Erin Baker Gentry, E. C., Collins, S. L., Panitchpakdi, M., Belda-Ferre, P., Stewart, A. K., Terrazas, M. C., … Dorrestein, P. C. (2024). Reverse metabolomics for the discovery of chemical structures from humans. NATURE, 626(7998). https://doi.org/10.1038/s41586-023-06906-8 Chappel, J. R., King, M. E., Fleming, J., Eberlin, L. S., Reif, D. M., & Baker, E. S. (2023, August 14). Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics. ANALYTICAL CHEMISTRY, Vol. 8. https://doi.org/10.1021/acs.analchem.3c02389 Foley, M. H., Walker, M. E., Stewart, A. K., O'Flaherty, S., Gentry, E. C., Patel, S., … Theriot, C. M. (2023, March 13). Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. NATURE MICROBIOLOGY, Vol. 3. https://doi.org/10.1038/s41564-023-01337-7 Ryan, J. P., Kostelic, M. M., Hsieh, C.-C., Powers, J., Aspinwall, C., Dodds, J. N., … Baker, E. S. (2023). Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 34(12), 2811–2821. https://doi.org/10.1021/jasms.3c00321 Cordova, A. C., Klaren, W. D., Ford, L. C., Grimm, F. A., Baker, E. S., Zhou, Y.-H., … Rusyn, I. (2023). Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams. TOXICS, 11(7). https://doi.org/10.3390/toxics11070586 Stewart, A. K., Foley, M. H., Dougherty, M. K., Mcgill, S. K., Gulati, A. S., Gentry, E. C., … Baker, E. S. (2023). Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems. ANALYTICAL CHEMISTRY, 95(41), 15357–15366. https://doi.org/10.1021/acs.analchem.3c03057 Butler, K. E., & Baker, E. S. (2022, September 22). A High-Throughput Ion Mobility Spectrometry-Mass Spectrometry Screening Method for Opioid Profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol. 9. https://doi.org/10.1021/jasms.2c00186 Bilbao, A., Gibbons, B. C., Stow, S. M., Kyle, J. E., Bloodsworth, K. J., Payne, S. H., … Fjeldsted, J. C. (2022). A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows. JOURNAL OF PROTEOME RESEARCH, 21(3), 798–807. https://doi.org/10.1021/acs.jproteome.1c00425 Valdiviezo, A., Aly, N. A., Luo, Y.-S., Cordova, A., Casillas, G., Foster, M. K., … Rusyn, I. (2022). 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. JOURNAL OF ENVIRONMENTAL SCIENCES, 115, 350–362. https://doi.org/10.1016/j.jes.2021.08.004 Doyle, M. G., Odenkirk, M. T., Stewart, A. K., Nelson, J. P., Baker, E. S., & Cruz, F. (2022, November 1). Assessing the Fate of Dissolved Organic Compounds in Landfill Leachate and Wastewater Treatment Systems. ACS ES&T WATER, Vol. 11. https://doi.org/10.1021/acsestwater.2c00320 Rainey, M. A., Watson, C. A., Asef, C. K., Foster, M. R., Baker, E. S., & Fernandez, F. M. (2022, December 6). CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics. ANALYTICAL CHEMISTRY, Vol. 12. https://doi.org/10.1021/acs.analchem.2c03491 Roman-Hubers, A. T., Cordova, A. C., Rohde, A. M., Chiu, W. A., McDonald, T. J., Wright, F. A., … Rusyn, I. (2022). Characterization of compositional variability in petroleum substances. FUEL, 317. https://doi.org/10.1016/j.fuel.2022.123547 Dodds, J. N., Wang, L., Patti, G. J., & Baker, E. S. (2022, January 28). Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses. ANALYTICAL CHEMISTRY, Vol. 1. https://doi.org/10.1021/acs.analchem.1c04430 Zhu, Y., Schrecke, S., Tang, S., Odenkirk, M. T., Walker, T., Stover, L., … Laganowsky, A. (2022). Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 144(16), 7048–7053. https://doi.org/10.1021/jacs.2c00612 Rampler, E., Baker, E. S., Kirkwood, K. I., Schwaiger-Haber, M., Tam, M., Jones, M. A., & Sherman, M. (2022, February 16). Empowering women and addressing underrepresentation in the field of mass spectrometry. EXPERT REVIEW OF PROTEOMICS, Vol. 2. https://doi.org/10.1080/14789450.2022.2039631 Valdiviezo, A., Kato, Y., Baker, E. S., Chiu, W. A., & Rusyn, I. (2022). Evaluation of Metabolism of a Defined Pesticide Mixture through Multiple In Vitro Liver Models. TOXICS, 10(10). https://doi.org/10.3390/toxics10100566 Butler, K. E., Dodds, J. N., Flick, T., Campuzano, I. D. G., & Baker, E. S. (2022). High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening. ANALYTICAL CHEMISTRY, 94(16), 6191–6199. https://doi.org/10.1021/acs.analchem.1c05533 Witchey, S. K., Doyle, M. G., Fredenburg, J. D., St Armour, G., Horman, B., Odenkirk, M. T., … Patisaul, H. B. (2022, September 8). Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters. NEUROENDOCRINOLOGY, Vol. 9. https://doi.org/10.1159/000526959 McDonald, J. G., Ejsing, C. S., Kopczynski, D., Holcapek, M., Aoki, J., Arita, M., … Ekroos, K. (2022, August 8). Introducing the Lipidomics Minimal Reporting Checklist. NATURE METABOLISM, Vol. 8. https://doi.org/10.1038/s42255-022-00628-3 Kostelic, M. M., Ryan, J. P., Brown, L. S., Jackson, T. W., Hsieh, C.-C., Zak, C. K., … Marty, M. T. (2022, August 18). Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry. ANALYTICAL CHEMISTRY, Vol. 8. https://doi.org/10.1021/acs.analchem.2c02378 Kostelic, M. M., Hsieh, C.-C., Sanders, H. M., Zak, C. K., Ryan, J. P., Baker, E. S., … Marty, M. T. (2022). Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 33(6), 1031–1037. https://doi.org/10.1021/jasms.2c00087 Roman-Hubers, A. T., Aeppli, C., Dodds, J. N., Baker, E. S., McFarlin, K. M., Letinski, D. J., … Rusyn, I. (2022). Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight. MARINE POLLUTION BULLETIN, 185. https://doi.org/10.1016/j.marpolbul.2022.114360 Foster, M. K., Rainey, M., Watson, C., Dodds, J. N., Kirkwood, K. I., Fernandez, F. M., & Baker, E. S. (2022). Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 56(12), 9133–9143. https://doi.org/10.1021/acs.est.2c00201 Kirkwood, K. I., Fleming, J., Nguyen, H., Reif, D. M., Baker, E. S., & Belcher, S. M. (2022). Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS). ENVIRONMENTAL SCIENCE & TECHNOLOGY, 56(6), 3441–3451. https://doi.org/10.1021/acs.est.1c06483 Kirkwood, K. I., Pratt, B. S., Shulman, N., Tamura, K., MacCoss, M. J., MacLean, B. X., & Baker, E. S. (2022, July 13). Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions. NATURE PROTOCOLS, Vol. 7. https://doi.org/10.1038/s41596-022-00714-6 Roman-Hubers, A. T., McDonald, T. J., Baker, E. S., Chiu, W. A., & Rusyn, I. (2021). A Comparative Analysis of Analytical Techniques for Rapid Oil Spill Identification. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 40(4), 1034–1049. https://doi.org/10.1002/etc.4961 Roman-Hubers, A. T., Cordova, A. C., Aly, N. A., McDonald, T. J., Lloyd, D. T., Wright, F. A., … Rusyn, I. (2021). Data Processing Workflow to Identify Structurally Related Compounds in Petroleum Substances Using Ion Mobility Spectrometry-Mass Spectrometry. ENERGY & FUELS, 35(13), 10529–10539. https://doi.org/10.1021/acs.energyfuels.1c00892 Kirkwood, K. I., Christopher, M. W., Burgess, J. L., Littau, S. R., Foster, K., Richey, K., … Baker, E. S. (2021, December 7). Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity. JOURNAL OF PROTEOME RESEARCH, Vol. 12. https://doi.org/10.1021/acs.jproteome.1c00820 Dodds, J. N., Alexander, N. L. M., Kirkwood, K. I., Foster, M. K. R., Hopkins, Z. R., Knappe, D. R. U., & Baker, E. S. (2021). [Review of From Pesticides to Per- and Polyfluoroalkyl Substances: An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics]. ANALYTICAL CHEMISTRY, 93(1), 641–656. https://doi.org/10.1021/acs.analchem.0c04359 Khadempour, L., Kyle, J. E., Webb-Robertson, B.-J. M., Nicora, C. D., Smith, F. B., Smith, R. D., … Burnum-Johnson, K. E. (2021). From Plants to Ants: Fungal Modification of Leaf Lipids for Nutrition and Communication in the Leaf-Cutter Ant Fungal Garden Ecosystem. MSYSTEMS, 6(2). https://doi.org/10.1128/msystems.01307-20 Odenkirk, M. T., Stratton, K. G., Bramer, L. M., Webb-Robertson, B.-J. M., Bloodsworth, K. J., Monroe, M. E., … Baker, E. S. (2021). From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions. BIOMOLECULES, 11(1). https://doi.org/10.3390/biom11010040 Dodds, J. N., & Baker, E. S. (2021). Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry-Mass Spectrometry. ANALYTICAL CHEMISTRY, 93(51), 17094–17102. https://doi.org/10.1021/acs.analchem.1c04267 Duncan, K. D., Sun, X., Baker, E. S., Dey, S. K., & Lanekoff, I. (2021). In situ imaging reveals disparity between prostaglandin localization and abundance of prostaglandin synthases. COMMUNICATIONS BIOLOGY, 4(1). https://doi.org/10.1038/s42003-021-02488-1 Ligare, M. R., Morrison, K. A., Hewitt, M. A., Reveles, J. U., Govind, N., Hernandez, H., … Johnson, G. E. (2021). Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au-7(PPh3)(7)H-5(2+). JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 12(10), 2502–2508. https://doi.org/10.1021/acs.jpclett.0c03664 Odenkirk, M. T., Reif, D. M., & Baker, E. S. (2021). Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. ANALYTICAL CHEMISTRY, 93(22), 7763–7773. https://doi.org/10.1021/acs.analchem.0c04850 Baker, E. S., & Knappe, D. R. U. (2021, December 2). Per- and polyfluoroalkyl substances (PFAS)-contaminants of emerging concern. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 12. https://doi.org/10.1007/s00216-021-03811-9 Koefeler, H. C., Ahrends, R., Baker, E. S., Ekroos, K., Han, X., Hoffmann, N., … Liebisch, G. (2021). [Review of Recommendations for good practice in MS-based lipidomics]. JOURNAL OF LIPID RESEARCH, 62. https://doi.org/10.1016/j.jlr.2021.100138 Luo, Y.-S., Chen, Z., Blanchette, A. D., Zhou, Y.-H., Wright, F. A., Baker, E. S., … Rusyn, I. (2021). Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes. FOOD AND CHEMICAL TOXICOLOGY, 149. https://doi.org/10.1016/j.fct.2021.111979 Spatial Distribution of Polycyclic Aromatic Hydrocarbon Contaminants after Hurricane Harvey in a Houston Neighborhood. (2021). Journal of Health & Pollution. https://doi.org/10.5696/2156-9614-11.29.210308 Butler, K. E., Takinami, Y., Rainczuk, A., Baker, E. S., & Roberts, B. R. (2021). Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase. FRONTIERS IN CHEMISTRY, 9. https://doi.org/10.3389/fchem.2021.614595 Aly, N. A., Dodds, J. N., Luo, Y.