={The secondary structures of DNA hairpins, pseudoknots and cruciforms are of great interest because of their possible role in materials applications and biological functions such as regulating transcription. To determine the stability of these structures, DNA sequences capable of forming each were analyzed with mass spectrometry, ion mobility, and molecular dynamics calculations. Nano-ESI mass spectra indicated that stoichiometries compatible with hairpin, pseudoknot, and cruciform structures were present. Ion mobility spectrometry (IMS) was utilized to obtain experimental collision cross sections for all complexes. These cross sections were compared with structures from molecular dynamics, and in all cases, the lowest-charge states could be matched with a structure for an intact hairpin, pseudoknot, or cruciform. However, as the charge states of the single-stranded hairpins and pseudoknots increased, their structures elongated, and all Watson-Crick pairs were broken.}, number={6}, journal={Journal of Physical Chemistry B}, author={Baker, Erin Shammel and Dupuis, Nicholas F. and Bowers, Michael T.}, year={2009}, pages={1722–1727} }
 @article{smargiasso_rosu_hsia_colson_baker_bowers_de pauw_gabelica_2008, title={G-quadruplex DNA assemblies: Loop length, cation identity, and multimer formation}, volume={130}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000258080600041&KeyUID=WOS:000258080600041}, DOI={10.1021/ja801535e}, abstractNote={G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGW(i)GGGW(j)GGGW(k)GGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K(+) inducing more parallel multimers than NH4(+) and Na(+). Structural possibilities are discussed for the new quadruplex higher-order assemblies.}, number={31}, journal={Journal of the American Chemical Society}, author={Smargiasso, Nicolas and Rosu, Frederic and Hsia, Wei and Colson, Pierre and Baker, Erin Shammel and Bowers, Michael T. and De Pauw, Edwin and Gabelica, Valerie}, year={2008}, pages={10208–10216} }
 @article{metz_page_baker_tang_ding_shen_smith_2008, title={High-resolution separations and improved ion production and transmission in metabolomics}, volume={27}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000255704800016&KeyUID=WOS:000255704800016}, DOI={10.1016/j.trac.2007.11.003}, abstractNote={The goal of metabolomics analyses is the detection and quantitation of as many sample components as reasonably possible in order to identify compounds or "features" that can be used to characterize the samples under study. When utilizing electrospray ionization to produce ions for analysis by mass spectrometry (MS), it is important that metabolome sample constituents be efficiently separated prior to ion production, in order to minimize ionization suppression and thereby extend the dynamic range of the measurement, as well as the coverage of the metabolome. Similarly, optimization of the MS inlet and interface can lead to increased measurement sensitivity. This perspective review will focus on the role of high resolution liquid chromatography (LC) separations in conjunction with improved ion production and transmission for LC-MS-based metabolomics. Additional emphasis will be placed on the compromise between metabolome coverage and sample analysis throughput.}, number={3}, journal={Trac-Trends in Analytical Chemistry}, author={Metz, Thomas O. and Page, Jason S. and Baker, Erin S. and Tang, Keqi and Ding, Jie and Shen, Yufeng and Smith, Richard D.}, year={2008}, pages={205–214} }
 @article{baker_tang_danielson_prior_smith_2008, title={Simultaneous fragmentation of multiple ions using IMS drift time dependent collision energies}, volume={19}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000254266400011&KeyUID=WOS:000254266400011}, DOI={10.1016/j.jasms.2007.11.018}, abstractNote={Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) was utilized to evaluate an ion collision energy ramping technique that simultaneously fragments a variety of species. To evaluate this technique, the fragmentation patterns of a mixture of ions ranging in mass, charge state, and drift time were analyzed to determine their optimal fragmentation conditions. The precursor ions were pulsed into the IMS-MS instrument and separated in the IMS drift cell based on mobility differences. Two differentially pumped short quadrupoles were used to focus the ions exiting the drift cell, and fragmentation was induced by collision induced dissociation (CID) between the conductance limiting orifice behind the second short quadrupole and before the first octopole in the mass spectrometer. To explore the fragmentation spectrum of each precursor ion, the bias voltages for the short quadrupoles and conductance limiting orifices were increased from 0 to 50 V above nonfragmentation voltage settings. An approximately linear correlation was observed between the optimal fragmentation voltage for each ion and its specific drift time, so a linear voltage gradient was employed to supply less collision energy to high mobility ions (e.g., small conformations or higher charge state ions) and more to low mobility ions. Fragmentation efficiencies were found to be similar for different ions when the fragmentation voltage was linearly ramped with drift time, but varied drastically when only a single voltage was used.}, number={3}, journal={Journal of the American Society For Mass Spectrometry}, author={Baker, Erin Shammel and Tang, Keqi and Danielson, William F., III and Prior, David C. and Smith, Richard D.}, year={2008}, pages={411–419} }
