@article{knizner_bagley_pu_elsen_williams_muddiman_2022, title={Normalization techniques for high-throughput screening by infrared matrix-assisted laser desorption electrospray ionization mass spectrometry}, volume={57}, ISSN={["1096-9888"]}, DOI={10.1002/jms.4869}, abstractNote={Abstract Mass spectrometry (MS) is an effective analytical tool for high‐throughput screening (HTS) in the drug discovery field. Infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) MS is a high‐throughput platform that has achieved analysis times of sub‐seconds‐per‐sample. Due to the high‐throughput analysis speed, methods are needed to increase the analyte signal while decreasing the variability in IR‐MALDESI‐MS analyses to improve data quality and reduce false‐positive hits. The Z‐factor is used as a statistic of assay quality that can be improved by reducing the variation of target ion abundances or increasing signal. Herein we report optimal solvent compositions for increasing measured analyte abundances with direct analysis by IR‐MALDESI‐MS. We also evaluate normalization strategies, such as adding a normalization standard that is similar or dissimilar in structure to the model target drug, to reduce the variability of measured analyte abundances with direct analyses by IR‐MALDESI‐MS in both positive and negative ionization modes.}, number={6}, journal={JOURNAL OF MASS SPECTROMETRY}, author={Knizner, Kevan T. and Bagley, Michael C. and Pu, Fan and Elsen, Nathaniel L. and Williams, Jon D. and Muddiman, David C.}, year={2022}, month={Jun} }
 @article{knizner_bagley_garrard_hauschild_pu_elsen_williams_muddiman_2022, title={Optimized C-Trap Timing of an Orbitrap 240 Mass Spectrometer for High-Throughput Screening and Native MS by IR-MALDESI}, volume={33}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.1c00319}, abstractNote={Infrared matrix-assisted laser desorption ionization (IR-MALDESI) is a hybrid mass spectrometry ionization source that combines the benefits of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) making it a great analytical tool for high-throughput screening (HTS) analyses. IR-MALDESI is coupled to an Orbitrap Exploris 240 mass spectrometer that utilizes a bent quadrupole (C-trap) to inject accumulated ions into the high-field Orbitrap mass analyzer. Here, we present a study on the optimized C-trap timing for HTS analyses by IR-MALDESI mass spectrometry. The timing between initial ion generation and the C-trap opening time was optimized to reduce unnecessary ambient ion accumulation in the mass spectrometer. The time in which the C-trap was held open, the ion accumulation time, was further optimized to maximize the accumulation of analyte ions generated using IR-MALDESI. The resulting C-trap opening scheme benefits small-molecule HTS analyses by IR-MALDESI by maximizing target ion abundances, minimizing ambient ion abundances, and minimizing the total analysis time per sample. The proposed C-trap timing scheme for HTS does not translate to large molecules; a NIST monoclonal antibody standard reference material was analyzed to demonstrate that larger analytes require longer ion accumulation times and that IR-MALDESI can measure intact antibodies in their native state.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Knizner, Kevan T. and Bagley, Michael C. and Garrard, Kenneth P. and Hauschild, Jan-Peter and Pu, Fan and Elsen, Nathaniel L. and Williams, Jon D. and Muddiman, David C.}, year={2022}, month={Feb}, pages={328–334} }
 @article{bagley_muddiman_2021, title={Investigations of beta-carotene radical cation formation in infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI)}, volume={35}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.9133}, abstractNote={RATIONALE
Radical cationization of endogenous hydrocarbons in cherry tomatoes was previously reported using IR-MALDESI, a mass spectrometry imaging technique that operates at ambient conditions and requires no sample derivatization. Due to the surprising nature of this odd-electron ionization, successive experiments were performed on β-carotene to determine the amount of radical cationization across different sampling conditions.


METHODS
β-Carotene was analyzed across a variety of sample states using IR-MALDESI followed by Orbitrap mass spectrometry analysis. First, as a standard in ethanol in a well plate. Second, as particulates on printer paper and, third, particulates covered by an ice matrix. These techniques were also performed on a β-carotene standard either in solution with a reducing agent (ascorbic acid) or with ascorbic acid in the electrospray solution.