-S., Grimm, F. A., Foster, M. K., Rusyn, I., & Baker, E. S. (2021, October 20). Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 10. https://doi.org/10.1007/s00216-021-03686-w Butler, K. E., Kalmar, J. G., Muddiman, D. C., & Baker, E. S. (2021, August 4). Utilizing liquid chromatography, ion mobility spectrometry, and mass spectrometry to assess INLIGHT (TM) derivatized N-linked glycans in biological samples. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 8. https://doi.org/10.1007/s00216-021-03570-7 Ekelof, M., Dodds, J. N., Khodjaniyazova, S., Garrard, K. P., Baker, E. S., & Muddiman, D. C. (2020). Coupling IR-MALDESI with Drift Tube Ion Mobility-Mass Spectrometry for High-Throughput Screening and Imaging Applications. Journal of the American Society for Mass Spectrometry, 31(3), 642–650. https://doi.org/10.1021/jasms.9b00081 Kalmar, J. G., Butler, K. E., Baker, E. S., & Muddiman, D. C. (2020). Enhanced protocol for quantitativeN-linked glycomics analysis using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)(TM). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 412(27), 7569–7579. https://doi.org/10.1007/s00216-020-02892-2 Soper-Hopper, M. T., Vandegrift, J., Baker, E. S., & Fernandez, F. M. (2020). Metabolite collision cross section prediction without energy-minimized structures. The Analyst, 145(16), 5414–5418. https://doi.org/10.1039/d0an00198h Orwoll, E. S., Wiedrick, J., Nielson, C. M., Jacobs, J., Baker, E. S., Piehowski, P., … Lapidus, J. (2020). Proteomic assessment of serum biomarkers of longevity in older men. AGING CELL, 19(11). https://doi.org/10.1111/acel.13253 Luo, Y.-S., Aly, N. A., McCord, J., Strynar, M. J., Chiu, W. A., Dodds, J. N., … Rusyn, I. (2020). Rapid Characterization of Emerging Per- and Polyfluoroalkyl Substances in Aqueous Film-Forming Foams Using Ion Mobility Spectrometry-Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 54(23), 15024–15034. https://doi.org/10.1021/acs.est.0c04798 Dodds, J. N., Hopkins, Z. R., Knappe, D. R. U., & Baker, E. S. (2020). Rapid Characterization of Per- and Polyfluoroalkyl Substances (PFAS) by Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS). Analytical Chemistry, 92(6), 4427–4435. https://doi.org/10.1021/acs.analchem.9b05364 Odenkirk, M. T., Zin, P. P. K., Ash, J. R., Reif, D. M., Fourches, D., & Baker, E. S. (2020). Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems. ANALYST, 145(22), 7197–7209. https://doi.org/10.1039/d0an01638a Aly, N. A., Luo, Y.-S., Liu, Y., Casillas, G., McDonald, T., Kaihatu, J., … Rusyn, I. (2020). Temporal and spatial analysis of per and polyfluoroalkyl substances in surface waters of Houston ship channel following a large-scale industrial fire incident. Environmental Pollution, 265(B), 115009. https://doi.org/10.1016/j.envpol.2020.115009 Odenkirk, M. T., Stratton, K. G., Gritsenko, M. A., Bramer, L. M., Webb-Robertson, B.-J. M., Bloodsworth, K. J., … Baker, E. S. (2020). Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools. MOLECULAR OMICS, 16(6). https://doi.org/10.1039/d0mo00074d Odenkirk, M. T., & Baker, E. S. (2020). Utilizing Drift Tube Ion Mobility Spectrometry for the Evaluation of Metabolites and Xenobiotics. ION MOBILITY-MASS SPECTROMETRY: METHODS AND PROTOCOLS, Vol. 2084, pp. 35–54. https://doi.org/10.1007/978-1-0716-0030-6_2 Eugenia Monge, M., Dodds, J. N., Baker, E. S., Edison, A. S., & Fernandez, F. M. (2019). Challenges in Identifying the Dark Molecules of Life. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 12, Vol. 12, pp. 177–199. https://doi.org/10.1146/annurev-anchem-061318-114959 Zheng, X., Smith, F. B., Aly, N. A., Cai, J., Smith, R. D., Patterson, A. D., & Baker, E. S. (2019). Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 411(19), 4673–4682. https://doi.org/10.1007/s00216-019-01869-0 Zhang, Y., Zhong, Y., Connor, A. L., Miller, D. P., Cao, R., Shen, J., … Gong, B. (2019). Folding and Assembly of Short α, β, Î-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures. Journal of the American Chemical Society, 141(36), 14239–14248. https://doi.org/10.1021/jacs.9b06094 Dodds, J. N., & Baker, E. S. (2019). Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 30(11), 2185–2195. https://doi.org/10.1007/s13361-019-02288-2 Chouinard, C. D., Nagy, G., Smith, R. D., & Baker, E. S. (2019). Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. In Comprehensive Analytical Chemistry (Vol. 83, pp. 123–159). https://doi.org/10.1016/bs.coac.2018.11.001 Burnum-Johnson, K. E., Zheng, X., Dodds, J. N., Ash, J., Fourches, D., Nicora, C. D., … Baker, E. S. (2019). [Review of Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples]. TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 116, 292–299. https://doi.org/10.1016/j.trac.2019.04.022 Baker, E. S., & Patti, G. J. (2019). Perspectives on Data Analysis in Metabolomics: Points of Agreement and Disagreement from the 2018 ASMS Fall Workshop. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 30(10), 2031–2036. https://doi.org/10.1007/s13361-019-02295-3 Plante, P.