 @article{baker_bowers_2007, title={B-DNA helix stability in a solvent-free environment}, volume={18}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000248062200004&KeyUID=WOS:000248062200004}, DOI={10.1016/j.jasms.2007.03.001}, abstractNote={B-DNA is the most common DNA helix conformation under physiological conditions. However, when the amount of water in a DNA solution is decreased, B-to-A helix transitions have been observed. To understand what type of helix conformations exist in a solvent-free environment, a series of poly d(CG)n and mixed sequence DNA duplexes from 18 to 30 bp were examined with circular dichroism (CD), ESI-MS, ion mobility, and molecular dynamics. From the CD spectra, it was observed that all sequences had B-form helices in solution. However, the solvent-free results were more complex. For the poly d(CG)n series, the 18 bp duplex had an A-form helix conformation, both A- and B-helices were present for the 22 bp duplex, and only B-helices were observed for the 26 and 30 bp duplexes. Since these sequences were all present as B-DNA in solution, the observed solvent-free structures illustrate that smaller helices with fewer base pairs convert to A-DNA more easily than larger helices in the absence of solvent. A similar trend was observed for the mixed sequence duplexes where both an A- and B-helix were present for the 18 bp duplex, while only B-helices occur for the larger 22, 26, and 30 bp duplexes. Since the solvent-free B-helices appear at smaller sizes for the mixed sequences than for the pure d(CG)n duplexes, the pure d(CG)n duplexes have a greater A-philicity.}, number={7}, journal={Journal of the American Society For Mass Spectrometry}, author={Baker, Erin Shammel and Bowers, Michael T.}, year={2007}, pages={1188–1195} }
 @article{baker_clowers_li_tang_tolmachev_prior_belov_smith_2007, title={Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures}, volume={18}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000248062200003&KeyUID=WOS:000248062200003}, DOI={10.1016/j.jasms.2007.03.031}, abstractNote={The ability of ion mobility spectrometry coupled with mass spectrometry (IMS-MS) to characterize biological mixtures has been illustrated over the past eight years. However, the challenges posed by the extreme complexity of many biological samples have demonstrated the need for higher resolution IMS-MS measurements. We have developed a higher resolution ESI-IMS-TOF MS by utilizing high-pressure electrodynamic ion funnels at both ends of the IMS drift cell and operating the drift cell at an elevated pressure compared with that conventionally used. The ESI-IMS-TOF MS instrument consists of an ESI source, an hourglass ion funnel used for ion accumulation/injection into an 88 cm drift cell, followed by a 10 cm ion funnel and a commercial orthogonal time-of-flight mass spectrometer providing high mass measurement accuracy. It was found that the rear ion funnel could be effectively operated as an extension of the drift cell when the DC fields were matched, providing an effective drift region of 98 cm. The resolution of the instrument was evaluated at pressures ranging from 4 to 12 torr and ion mobility drift voltages of 16 V/cm (4 torr) to 43 V/cm (12 torr). An increase in resolution from 55 to 80 was observed from 4 to 12 torr nitrogen drift gas with no significant loss in sensitivity. The choice of drift gas was also shown to influence the degree of ion heating and relative trapping efficiency within the ion funnel.}, number={7}, journal={Journal of the American Society For Mass Spectrometry}, author={Baker, Erin Shammel and Clowers, Brian H. and Li, Fumin and Tang, Keqi and Tolmachev, Aleksey V. and Prior, David C. and Belov, Mikhail E. and Smith, Richard D.}, year={2007}, pages={1176–1187} }
 @article{shvartsburg_mashkevich_baker_smith_2007, title={Optimization of algorithms for ion mobility calculations}, volume={111}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000244735000032&KeyUID=WOS:000244735000032}, DOI={10.1021/jp066953m}, abstractNote={Ion mobility spectrometry (IMS) is increasingly employed to probe the structures of gas-phase ions, particularly those of proteins and other biological macromolecules. This process involves comparing measured mobilities to those computed for potential geometries, which requires evaluation of orientationally averaged cross sections using some approximate treatment of ion-buffer gas collisions. Two common models are the projection approximation (PA) and exact hard-spheres scattering (EHSS) that represent ions as collections of hard spheres. Though calculations for large ions and/or conformer ensembles take significant time, no algorithmic optimization had been explored. Previous EHSS programs were dominated by ion rotation operations that allow orientational averaging. We have developed two new algorithms for PA and EHSS calculations: one simplifies those operations and greatly reduces their number, and the other disposes of them altogether by propagating trajectories from a random origin. The new algorithms were tested for a representative set of seven ion geometries including diverse sizes and shapes. While the best choice depends on the geometry in a nonobvious way, the difference between the two codes is generally modest. Both are much more efficient than the existing software, for example faster than the widely used Mobcal (implementing EHSS) approximately 10-30-fold.