RESULTS
Tandem mass spectrometry confirmed the presence of the radical cation of β-Carotene by comparing fragments against NIST and METLIN databases. It was always analyzed as a radical cation when sampled from solution, where ascorbic acid increased radical cation abundance when in solution with β-Carotene. Mixed-mode ionization between radical cationization and proton adduction was observed from dried particulates using IR-MALDESI.


CONCLUSIONS
There are several potential mechanisms for β-carotene radical cationization prior to IR-MALDESI analysis with multiphoton-ionization, thermal degradation, and/or reaction with oxygen appears to be the most logical explanation. Furthermore, although is not the primary cause, changing certain aspects of sample conditions can result in significant mixed-mode ionization with competing protonation.}, number={16}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bagley, M. Caleb and Muddiman, David C.}, year={2021}, month={Aug} }
 @article{bagley_garrard_muddiman_2021, title={The development and application of matrix assisted laser desorption electrospray ionization: The teenage years}, volume={5}, ISSN={["1098-2787"]}, DOI={10.1002/mas.21696}, abstractNote={In the past 15 years, ambient ionization techniques have witnessed a significant incursion into the field of mass spectrometry imaging, demonstrating their ability to provide complementary information to matrix-assisted laser desorption ionization. Matrix-assisted laser desorption electrospray ionization is one such technique that has evolved since its first demonstrations with ultraviolet lasers coupled to Fourier transform-ion cyclotron resonance mass spectrometers to extensive use with infrared lasers coupled to orbitrap-based mass spectrometers. Concurrently, there have been transformative developments of this imaging platform due to the high level of control the principal group has retained over the laser technology, data acquisition software (RastirX), instrument communication, and image processing software (MSiReader). This review will discuss the developments of MALDESI since its first laboratory demonstration in 2005 to the most recent advances in 2021.}, journal={MASS SPECTROMETRY REVIEWS}, author={Bagley, Michael Caleb and Garrard, Kenneth P. and Muddiman, David C.}, year={2021}, month={May} }
 @article{jaiswal_yerke_bagley_ekelof_weber_haddad_fodor_muddiman_williams_2020, title={3D Imaging and metabolomic profiling reveal higher neuroactive kavalactone contents in lateral roots and crown root peels of Piper methysticum (kava)}, volume={9}, ISSN={["2047-217X"]}, DOI={10.1093/gigascience/giaa096}, abstractNote={Abstract Background Kava is an important neuroactive medicinal plant. While kava has a large global consumer footprint for its clinical and recreational use, factors related to its use lack standardization and the tissue-specific metabolite profile of its neuroactive constituents is not well understood. Results Here we characterized the metabolomic profile and spatio-temporal characteristics of tissues from the roots and stems using cross-platform metabolomics and a 3D imaging approach. Gas chromatography–mass spectrometry and liquid chromatography–mass spectrometry revealed the highest content of kavalactones in crown root peels and lateral roots. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging revealed a unique tissue-specific presence of each target kavalactone. X-ray micro-computed tomography analysis demonstrated that lateral roots have morphological characteristics suitable for synthesis of the highest content of kavalactones. Conclusions These results provide mechanistic insights into the social and clinical practice of the use of only peeled roots by linking specific tissue characteristics to concentrations of neuroactive compounds.}, number={9}, journal={GIGASCIENCE}, author={Jaiswal, Yogini S. and Yerke, Aaron M. and Bagley, M. Caleb and Ekelof, Mans and Weber, Daniel and Haddad, Daniel and Fodor, Anthony and Muddiman, David C. and Williams, Leonard L.}, year={2020}, month={Sep} }