-L., Francovic-Fontaine, E., May, J. C., McLean, J. A., Baker, E. S., Laviolette, F., … Corbeil, J. (2019). Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS. ANALYTICAL CHEMISTRY, 91(8), 5191–5199. https://doi.org/10.1021/acs.analchem.8b05821 Orton, D. J., Tfaily, M. M., Moore, R. J., Lamarche, B. L., Zheng, X., Fillmore, T. L., … Baker, E. S. (2018). A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements. Analytical Chemistry, 90(1), 737–744. https://doi.org/10.1021/acs.analchem.7b02986 Bilbao, A., Gibbons, B. C., Slysz, G. W., Crowell, K. L., Monroe, M. E., Ibrahim, Y. M., … Baker, E. S. (2018). An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies. International Journal of Mass Spectrometry, 427, 91–99. https://doi.org/10.1016/j.ijms.2017.11.003 Kedia, K., Wendler, J. P., Baker, E. S., Burnum-Johnson, K. E., Jarsberg, L. G., Stratton, K. G., … Nahid, P. (2018). Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis. Tuberculosis, 112, 52–61. https://doi.org/10.1016/j.tube.2018.07.005 Kyle, J. E., Clair, G., Bandyopadhyay, G., Misra, R. S., Zink, E. M., Bloodsworth, K. J., … Ansong, C. (2018). Cell type-resolved human lung lipidome reveals cellular cooperation in lung function. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-31640-x Horney, J. A., Casillas, G. A., Baker, E., Stone, K. W., Kirsch, K. R., Camargo, K., … McDonald, T. J. (2018). Comparing residential contamination in a Houston environmental justice neighborhood before and after Hurricane Harvey. PLoS ONE, 13(2). https://doi.org/10.1371/journal.pone.0192660 Nagy, G., Chouinard, C. D., Attah, I. K., Webb, I. K., Garimella, S. V. B., Ibrahim, Y. M., … Smith, R. D. (2018). Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations. Electrophoresis, 39(24), 3148–3155. https://doi.org/10.1002/elps.201800294 Barran, P., & Baker, E. (2018). Editorial overview: Omics. Current Opinion in Chemical Biology, 42, A1–A2. https://doi.org/10.1016/j.cbpa.2018.02.007 Kyle, J. E., Aly, N., Zheng, X., Burnum-Johnson, K. E., Smith, R. D., & Baker, E. S. (2018). Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry. Bioanalysis, 10(5), 279–289. https://doi.org/10.4155/bio-2017-0245 Baker, E. S., & Ogorzalek Loo, R. (2018). Guest editor's personal foreward. International Journal of Mass Spectrometry, 427, 1–3. https://doi.org/10.1016/j.ijms.2018.03.002 Orwoll, E. S., Wiedrick, J., Jacobs, J., Baker, E. S., Piehowski, P., Petyuk, V., … Lapidus, J. (2018). High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men. Aging Cell, 17(2). https://doi.org/10.1111/acel.12717 Chouinard, C. D., Nagy, G., Webb, I. K., Shi, T., Baker, E. S., Prost, S. A., … Smith, R. D. (2018). Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry. Analytical Chemistry, 90(18), 10889–10896. https://doi.org/10.1021/acs.analchem.8b02397 Dautel, S., Khan, N., Brandvold, K. R., Brislawn, C. J., Hutchison, J., Weitz, K. K., … Bernstein, H. C. (2018). Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism. https://doi.org/10.1101/296020 Poad, B. L. J., Zheng, X., Mitchell, T. W., Smith, R. D., Baker, E. S., & Blanksby, S. J. (2018). Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses. Analytical Chemistry, 90(2), 1292–1300. https://doi.org/10.1021/acs.analchem.7b04091 Chouinard, C. D., Nagy, G., Webb, I. K., Garimella, S. V. B., Baker, E. S., Ibrahim, Y. M., & Smith, R. D. (2018). Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations. Analytical Chemistry, 90(18), 11086–11091. https://doi.org/10.1021/acs.analchem.8b02990 Zheng, X., Smith, R. D., & Baker, E. S. (2018). Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches. Current Opinion in Chemical Biology, 42, 111–118. https://doi.org/10.1016/j.cbpa.2017.11.009 Nicora, C. D., Burnum-Johnson, K. E., Nakayasu, E. S., Casey, C. P., White, R. A., Chowdhury, T. R., … Baker, E. S. (2018). The MPLEx protocol for multi-omic analyses of soil samples. Journal of Visualized Experiments, 2018(135). https://doi.org/10.3791/57343 Garabedian, A., Benigni, P., Ramirez, C. E., Baker, E. S., Liu, T., Smith, R. D., & Fernandez-Lima, F. (2018). Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. Journal of the American Society for Mass Spectrometry, 29(5), 817–826. https://doi.org/10.1007/s13361-017-1787-8 Nagy, G., Attah, I. K., Garimella, S. V. B., Tang, K., Ibrahim, Y. M., Baker, E. S., & Smith, R. D. (2018). Unraveling the isomeric heterogeneity of glycans: Ion mobility separations in structures for lossless ion manipulations. Chemical Communications, 54(83), 11701–11704. https://doi.org/10.1039/c8cc06966b MacLean, B. X., Pratt, B. S., Egertson, J. D., MacCoss, M. J., Smith, R. D., & Baker, E. S. (2018). Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. Journal of the American Society for Mass Spectrometry, 29(11), 2182–2188. https://doi.org/10.1007/s13361-018-2028-5 Zheng, X., Dupuis, K. T., Aly, N. A., Zhou, Y., Smith, F. B., Tang, K., … Baker, E. S. (2018). Utilizing Ion Mobility Spectrometry and Mass Spectrometry for the Analysis of Polycyclic Aromatic Hydrocarbons, Polychlorinated Biphenyls, Polybrominated Diphenyl Ethers and Their Metabolites. Analytica Chimica Acta, 1037, 265–273. https://doi.org/10.1016/j.aca.2018.02.054 Zheng, X., Aly, N. A., Zhou, Y., Dupuis, K. T., Bilbao, A., Paurus, V. L., … Baker, E. S. (2017). A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. Chemical Science, 8(11), 7724–7736. https://doi.org/10.1039/c7sc03464d Stow, S. M., Causon, T. J., Zheng, X., Kurulugama, R. T., Mairinger, T., May, J. C., … Fjeldsted, J. C. (2017). An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements. Analytical Chemistry, 89(17), 9048–9055. https://doi.org/10.1021/acs.analchem.7b01729 Burnum-Johnson, K. E., Baker, E. S., & Metz, T. O. (2017). Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging. Placenta, 60, S67–S72. https://doi.org/10.1016/j.placenta.2017.03.016 Kyle, J. E., Casey, C. P., Stratton, K. G., Zink, E. M., Kim, Y.-M., Zheng, X., … Baker, E. S. (2017). Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies. Rapid Communications in Mass Spectrometry, 31(5), 447–456. https://doi.org/10.1002/rcm.7808 Deng, L., Garimella, S. V. B., Hamid, A. M., Webb, I. K., Attah, I. K., Norheim, R. V., … Smith, R. D. (2017). 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). Analytical Chemistry, 89(12), 6432–6439. https://doi.org/10.1021/acs.analchem.7b00189 Heyman, H. M., Zhang, X., Tang, K., Baker, E. S., & Metz, T. O. (2017). Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications. In Encyclopedia of Spectroscopy and Spectrometry (pp. 376–384). https://doi.org/10.1016/B978-0-12-409547-2.12132-8 Zheng, X., Wojcik, R., Zhang, X., Ibrahim, Y. M., Burnum-Johnson, K. E., Orton, D. J., … Baker, E. S. (2017). Coupling front-end separations, ion mobility spectrometry, and mass spectrometry for enhanced multidimensional biological and environmental analyses. In Annual Review of Analytical Chemistry (Vol. 10, pp. 71–92). https://doi.org/10.1146/annurev-anchem-061516-045212 Zheng, X., Deng, L., Baker, E. S., Ibrahim, Y. M., Petyuk, V. A., & Smith, R. D. (2017). Distinguishing D- and L-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry. Chemical Communications, 53(56), 7913–7916. https://doi.org/10.1039/c7cc03321d Zheng, X., Zhang, X., Schocker, N. S., Renslow, R. S., Orton, D. J., Khamsi, J., … Baker, E. S. (2017). Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses. Analytical and Bioanalytical Chemistry, 409(2), 467–476. https://doi.org/10.1007/s00216-016-9866-4 Nielson, C. M., Wiedrick, J., Shen, J., Jacobs, J., Baker, E. S., Baraff, A., … Orwoll, E. S. (2017). Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics. Journal of Bone and Mineral Research, 32(7), 1559–1567. https://doi.org/10.1002/jbmr.3125 Metz, T. O., Baker, E. S., Schymanski, E. L., Renslow, R. S., Thomas, D. G., Causon, T. J., … Teeguarden, J. G. (2017). Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go? Bioanalysis, 9(1), 81–98. https://doi.org/10.4155/bio-2016-0244 Ligare, M. R., Baker, E. S., Laskin, J., & Johnson, G. E. (2017). Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry. Chemical Communications, 53(53), 7389–7392. https://doi.org/10.1039/c7cc02251d Wojcik, R., Webb, I. K., Deng, L., Garimella, S. V. B., Prost, S. A., Ibrahim, Y. M., … Smith, R. D. (2017). Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations. International Journal of Molecular Sciences, 18(1). https://doi.org/10.3390/ijms18010183 Ibrahim, Y. M., Hamid, A. M., Deng, L., Garimella, S. V. B., Webb, I. K., Baker, E. S., & Smith, R. D. (2017). New frontiers for mass spectrometry based upon structures for lossless ion manipulations. Analyst, 142(7), 1010–1021. https://doi.org/10.1039/c7an00031f Ma, J., Casey, C. P., Zheng, X., Ibrahim, Y. M., Wilkins, C. S., Renslow, R. S., … Metz, T. O. (2017). PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. Bioinformatics (Oxford, England), 33(17), 2715–2722. https://doi.org/10.1093/bioinformatics/btx305 Rosnow, J., Anderson, L. N., Nair, R. N., Baker, E. S., & Wright, A. T. (2017). Profiling microbial lignocellulose degradation and utilization by emergent omics technologies. Critical Reviews in Biotechnology, 37(5), 626–640. https://doi.org/10.1080/07388551.2016.1209158 Deng, L., Webb, I. K., Garimella, S. V. B., Hamid, A. M., Zheng, X., Norheim, R. V., … Smith, R. D. (2017). Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations. Analytical Chemistry, 89(8), 4628–4634. https://doi.org/10.1021/acs.analchem.7b00185 Zheng, X., Renslow, R. S., Makola, M. M., Webb, I. K., Deng, L., Thomas, D. G., … Baker, E. S. (2017). Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry. Journal of Physical Chemistry Letters, 8(7), 1381–1388. https://doi.org/10.1021/acs.jpclett.6b03015 Webb, I. K., Garimella, S. V. B., Norheim, R. V., Baker, E. S., Ibrahim, Y. M., & Smith, R. D. (2016). A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation. Journal of the American Society For Mass Spectrometry, 27(7), 1285–1288. https://doi.org/10.1007/s13361-016-1397-x Jansson, J. K., & Baker, E. S. (2016). A multi-omic future for microbiome studies. Nature Microbiology, 1(5). https://doi.org/10.1038/NMICROBIOL.2016.49 Hamid, A. M., Garimella, S. V. B., Ibrahim, Y. M., Deng, L., Zheng, X., Webb, I. K., … Smith, R. D. (2016). Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations. Analytical Chemistry, 88(18), 8949–8956. https://doi.org/10.1021/acs.analchem.6b01914 Ibrahim, Y. M., Garimella, S. V. B., Prost, S. A., Wojcik, R., Norheim, R. V., Baker, E. S., … Smith, R. D. (2016). Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform. Analytical Chemistry, 88(24), 12152–12160. https://doi.org/10.1021/acs.analchem.6b03027 Deng, L., Ibrahim, Y. M., Garimella, S. V. B., Webb, I. K., Hamid, A. M., Norheim, R. V., … Smith, R. D. (2016). Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations. Analytical Chemistry, 88(20), 10143–10150. https://doi.org/10.1021/acs.analchem.6b02678 Deng, L., Ibrahim, Y. M., Baker, E. S., Aly, N. A., Hamid, A. M., Zhang, X., … Smith, R. D. (2016). Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry. Chemistryselect, 1(10), 2396–2399. https://doi.org/10.1002/slct.201600460 Cong, Y., Katipamula, S., Trader, C. D., Orton, D. J., Geng, T., Baker, E. S., & Kelly, R. T. (2016). Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform. Lab on a Chip, 16(9), 1544–1548. https://doi.org/10.1039/c6lc00183a Chen, T.-C., Ibrahim, Y. M., Webb, I. K., Garimella, S. V. B., Zhang, X., Hamid, A. M., … Smith, R. D. (2016). Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations. Analytical Chemistry, 88(3), 1728–1733. https://doi.org/10.1021/acs.analchem.5b03910 Zhang, X., Romm, M., Zheng, X., Zink, E. M., Kim, Y.-M., Burnum-Johnson, K. E., … Baker, E. S. (2016). SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. Clinical Mass Spectrometry, 2, 1–10. https://doi.org/10.1016/j.clinms.2016.11.002 Burnum-Johnson, K. E., Nie, S., Casey, C. P., Monroe, M. E., Orton, D. J., Ibrahim, Y. M., … Smith, R. D. (2016). Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. Molecular Cellular Proteomics, 15(12), 3694–3705. https://doi.org/10.1074/mcp.M116.061143 Garimella, S. V. B., Ibrahim, Y. M., Tang, K., Webb, I. K., Baker, E. S., Tolmachev, A. V., … Smith, R. D. (2016). Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry. Journal of the American Society For Mass Spectrometry, 27(6), 1128–1135. https://doi.org/10.1007/s13361-016-1371-7 Garimella, S. V. B., Hamid, A. M., Deng, L., Ibrahim, Y. M., Webb, I. K., Baker, E. S., … Smith, R. D. (2016). Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations Using Compression Ratio Ion Mobility Programming. Analytical Chemistry, 88(23), 11877–11885. https://doi.org/10.1021/acs.analchem.6b03660 Liu, R., Cheng, S., Baker, E. S., Smith, R. D., Zeng, X. C., & Gong, B. (2016). Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers. Chemical Communications, 52(19), 3773–3776. https://doi.org/10.1039/c6cc00224b Liu, R., Chen, S., Baker, E. S., Smith, R. D., Zeng, X. C., & Gong, B. (2016). Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers (vol 52, pg 3773, 2016). Chemical Communications, 52(29), 5205. https://doi.org/10.1039/c6cc90142e Khadempour, L., Burnum-Johnson, K. E., Baker, E. S., Nicora, C. D., Webb-Robertson, B.-J. M., White, R. A., III, … Currie, C. R. (2016). The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates. Molecular Ecology, 25(22), 5795–5805. https://doi.org/10.1111/mec.13872 White, R. A., III, Callister, S. J., Moore, R. J., Baker, E. S., & Jansson, J. K. (2016). The past, present and future of microbiome analyses. Nature Protocols, 11(11), 4–8. https://doi.org/10.1038/nprot.2016.148 Deng, L., Ibrahim, Y. M., Hamid, A. M., Garimella, S. V. B., Webb, I. K., Zheng, X., … Smith, R. D. (2016). Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module. Analytical Chemistry, 88(18), 8957–8964. https://doi.org/10.1021/acs.analchem.6b01915 Kyle, J. E., Zhang, X., Weitz, K. K., Monroe, M. E., Ibrahim, Y. M., Moore, R. J., … Baker, E. S. (2016). Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. Analyst, 141(5), 1649–1659. https://doi.org/10.1039/c5an02062j Ibrahim, Y. M., Baker, E. S., Danielson, W. F., Norheim, R. V., Prior, D. C., Anderson, G. A., … Smith, R. D. (2015). Development of a new ion mobility (quadrupole) time-of-flight mass spectrometer. International Journal of Mass Spectrometry, 377(1), 655–662. https://doi.org/10.1016/j.ijms.2014.07.034 Zhang, X., Ibrahim, Y. M., Chen, T.-C., Kyle, J. E., Norheim, R. V., Monroe, M. E., … Baker, E. S. (2015). Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations. Analyst, 140(20), 6955–6963. https://doi.org/10.1039/c5an00897b Baker, E. S., Burnum-Johnson, K. E., Ibrahim, Y. M., Orton, D. J., Monroe, M. E., Kelly, R. T., … Smith, R. D. (2015). Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics, 15(16), 2766–2776. https://doi.org/10.1002/pmic.201500048 Zhang, X., Garimella, S. V. B., Prost, S. A., Webb, I. K., Chen, T.