}, number={10}, journal={Journal of Physical Chemistry a}, author={Shvartsburg, Alexandre A. and Mashkevich, Stefan V. and Baker, Erin Shammel and Smith, Richard D.}, year={2007}, pages={2002–2010} }
 @article{gabelica_baker_teulade-fichou_de pauw_bowers_2007, title={Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: The role of central cations and small planar ligands}, volume={129}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000243683800042&KeyUID=WOS:000243683800042}, DOI={10.1021/ja065989p}, abstractNote={A promising approach for anticancer strategies is the stabilization of telomeric DNA into a G-quadruplex structure. To explore the intrinsic stabilization of folded G-quadruplexes, we combined electrospray ionization mass spectrometry, ion mobility spectrometry, and molecular modeling studies to study different DNA sequences known to form quadruplexes. Two telomeric DNA sequences of different lengths and two DNA sequences derived from the NHE III1 region of the c-myc oncogene (Pu22 and Pu27) were studied. NH4+ and the ligands PIPER, TMPyP4, and the three quinacridines MMQ1, MMQ3, and BOQ1 were complexed with the DNA sequences to determine their effect on the stability of the G-quadruplexes. Our results demonstrate that G-quadruplex intramolecular folds are stabilized by NH4+ cations and the ligands listed. Furthermore, the ligands can be classified according to their ability to stabilize the quadruplexes and end stacking is shown to be the dominant mode for ligand attachment. In all cases our solvent-free experimental observations and theoretical modeling reveal structures that are highly relevant to the solution-phase structures.}, number={4}, journal={Journal of the American Chemical Society}, author={Gabelica, Valerie and Baker, Erin Shammel and Teulade-Fichou, Marie-Paule and De Pauw, Edwin and Bowers, Michael T.}, year={2007}, pages={895–904} }
 @article{tang_shvartsburg_li_ibrahim_prior_buschbach_baker_smith_2006, title={ANYL 227-Exploring the conformational diversity of proteins and peptides using high-resolution FAIMS and IMS}, volume={232}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000207781601223&KeyUID=WOS:000207781601223}, journal={Abstracts of Papers of the American Chemical Society}, author={Tang, Keqi and Shvartsburg, Alexandre A. and Li, Fumin and Ibrahim, Yehia and Prior, David C. and Buschbach, Michael A. and Baker, Erin S. and Smith, Richard D.}, year={2006} }
 @article{baker_lee_sessler_bowers_2006, title={Cyclo[n]pyrroles: Size and site-specific binding to G-quadruplexes}, volume={128}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000235787200039&KeyUID=WOS:000235787200039}, DOI={10.1021/ja0564968}, abstractNote={Inhibiting the enzyme telomerase by stabilizing the G-quadruplex has potential in anticancer drug design. Diprotonated cyclo[n]pyrroles represent a set of expanded porphyrin analogues with structures similar to that of telomestatin, a natural product known to bind to and stabilize G-quadruplexes. As a first step toward testing whether cyclo[n]pyrroles display a similar function, a series of diprotonated cyclo[n]pyrroles (where n = 6, 7, and 8) was each added to the human telomere repeat sequence d(T(2)AG(3))(4) and examined with mass spectrometry, ion mobility, and molecular dynamics calculations. Nano-ESI-MS indicated that the smaller the cyclo[n]pyrrole, the more strongly it binds to the telomeric sequence. It was also found that cyclo[6]pyrrole bound to d(T(2)AG(3))(4) better than octaethylporphyrin, a finding rationalized by cyclo[6]pyrrole having a 2+ charge, while octaethylporphyrin bears no charge. Ion mobility measurements were used to measure the collision cross section of each d(T(2)AG(3))(4)/cyclo[n]pyrrole complex. Only one peak was observed in the arrival time distributions for all complexes, and the experimental cross sections indicated that only structures with d(T(2)AG(3))(4) in an antiparallel G-quadruplex arrangement and each cyclo[n]pyrrole externally stacked below the G-quartets occur under these experimental conditions. When the cyclo[n]pyrroles were intercalated or nonspecifically bound to the quadruplex, or if conformations different than antiparallel were considered for d(T(2)AG(3))(4), the theoretical cross sections did not match experiment. On this basis, it is inferred that (1) external stacking represents the dominant binding mode for the interaction of cyclo[n]pyrroles with d(T(2)AG(3))(4) and (2) the overall size and charge of the cyclo[n]pyrroles play important roles in defining the binding strength.}, number={8}, journal={Journal of the American Chemical Society}, author={Baker, ES and Lee, JT and Sessler, JL and Bowers, MT}, year={2006}, pages={2641–2648} }