 @article{garrard_ekelöf_khodjaniyazova_bagley_muddiman_2020, title={A Versatile Platform for Mass Spectrometry Imaging of Arbitrary Spatial Patterns}, volume={31}, ISSN={1044-0305 1879-1123}, url={http://dx.doi.org/10.1021/jasms.0c00128}, DOI={10.1021/jasms.0c00128}, abstractNote={A vision-system driven platform, RastirX, has been constructed for mass spectrometry imaging (MSI) of arbitrary two-dimensional patterns. The user identifies a region of interest (ROI) by drawing on a live video image of the sample with the computer mouse. Motion commands are automatically generated to move the sample to acquire scan data for the pixels in the ROI. Synchronization of sample stage motion with laser firing and mass spectrometer (MS) scan acquisition is fully automated. RastirX saves a co-registered optical image and the scan location information needed to convert raw MS data into imzML format. Imaging an arbitrarily shaped ROI instead of the minimal enclosing rectangle reduces contamination from off-sample material and significantly reduces acquisition time.}, number={12}, journal={Journal of the American Society for Mass Spectrometry}, publisher={American Chemical Society (ACS)}, author={Garrard, Kenneth P. and Ekelöf, Måns and Khodjaniyazova, Sitora and Bagley, M. Caleb and Muddiman, David C.}, year={2020}, month={Jun}, pages={2547–2552} }
 @article{bagley_ekelof_muddiman_2020, title={Determination of Optimal Electrospray Parameters for Lipidomics in Infrared-Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry Imaging}, volume={31}, ISSN={["1879-1123"]}, DOI={10.1021/jasms.9b00063}, abstractNote={Infrared matrix-assisted laser desorption ionization (IR-MALDESI) is an ambient mass spectrometry imaging (MSI) technique that relies on electrospray ionization (ESI) for ion generation of desorbed neutrals. Although many mechanisms in IR-MALDESI have been studied in depth, there has not yet been a comprehensive study of how the ESI parameters change the profiles of tissue specific lipids. Acetonitrile (ACN)/water and methanol (MeOH)/water solvent systems and compositions were varied across a series of applied ESI voltages during IR-MALDESI analysis of rat liver tissue. Gradients of 12 min were run from 5 to 95% organic solvent in both positive and negative polarities across 11 voltages between 2.25 and 4.5 kV. These experiments informed longer gradients (25-30 min) across shorter solvent gradient ranges with fewer voltages. Optimal ESI parameters for lipidomics were determined by the number and abundance of detected lipids and the relative proportion of background ions. In positive polarity, the best solvent composition was 60-75% ACN/40-25% H2O with 0.2% formic acid at 3.2 kV applied voltage. The best parameters for negative polarity analysis are 45-55% ACN/55-45% H2O with 1 mM of acetic acid for voltages between 2.25 and 3.2 kV. Using these defined parameters, IR-MALDESI positive polarity lipidomics studies can increase lipid abundances 3-fold, with 15% greater coverage, while an abundance increase of 1.5-fold and 10% more coverage can be achieved relative to commonly used parameters in negative polarity.}, number={2}, journal={JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY}, author={Bagley, M. Caleb and Ekelof, Mans and Muddiman, David C.}, year={2020}, month={Feb}, pages={319–325} }
 @article{bagley_stepanova_ekelof_alonso_muddiman_2020, title={Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings}, volume={34}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.8616}, abstractNote={RATIONALE
Mass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due numerous biological considerations, established methods for the relative quantification of analytes using IR-MALDESI mass spectrometry imaging are not viable options. In this study, we report a method for quantification of auxin-related compounds using stable-isotope-labelled (SIL) indole-3-acetic acid (IAA) doped into agarose substrate.


METHODS
Wild-type Arabidopsis thaliana seedlings, sur2 and wei8 tar2 loss-of-function mutants, and YUC1 gain-of-function line were grown for 3 days in the dark in standard growth medium. SIL-IAA was doped into a 1% low-melting-point agarose gel and seedlings were gently laid on top for IR-MALDESI imaging with Orbitrap mass spectrometry analysis. Relative quantification was performed post-acquisition by normalization of auxin-related compounds to SIL-IAA in the agarose. Amounts of auxin-related compounds were compared between genotypes to distinguish the effects of the mutations on the accumulation of indolic metabolites of interest.


RESULTS
IAA added to agarose was found to maintain stability, with repeatability and abundance features of IAA comparable with those of other compounds used in other methods for relative quantification in IR-MALDESI analyses. Indole-3-acetaldoxime was increased in sur2 mutants compared with wildtype and other mutants. Other auxin-related metabolites were either below the limits of quantification or successfully quantified but showing little difference among mutants.