-C., Tang, K., … Smith, R. D. (2015). Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations. Analytical Chemistry, 87(12), 6010–6016. https://doi.org/10.1021/acs.analchem.5b00214 Garimella, S. V. B., Ibrahim, Y. M., Webb, I. K., Ipsen, A. B., Chen, T.-C., Tolmachev, A. V., … Smith, R. D. (2015). Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90° turn and a switch. The Analyst, 140(20), 6845–6852. https://doi.org/10.1039/c5an00844a Wu, C., Liu, T., Baker, E. S., Rodland, K. D., & Smith, R. D. (2015). Mass Spectrometry for Biomarker Development. In V. R. Preedy & V. B. Patel (Eds.), General Methods in Biomarker Research and their Applications (pp. 17–48). New York, NY: Springer. Wu, C., Liu, T., Baker, E. S., Rodland, K. D., & Smith, R. D. (2015). Mass spectrometry for biomarker development. In General Methods in Biomarker Research and their Applications (Vol. 1-2, pp. 17–48). https://doi.org/10.1007/978-94-007-7696-8_21 Cha, J., Burnum-Johnson, K. E., Bartos, A., Li, Y., Baker, E. S., Tilton, S. C., … Dey, S. K. (2015). Muscle Segment Homeobox Genes Direct Embryonic Diapause by Limiting Inflammation in the Uterus. Journal of Biological Chemistry, 290(24), 15337–15349. https://doi.org/10.1074/jbc.M115.655001 Baker, E. S., Burnum-Johnson, K. E., Jacobs, J. M., Diamond, D. L., Brown, R. N., Ibrahim, Y. M., … Smith, R. D. (2014). Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry*. Molecular Cellular Proteomics, 13(4), 1119–1127. https://doi.org/10.1074/mcp.M113.034595 Prost, S. A., Crowell, K. L., Baker, E. S., Ibrahim, Y. M., Clowers, B. H., Monroe, M. E., … Payne, S. H. (2014). Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements. The Journal of the American Society for Mass Spectrometry, 25(12), 2020–2027. https://doi.org/10.1007/s13361-014-0895-y Baker, E. S., Muddiman, D. C., & Loo, J. A. (2014, December). Focus on Advancing High Performance Mass Spectrometry, Honoring Dr. Richard D. Smith, Recipient of the 2013 Award for a Distinguished Contribution in Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol. 25, pp. 1997–1999. https://doi.org/10.1007/s13361-014-1007-8 Ibrahim, Y. M., Garimella, S. V. B., Tolmachev, A. V., Baker, E. S., & Smith, R. D. (2014). Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel Trap. Analytical Chemistry, 86(11), 5295–5299. https://doi.org/10.1021/ac404250z Merkley, E. D., Baker, E. S., Crowell, K. L., Orton, D. J., Taverner, T., Ansong, C., … Adkins, J. N. (2013). Combining heavy isotope labeling, chemical cross-linking, ion mobility spectrometry, and mass spectrometry to study the structure of homomultimeric protein complexes. Abstracts of Papers of the American Chemical Society, 246. Retrieved from http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000329618401034&KeyUID=WOS:000329618401034 Crowell, K. L., Baker, E. S., Payne, S. H., Ibrahim, Y. M., Monroe, M. E., Slysz, G. W., … Smith, R. D. (2013). Increasing confidence of LC-MS identifications by utilizing ion mobility spectrometry. International Journal of Mass Spectrometry, 354, 312–317. https://doi.org/10.1016/j.ijms.2013.06.028 Crowell, K. L., Slysz, G. W., Baker, E. S., LaMarche, B. L., Monroe, M. E., Ibrahim, Y. M., … Smith, R. D. (2013). LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinformatics, 29(21), 2804–2805. https://doi.org/10.1093/bioinformatics/btt465 Merkley, E. D., Baker, E. S., Crowell, K. L., Orton, D. J., Taverner, T., Ansong, C., … Adkins, J. N. (2013). Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking. Journal of the American Society For Mass Spectrometry, 24(3), 444–449. https://doi.org/10.1007/s13361-012-0565-x Venceslau, S. S., Cort, J. R., Baker, E. S., Chu, R. K., Robinson, E. W., Dahl, C., … Pereira, I. A. C. (2013). Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction. Biochemical and Biophysical Research Communications, 441(4), 732–736. https://doi.org/10.1016/j.bbrc.2013.10.116 Hengel, S. M., Floyd, E., Baker, E. S., Zhao, R., Wu, S., & Pasa-Tolic, L. (2012). Evaluation of SDS Depletion Using an Affinity Spin Column and IMS-MS Detection. Proteomics, 12(21), 3138–3142. https://doi.org/10.1002/pmic.201200168 Baker, E. S., Liu, T., Petyuk, V. A., Burnum-Johnson, K. E., Ibrahim, Y. M., Anderson, G. A., & Smith, R. D. (2012). Mass spectrometry for translational proteomics: progress and clinical implications. Genome Medicine, 4(8). https://doi.org/10.1186/gm364 Angel, T. E., Aryal, U. K., Hengel, S. M., Baker, E. S., Kelly, R. T., Robinson, E. W., & Smith, R. D. (2012). Mass spectrometry-based proteomics: existing capabilities and future directions. Chemical Society Reviews, 41(10), 3912–3928. https://doi.org/10.1039/c2cs15331a Burnum, K. E., Hirota, Y., Baker, E. S., Yoshie, M., Ibrahim, Y. M., Monroe, M. E., … Dey, S. K. (2012). Uterine Deletion of Trp53 Compromises Antioxidant Responses in the Mouse Decidua. Endocrinology, 153(9), 4568–4579. https://doi.org/10.1210/en.2012-1335 Belov, M. E., Kurulugama, R., Lopez-Ferrer, D., Ibrahim, Y., & Baker, E. (2011). New