 @article{baker_bernstein_gabelica_de pauw_bowers_2006, title={G-quadruplexes in telomeric repeats are conserved in a solvent-free environment}, volume={253}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000238967500010&KeyUID=WOS:000238967500010}, DOI={10.1016/j.ijms.2006.03.016}, abstractNote={The structural properties of G-quadruplex forming sequences, such as the human telomeric repeat d(T2AG3)n, are of great interest due to their role in cancer and cellular aging. To determine if G-quadruplexes are present in a solvent-free environment, different lengths of the telomeric repeat d(T2AG3)n (where n = 1, 2, 4 and 6) and dTG4T were investigated with mass spectrometry, ion mobility and molecular dynamics calculations. Nano-ESI-MS illustrated quadruplex stoichiometries compatible with G-quadruplex structures for each sequence, with dT2AG3 and dTG4T forming 4-strand complexes with two and three NH4+ adducts, d(T2AG3)2 a 2-strand complex, and d(T2AG3)4 and d(T2AG3)6 remaining single-stranded. Experimental cross sections were obtained for all species using ion mobility methods. In all cases, these could be quantitatively matched to model cross sections with specific strand orientations (parallel/antiparallel) and structures. For each species, the solvent-free structures agreed with the solution CD measurements, but the ion mobility/modeling procedure often gave much more detailed structural information.}, number={3}, journal={International Journal of Mass Spectrometry}, author={Baker, Erin Shammel and Bernstein, Summer L. and Gabelica, Valerie and De Pauw, Edwin and Bowers, Michael T.}, year={2006}, pages={225–237} }
 @article{bowers_bernstein_baker_wyttenbach_shea_teplow_2006, title={Non-covalent complexes of biological interest: Nucleotide-drug interactions and peptide/protein self assembly}, volume={231}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000238125900429&KeyUID=WOS:000238125900429}, journal={Abstracts of Papers of the American Chemical Society}, author={Bowers, Michael T. and Bernstein, Summer L. and Baker, Erin Shammel and Wyttenbach, Thomas and Shea, Joan-Emma and Teplow, David B.}, year={2006} }
 @article{baker_hong_gaylord_bazan_bowers_2006, title={PNA/dsDNA complexes: Site specific binding and dsDNA biosensor applications}, volume={128}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000238590000035&KeyUID=WOS:000238590000035}, DOI={10.1021/ja060069s}, abstractNote={The ability of peptide nucleic acids (PNA) to form specific higher-order (i.e., three- and four-stranded) complexes with DNA makes it an ideal structural probe for designing strand-specific dsDNA biosensors. Higher-order complexes are formed between a dye-labeled charge-neutral PNA probe and complementary dsDNA. Addition of a light-harvesting cationic conjugated polymer (CCP) yields supramolecular structures held together by electrostatic forces that incorporate the CCP and the dye-labeled PNA/DNA complexes. Optimization of optical properties allows for excitation of the CCP and subsequent fluorescence resonance energy transfer (FRET) to the PNA-bound dye. In the case of noncomplementary dsDNA, complexation between the probe and target does not occur, and dye emission is weak. The binding between PNA and noncomplementary and complementary dsDNA was examined by several methods. Gel electrophoresis confirms specificity of binding and the formation of higher-order complexes. Nano-electrospray mass spectrometry gives insight into the stoichiometric composition, including PNA/DNA, PNA(2)/DNA, PNA/DNA(2), and PNA(2)/DNA(2) complexes. Finally, structural characteristics and binding-site specificity were examined using ion mobility mass spectrometry in conjunction with molecular dynamics. These results give possible conformations for each of the higher-order complexes formed and show exclusive binding of PNA to the complementary stretch of DNA for all PNA/DNA complexes. Overall, the capability and specificity of binding indicates that the CCP/PNA assay is a feasible detection method for dsDNA and eliminates the need for thermal denaturing steps typically required for DNA hybridization probe assays.}, number={26}, journal={Journal of the American Chemical Society}, author={Baker, ES and Hong, JW and Gaylord, BS and Bazan, GC and Bowers, MT}, year={2006}, pages={8484–8492} }