CONCLUSIONS
Agarose was shown to be an appropriate sampling surface for IR-MALDESI mass spectrometry imaging of Arabidopsis seedlings. SIL-IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations.}, number={6}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bagley, M. Caleb and Stepanova, Anna N. and Ekelof, Mans and Alonso, Jose M. and Muddiman, David C.}, year={2020}, month={Mar} }
 @article{bagley_pace_ekelof_muddiman_2020, title={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging analysis of endogenous metabolites in cherry tomatoes}, volume={145}, ISSN={["1364-5528"]}, DOI={10.1039/d0an00818d}, abstractNote={We report the spatially resolved metabolic profiling of cherry tomatoes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI), a mass spectrometry imaging (MSI) technique that operates at ambient conditions and requires no sample derivatization. Tomatoes were flash frozen, cryosectioned and imaged with adequate spatial resolution to distinguish between the major tissue structures of a tomato including the skin, mesocarp, endocarp, locular tissue, septum, placenta, seed and seed coating. Metabolites were imaged from 100-1200 m/z, enabling significant coverage of a diverse array of metabolites including amino acids and lipids along with the major secondary metabolite classes: terpenes, phenolics, glycosides, and alkaloids. During the metabolic profiling, we found endogenous carotenoid hydrocarbons, namely lycopene or its structural isomer β-carotene, ionized as radical cations. To our knowledge, this is the first demonstration of ionizing hydrocarbons in the MSI field.}, number={16}, journal={ANALYST}, author={Bagley, M. Caleb and Pace, Crystal L. and Ekelof, Mans and Muddiman, David C.}, year={2020}, month={Aug}, pages={5516–5523} }
 @article{bagley_ekelof_rock_patisaul_muddiman_2018, title={IR-MALDESI mass spectrometry imaging of underivatized neurotransmitters in brain tissue of rats exposed to tetrabromobisphenol A}, volume={410}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-018-1420-0}, abstractNote={There is a pressing need to develop tools for assessing possible neurotoxicity, particularly for chemicals where the mode of action is poorly understood. Tetrabromobisphenol A (TBBPA), a highly abundant brominated flame retardant, has lately been targeted for neurotoxicity analysis by concerned public health entities in the EU and USA because it is a suspected thyroid disruptor and neurotoxicant. In this study, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) coupled to a Q Exactive Plus mass spectrometer was used for the analysis of neurotransmitters in the brains of rats exposed to TBBPA in gestation and lactation through their mothers. Three neurotransmitters of interest were studied in three selected regions of the brain: caudate putamen, substantia nigra (SN), and dorsal raphe. Stable isotope labeled (SIL) standards were used as internal standards and a means to achieve relative quantification. This study serves as a demonstration of a new application of IR-MALDESI, namely that neurotransmitter distributions can be confidently and rapidly imaged without derivatization.}, number={30}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Bagley, M. Caleb and Ekelof, Mans and Rock, Kylie and Patisaul, Heather and Muddiman, David C.}, year={2018}, month={Dec}, pages={7979–7986} }
 @article{zhang_zhang_nazari_bagley_miller_williams_muddiman_lindsey_2017, title={Mass spectrometric detection of chlorophyll a and the tetrapyrrole secondary metabolite tolyporphin A in the filamentous cyanobacterium HT-58-2. Approaches to high-throughput screening of intact cyanobacteria}, volume={21}, ISSN={["1099-1409"]}, DOI={10.1142/s108842461750078x}, abstractNote={Tolyporphins are unusual tetrapyrrole macrocycles produced by the filamentous cyanobacterium–microbial community HT-58-2, the only known source to date. Numerous cyanobacterial samples have been collected worldwide but most have not been screened for secondary metabolites. Identification of tolyporphins typically has entailed lipophilic extraction followed by chromatographic fractionation and spectroscopic and/or mass spectrometric analysis. For quantitation, lengthy lipophilic extraction, sample processing and HPLC separation are needed. Examination by MALDI-TOF-MS (with the matrix 1,5-diaminonaphthalene) of lipophilic crude extracts of small-scale HT-58-2 samples (2 mL) without chromatographic fractionation enabled semi-quantitation of tolyporphin A over a 41-day growth period. Screening for tolyporphin A in intact or slightly sheared and vortexed HT-58-2 samples (no lipophilic extraction), and confirmation of identity by tandem MS, were carried out by IR-MALDESI-FTMS. Tolyporphin A was identified by th...}, number={11}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Zhang, Yunlong and Zhang, Ran and Nazari, Milad and Bagley, Michael C. and Miller, Eric S. and Williams, Philip G. and Muddiman, David C. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={759–768} }