Developments in LC-MS and Other Hyphenated Techniques. In Sample Preparation in Biological Mass Spectrometry (pp. 981–1030). https://doi.org/10.1007/978-94-007-0828-0_47 Buchko, G. W., Niemann, G., Baker, E. S., Belov, M. E., Smith, R. D., Heffron, F., … McDermott, J. E. (2010). A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins. Molecular Biosystems, 6(12), 2448–2458. https://doi.org/10.1039/c0mb00097c Baker, E. S., Livesay, E. A., Orton, D. J., Moore, R. J., Danielson, W. F., III, Prior, D. C., … Belov, M. E. (2010). An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies. Journal of Proteome Research, 9(2), 997–1006. https://doi.org/10.1021/pr900888b Ibrahim, Y. M., Prior, D. C., Baker, E. S., Smith, R. D., & Belov, M. E. (2010). Characterization of an ion mobility-multiplexed collision-induced dissociation-tandem time-of-flight mass spectrometry approach. International Journal of Mass Spectrometry, 293(1-3), 34–44. https://doi.org/10.1016/j.ijms.2010.03.009 Belov, M. E., Baker, E. S., Ibrahim, Y. M., Prior, D. C., Danielson, W. F., Kurulugama, R. T., … Smith, R. D. (2010). Ion mobility separations in high throughput proteomics: A novel approach to protein detection and quantitation. Abstracts of Papers of the American Chemical Society, 240. Retrieved from http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000208164705803&KeyUID=WOS:000208164705803 Shah, A. R., Agarwal, K., Baker, E. S., Singhal, M., Mayampurath, A. M., Ibrahim, Y. M., … Smith, R. D. (2010). Machine learning based prediction for peptide drift times in ion mobility spectrometry. Bioinformatics, 26(13), 1601–1607. https://doi.org/10.1093/bioinformatics/btq245 Baker, E. S., Dupuis, N. F., & Bowers, M. T. (2009). Aminoglycoside antibiotics: A-site specific binding to 16S. International Journal of Mass Spectrometry, 283(1-3), 105–111. https://doi.org/10.1016/j.ijms.2009.02.010 Page, J. S., Marginean, I., Baker, E. S., Kelly, R. T., Tang, K., & Smith, R. D. (2009). Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet. Journal of the American Society For Mass Spectrometry, 20(12), 2265–2272. https://doi.org/10.1016/j.jasms.2009.08.018 Baker, E. S., Dupuis, N. F., & Bowers, M. T. (2009). DNA Hairpin, Pseudoknot, and Cruciform Stability in a Solvent-Free Environment. Journal of Physical Chemistry B, 113(6), 1722–1727. https://doi.org/10.1021/jp807529m Smargiasso, N., Rosu, F., Hsia, W., Colson, P., Baker, E. S., Bowers, M. T., … Gabelica, V. (2008). G-quadruplex DNA assemblies: Loop length, cation identity, and multimer formation. Journal of the American Chemical Society, 130(31), 10208–10216. https://doi.org/10.1021/ja801535e Metz, T. O., Page, J. S., Baker, E. S., Tang, K., Ding, J., Shen, Y., & Smith, R. D. (2008). High-resolution separations and improved ion production and transmission in metabolomics. Trac-Trends in Analytical Chemistry, 27(3), 205–214. https://doi.org/10.1016/j.trac.2007.11.003 Baker, E. S., Tang, K., Danielson, W. F., III, Prior, D. C., & Smith, R. D. (2008). 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Duplex formation and the onset of helicity in oligonucleotides. Abstracts of Papers of the American Chemical Society, 227, U258. Retrieved from http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000223655701333&KeyUID=WOS:000223655701333 Gidden, J., Ferzoco, A., Baker, E. S., & Bowers, M. T. (2004). Duplex formation and the onset of helicity in poly d(CG)(n) oligonucleotides in a solvent-free environment. Journal of the American Chemical Society, 126(46), 15132–15140. https://doi.org/10.1021/ja046433+ Baker, E. S., Gidden, J., Anderson, S. E., Haddad, T. S., & Bowers, M. T. (2004). Isomeric structural characterization of polyhedral oligomeric silsesquioxanes (POSS) with styryl and epoxy phenyl capping agents. Nano Letters, 4(5), 779–785. https://doi.org/10.1021/nl049957g Jackson, A. T., Scrivens, J. H., Williams, J. P., Baker, E. S., Gidden, J., & Bowers, M. T. (2004). Microstructural and Conformational Studies of Polyether Copolymers. The International Journal of Mass Spectrometry, 238(3), 287–297. https://doi.org/10.1016/j.ijms.2004.09.025 Baker, E. S., Gidden, J., Simonsick, W. J., Grady, M. C., & Bowers, M. T. (2004). Sequence Dependent Conformations of Glycidyl Methacrylate/Butyl Methacrylate Copolymers in the Gas Phase. The International Journal of Mass Spectrometry, 238(3), 279–286. https://doi.org/10.1016/j.ijms.2004.04.020 Baker, E. S., Gidden, J., Ferzoco, A., & Bowers, M. T. (2004). Sodium stabilization of dinucleotide multiplexes in the gas phase. Physical Chemistry Chemical Physics, 6(10), 2786–2795. https://doi.org/10.1039/b315727j Wyttenbach, T., Baker, E. S., Bernstein, S. L., Ferzoco, A., Gidden, J., Liu, D. F., & Bowers, M. T. (2004). The ion mobility mass spectrometry method and its application to duplex formation of oligonucleotides and aggregation of proteins. In Advances in Mass Spectrometry, Vol 16 (Vol. 16, pp. 189–200). 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