 @article{baker_bushnell_wecksler_lim_manard_dupuis_ford_bowers_2005, title={Probing shapes of bichromophoric metal-organic complexes using ion mobility mass spectrometry}, volume={127}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000234258700053&KeyUID=WOS:000234258700053}, DOI={10.1021/ja0553699}, abstractNote={Ion mobility mass spectrometry (IM-MS) was used to probe the structures of several metal complexes carrying pendant chromophores. The three complexes investigated were the copper(II) complex Cu(DAC)2+ (DAC = 1,8-bis(9-methylanthracyl)cyclam, cyclam = 1,4,8,11-tetraazacyclotetradecane), the N-nitrosylated ligand DAC-NO, and the Roussin's red salt ester (mu-S,mu-S')-protoporphyrin-IX-bis(2-thioethyl ester)tetranitrosyldiiron (PPIX-RSE). From the IM-MS data coupled with theoretical calculations, it was found that [Cu(II)(DAC - H)]+ exists as a single conformer, with one anthracenyl group above the cyclam and the other below, similar to the crystal structure of Cu(II)(DAC)2+. The metal-free N-nitrosylated ligand (DAC-NO + H)+ has two conformations: one family of structures has one anthracenyl group above the cyclam and one below, while the other has both anthracenyl groups on the same side of the cyclam. These observations are consistent with 1H NMR data for the neutral DAC-NO complex that indicate the presence of two geometric isomers in solution. The third species, PPIX-RSE, has a porphyrin chromophore covalently linked to an Fe2S2(NO)4 cluster for use as a precursor for the photochemical delivery of nitric oxide in single- and two-photon excitation processes. Ion mobility indicates the presence of two (PPIX-RSE + H)+ conformations, consistent with the previous interpretation of the bimodal fluorescence lifetime decay seen for PPIX-RSE. DFT structures, in good agreement with the IM-MS cross sections, indicate two "bent" conformations with the planes of the porphyrin and Fe2S2 rings at different angles with respect to each other.}, number={51}, journal={Journal of the American Chemical Society}, author={Baker, E.S. and Bushnell, J.E. and Wecksler, S.R. and Lim, M.D. and Manard, M.J. and Dupuis, N.F. and Ford, P.C. and Bowers, M.T.}, year={2005}, pages={18222–18228} }
 @article{baker_manard_gidden_bowers_2005, title={Structural analysis of metal interactions with the dinucleotide duplex, dCG center dot dCG, using ion mobility mass spectrometry}, volume={109}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000227734500002&KeyUID=WOS:000227734500002}, DOI={10.1021/jp0501190}, abstractNote={The metal binding properties of the dinucleotide duplex, dCG x dCG, were analyzed in the gas phase with ion mobility mass spectrometry. Both MALDI and ESI were used to generate [M(dCG x dCG)]+ complexes. The collision cross section of each complex was measured in helium using ion mobility based methods and compared to calculated cross sections of theoretical structures. When metal cations classified as hard acids were combined with dCG x dCG, the [M(dCG x dCG)]+ complex organized into a globular structure. However, when soft acid metal cations were examined, a structure was observed where the two C-G base pairs were Watson-Crick bound.}, number={11}, journal={Journal of Physical Chemistry B}, author={Baker, ES and Manard, MJ and Gidden, J and Bowers, MT}, year={2005}, pages={4808–4810} }
 @article{baker_bernstein_bowers_2005, title={Structural characterization of G-quadruplexes in deoxyguanosine clusters using ion mobility mass spectrometry}, volume={16}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000230045500003&KeyUID=WOS:000230045500003}, DOI={10.1016/j.jasms.2005.03.012}, abstractNote={The aggregation and conformation of deoxyguanosine (dG) in an ammonium acetate buffer solution were examined using mass spectrometry, ion mobility, and molecular mechanics/dynamics calculations. The nano-ESI mass spectrum indicated that 4 and 6 dGs cluster with 1 NH4+; 11 dGs with 2 NH4+; 14, 16, and 17 dGs with 3 NH4+; and 23 dGs with 4 NH4+. The collision cross sections with helium were measured and compared with calculated cross sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct arrival time distribution (ATD) peaks were observed for (4dG + NH4)+. One peak was assigned to the quadruplex structure of (4dG + NH4)+, while the other two peaks corresponded to the quadruplex structures of (8dG + 2NH4)2+ and (12dG + 3NH4)3+, all with the same m/z. Four ATD peaks were observed for (6dG + NH4)+ and assigned to the globular structure of (6dG + NH4)+, and the quadruplex structures of (12dG + 2NH4)2+, (18dG + 3NH4)3+, and (24dG + 4NH4)4+. Two ATD peaks were observed for (11dG + 2NH4)2+ and assigned to the quadruplex structures of (11dG + 2NH4)2+ and (22dG + 4NH4)4+. All of the other clusters in the mass spectrum (14, 16, and 17 dGs with 3 NH4+ and 23 dGs with 4 NH4+) only had one peak in their ATDs and in all cases the theoretical structures in a quadruplex arrangement agreed with the experimental cross sections. These results provide compelling evidence that quadruplexes are present in solution and retain their structure during the spray process, dehydration, and detection.}, number={7}, journal={Journal of the American Society For Mass Spectrometry}, author={Baker, ES and Bernstein, SL and Bowers, MT}, year={2005}, pages={989–997} }
 @article{gidden_baker_ferzoco_bowers_2005, title={Structural motifs of DNA complexes in the gas phase}, volume={240}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000226540400003&KeyUID=WOS:000226540400003}, DOI={10.1016/j.ijms.2004.09.011}, abstractNote={DNA duplexes are known to be quite stable in the condensed phase but recent mass spectrometry results have shown that DNA complexes are also stable (at least for a limited time) in the gas phase. However, very little is known about the overall shape of the complexes in a solvent-free environment and what factors influence that shape. In this article, we present recent ion mobility and molecular modeling results that address some issues concerning the gas-phase conformations of DNA duplexes. Examples include the effect of metal ions on Watson–Crick base pairing, investigating the onset of helicity in duplexes as a function of strand length, comparison of the stability of C·G and A·T base pairs, and examining the formation of quadruplex structures.}, number={3}, journal={International Journal of Mass Spectrometry}, author={Gidden, J and Baker, ES and Ferzoco, A and Bowers, MT}, year={2005}, pages={183–193} }
 @article{anderson_baker_mitchell_haddad_bowers_2005, title={Structure of hybrid polyhedral oligomeric silsesquioxane propyl methacrylate oligomers using ion mobility mass spectrometry and molecular mechanics}, volume={17}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000229138600009&KeyUID=WOS:000229138600009}, DOI={10.1021/cm047868z}, abstractNote={Ion mobility and molecular modeling methods were used to examine the gas phase conformational properties of polyhedral oligomeric silsesquioxanes (POSS) propyl methacrylate (PMA) oligomers. MALDI was utilized to generate sodiated [(PMA)Cp7T8]xNa+ ions, x = 1, 2, and 3, and their collision cross-sections were measured in helium using ion mobility based methods. Experimental results indicate only one conformer for the Na+1-mer and Na+3-mer, but two or more conformers for the Na+2-mer. Theoretical modeling of the Na+1-mer using the AMBER suite of programs indicates only one family of low-energy structures is found, in which the sodium ion binds to the carbonyl oxygen on the PMA and 4 oxygens on one face of the POSS cage. The calculated cross-section of this family agrees very well with the experimental value, with <2% deviation. For the Na+2-mer, theory predicts three separate conformer families based on whether the backbone attachments to the two POSS cages are “cis”, “extended trans” (larger), or “trans” (...}, number={10}, journal={Chemistry of Materials}, author={Anderson, SE and Baker, ES and Mitchell, C and Haddad, TS and Bowers, MT}, year={2005}, pages={2537–2545} }
 @article{baker_hong_gidden_bartholomew_bazan_bowers_2004, title={Diastereomer assignment of an olefin-linked bis-paracyclophane by ion mobility mass spectrometry}, volume={126}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000221526800027&KeyUID=WOS:000221526800027}, DOI={10.1021/ja039486k}, abstractNote={trans-1,2-Bis([2.2]paracyclophanyl)ethene (1) exists as a pair of diastereomers whose conformations, and thus effective collision cross sections, are quite different. The two forms can be obtained by different transition metal-catalyzed reactions. To assign meso and racemic structures, a novel method is reported in which experimental gas-phase ion mobility data are compared with theoretical structures obtained from molecular mechanics calculations.}, number={20}, journal={Journal of the American Chemical Society}, author={Baker, ES and Hong, JW and Gidden, J and Bartholomew, GP and Bazan, GC and Bowers, MT}, year={2004}, pages={6255–6257} }
 @article{gidden_baker_ferzoco_bowers_2004, title={Duplex formation and the onset of helicity in oligonucleotides.}, volume={227}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000223655701333&KeyUID=WOS:000223655701333}, journal={Abstracts of Papers of the American Chemical Society}, author={Gidden, J and Baker, ES and Ferzoco, A and Bowers, MT}, year={2004}, pages={U258} }
 @article{gidden_ferzoco_baker_bowers_2004, title={Duplex formation and the onset of helicity in poly d(CG)(n) oligonucleotides in a solvent-free environment}, volume={126}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000225233600035&KeyUID=WOS:000225233600035}, DOI={10.1021/ja046433+}, abstractNote={The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.}, number={46}, journal={Journal of the American Chemical Society}, author={Gidden, J and Ferzoco, A and Baker, ES and Bowers, MT}, year={2004}, pages={15132–15140} }
 @article{baker_gidden_anderson_haddad_bowers_2004, title={Isomeric structural characterization of polyhedral oligomeric silsesquioxanes (POSS) with styryl and epoxy phenyl capping agents}, volume={4}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000221410000004&KeyUID=WOS:000221410000004}, DOI={10.1021/nl049957g}, abstractNote={Ion mobility and molecular modeling methods were used to examine the gas-phase structures of sodiated POSS capped with styryl and epoxy phenyl substituents (Na+StyxEp8-xT8). Results were obtained for x = 5−7 and indicated that three distinct isomers with different collision cross-sections were present for each value of x. Theoretical modeling also yielded three different families of structures for each POSS system, and their calculated cross-sections agreed very well with experimental values (<1% difference). For Na+Sty7EpT8, the three families differ in the number of “paired” Sty groups. For Na+Sty6Ep2T8 and Na+Sty5Ep3T8, the three isomers correspond to the three different ways the Ep groups can be positioned on the POSS cage.}, number={5}, journal={Nano Letters}, author={Baker, ES and Gidden, J and Anderson, SE and Haddad, TS and Bowers, MT}, year={2004}, pages={779–785} }
 @article{jackson_scrivens_williams_baker_gidden_bowers_2004, title={Microstructural and Conformational Studies of Polyether Copolymers}, volume={238}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000225740000010&KeyUID=WOS:000225740000010}, DOI={10.1016/j.ijms.2004.09.025}, abstractNote={A combined structural/conformational study of ethylene oxide/propylene oxide (EO/PO) copolymers has been undertaken. Electrospray ionisation (ESI) and matrix-assisted laser desorption/ionisation (MALDI) methods have been utilised and ESI-tandem mass spectrometry (MS/MS) product ion spectra, including accurate mass measurements, utilised to establish fragmentation pathways. This has enabled end group and sequence information to be obtained. Ion mobility mass spectrometry experimental, along with theoretical, approaches has been used in tandem to probe the gas-phase conformation of selected cationised species from the block and random copolymers. The cross-sections established from these measurements and calculations have been shown to be dependent on molecular weight of the oligomer and radii of the cation but largely independent of the sequence of the ion in the gas-phase. The ion mobility results have been used to aid the understanding of the fragmentation of these copolymers by means of ESI-MS/MS.}, number={3}, journal={The International Journal of Mass Spectrometry}, author={Jackson, A.T. and Scrivens, J.H. and Williams, J.P. and Baker, E.S. and Gidden, J. and Bowers, M.T.}, year={2004}, month={Nov}, pages={287–297} }
 @article{baker_gidden_simonsick_grady_bowers_2004, title={Sequence Dependent Conformations of Glycidyl Methacrylate/Butyl Methacrylate Copolymers in the Gas Phase}, volume={238}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000225740000009&KeyUID=WOS:000225740000009}, DOI={10.1016/j.ijms.2004.04.020}, abstractNote={Sequence dependent conformations of a series of glycidyl methacrylate/butyl methacrylate (GMA/BMA) copolymers cationized by sodium were analyzed in the gas phase using ion mobility methods. GMA and BMA have the same nominal mass but vary in exact mass by 0.036 Da (CH4 versus O). Matrix assisted laser desorption/ionization (MALDI) was used to form Na + (GMA/BMA) copolymer ions and their collision cross-sections were measured in helium using ion mobility methods. The copolymer sequences from Na + (GMA/BMA)3 to Na + (GMA/BMA)5 (i.e. for the trimer to the pentamer) were studied. Analysis by molecular mechanics/dynamics indicates that each copolymer (regardless of sequence) forms a ring around the sodium ions due to Na + /oxygen electrostatic interactions. However, the structures vary in size, since the epoxy oxygen atoms in the glycidyl groups are attracted to the sodium ions while the carbon-composed butyl groups are not. This allows copolymers with more GMA segments to fold tighter (more spherically) around the sodium ion and have smaller cross-sections than copolymers with a larger amount of BMA segments in the sequence. Due to this cross-sectional difference, the GMA/BMA sequence compositions of the trimer and tetramer could be quantified. © 2004 Elsevier B.V. All rights reserved.}, number={3}, journal={The International Journal of Mass Spectrometry}, author={Baker, E.S. and Gidden, J. and Simonsick, W.J. and Grady, M.C. and Bowers, M.T.}, year={2004}, month={Nov}, pages={279–286} }
 @article{baker_gidden_ferzoco_bowers_2004, title={Sodium stabilization of dinucleotide multiplexes in the gas phase}, volume={6}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-3042559886&partnerID=MN8TOARS}, DOI={10.1039/b315727j}, abstractNote={The aggregation and conformations of sodiated dinucleotides were studied in the gas phase. MALDI was used to generate [M − (n − 1)H + nNa]+ ions, yielding single-strand ions having n = 1–3, duplex ions with n = 1–7 and triplex ions with n = 3–10. Collision cross-sections of each sodiated complex were measured in helium using ion mobility based methods and compared to calculated cross-sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct single-strand conformers were observed: one with the nucleobases stacked, one with the planes oriented perpendicular to each other and one with the bases coplanar to each other. One conformer is observed for all of the duplexes except dTG·dTG, dGT·dGT and dTT·dTT (in which two conformers are observed depending on whether the guanine or thymine bases stack). For low values of n, the Na+ ions cluster around the two deprotonated phosphates. However, as n increases, the Na+ ions become more dispersed along the duplex. One conformer is also observed for all of the triplexes. For n = 3–6, three Na+ ions and the three phosphates form a quasi-planar ring with the additional Na+ ions resting above, below and in the middle of the ring. Cytosine and thymine also coordinate to the Na+ ions but adenine and guanine prefer to stack and do not coordinate to the Na+ ions in the ring. The addition of the seventh to tenth Na+ ions breaks the sodium-phosphate ring and the Na+ ions become scattered around the triplex. Differences between experimental and theoretical cross-sections (averaged over the lowest 5 kcal mol−1 structures) of each sodiated complex fell between 1–2%.}, number={10}, journal={Physical Chemistry Chemical Physics}, author={Baker, E.S. and Gidden, J. and Ferzoco, A. and Bowers, M.T.}, year={2004}, pages={2786–2795} }
 @inbook{wyttenbach_baker_bernstein_ferzoco_gidden_liu_bowers_2004, title={The ion mobility mass spectrometry method and its application to duplex formation of oligonucleotides and aggregation of proteins}, volume={16}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000226631200011&KeyUID=WOS:000226631200011}, booktitle={Advances in Mass Spectrometry, Vol 16}, author={Wyttenbach, T and Baker, ES and Bernstein, SL and Ferzoco, A and Gidden, J and Liu, DF and Bowers, MT}, year={2004}, pages={189–200} }
 @article{baker_gidden_fee_kemper_anderson_bowers_2003, title={3-dimensional structural characterization of cationized polyhedral oligomeric silsesquioxanes (POSS) with styryl and phenylethyl capping agents}, volume={227}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000182724200018&KeyUID=WOS:000182724200018}, DOI={10.1016/S1387-3806(03)00068-X}, abstractNote={The 3-dimensional gas-phase conformations of polyhedral oligomeric silsesquioxanes (POSS), R8Si8O12, capped with styryl and phenylethyl substituents (R) and cationized by sodium were examined. MALDI was used to generate sodiated styryl–POSS (Na+Sty8T8) and phenylethyl–POSS (Na+PhEt8T8) ions and their collision cross-sections in helium were measured using ion mobility-based methods. Five distinct conformers with different collision cross-sections were experimentally observed for Na+Sty8T8 while only one conformer was detected for Na+PhEt8T8. Theoretical modeling of Na+Sty8T8, using molecular mechanics/dynamics calculations, predicts three low-energy conformations. In each conformer, the Na+ ion binds to four oxygens on one side of the SiO cage and the styryl groups extend away from the cage. However, different numbers of styryl groups “pair” together (forming 2, 3 or 4 pairs), yielding three different conformations. The calculated cross-sections of these conformers match the largest three cross-sections obtained from the ion mobility experiments (∼2% error). If, however, one or two of the styryl groups are rotated so that the phenyl groups are “cis” with respect to the Si atom on the cage (i.e., the SiCCC dihedral angle changes from 180 to 0°) two smaller conformers are predicted by theory whose cross-sections match the smallest two values obtained from the ion mobility experiments (1–2% error). Theoretical modeling of Na+PhEt8T8 yields one low-energy conformation in which the Na+ ion binds to one oxygen on the SiO cage and is sandwiched between two phenyl groups. The remaining phenylethyl groups fold toward the SiO cage, yielding a significantly more compact structure than Na+Sty8T8 (∼20% smaller cross-section). The calculated cross-section of the predicted Na+PhEt8T8 structure agrees very well with the experimental cross-section obtained from the ion mobility experiments (∼1% error).}, number={1}, journal={International Journal of Mass Spectrometry}, author={Baker, E.S. and Gidden, J. and Fee, D.P. and Kemper, P.R. and Anderson, S.E. and Bowers, M.T.}, year={2003}, pages={205–216} }
 @article{application of ion mobility to the gas-phase conformational analysis of polyhedral oligomeric silsesquioxanes (poss)_2003, volume={222}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000180104600007&KeyUID=WOS:000180104600007}, DOI={10.1016/S1387-3806(02)00951-X}, abstractNote={Ion mobility experiments and molecular modeling calculations were used to investigate the gas-phase conformational properties of various polyhedral oligomeric silsesquioxanes (POSS) cationized by sodium. POSS, (RSiO3/2)n, has a rigid SiO cage with organic substituents attached to each Si atom. Na+POSS ions were formed by electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) and their collision cross-sections were measured in helium using ion mobility methods. Calculated cross-sections of theoretical models of the POSS ions, generated by molecular mechanics (MM) calculations, were compared to experiment for conformational identification. The calculations predict that the Na+ ion remains outside of the SiO cage and binds to one to two oxygen atoms in the cage or interacts with two neighboring organic substituents. Cross-sections of X-ray structures were also compared to the experimental and theoretical data to determine if any changes occur to POSS in the gas phase (compared to the condensed phase) and to provide a check for the geometries predicted by theory (which used untested Si parameters). Several types of POSS compounds were investigated that had different SiO cage sizes (Si6O9, Si8O12, Si10O15, Si12O18, …) and different “R” substituents such as cyclohexyl, cyclopropyl, vinyl, and phenyl groups. Experimental, theoretical, and X-ray cross-sections differed by <2% for each POSS compound.}, number={1-3}, journal={International Journal of Mass Spectrometry}, year={2003}, pages={63–73} }