Erin Marie Baker

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut

Foley, M. H., Walker, M. E., Stewart, A. K., O'Flaherty, S., Gentry, E. C., Patel, S., … Theriot, C. M. (2023, March 13). NATURE MICROBIOLOGY, Vol. 3.

A High-Throughput Ion Mobility Spectrometry-Mass Spectrometry Screening Method for Opioid Profiling

Butler, K. E., & Baker, E. S. (2022, September 22). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol. 9.

A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows

JOURNAL OF PROTEOME RESEARCH, 21(3), 798–807.

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.

Assessing the Fate of Dissolved Organic Compounds in Landfill Leachate and Wastewater Treatment Systems

Doyle, M. G., Odenkirk, M. T., Stewart, A. K., Nelson, J. P., Baker, E. S., & Cruz, F. (2022, November 1). ACS ES&T WATER, Vol. 11.

CCS Predictor 2.0: An Open-Source Jupyter Notebook Tool for Filtering Out False Positives in Metabolomics

Rainey, M. A., Watson, C. A., Asef, C. K., Foster, M. R., Baker, E. S., & Fernandez, F. M. (2022, December 6). ANALYTICAL CHEMISTRY, Vol. 12.

Characterization of compositional variability in petroleum substances

FUEL, 317.

Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses

Dodds, J. N., Wang, L., Patti, G. J., & Baker, E. S. (2022, January 28). ANALYTICAL CHEMISTRY, Vol. 1.

Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 144(16), 7048–7053.

Empowering women and addressing underrepresentation in the field of mass spectrometry

Rampler, E., Baker, E. S., Kirkwood, K. I., Schwaiger-Haber, M., Tam, M., Jones, M. A., & Sherman, M. (2022, February 16). EXPERT REVIEW OF PROTEOMICS, Vol. 2.

Evaluation of Metabolism of a Defined Pesticide Mixture through Multiple In Vitro Liver Models

TOXICS, 10(10).

High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening

ANALYTICAL CHEMISTRY, 94(16), 6191–6199.

Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters

Witchey, S. K., Doyle, M. G., Fredenburg, J. D., St Armour, G., Horman, B., Odenkirk, M. T., … Patisaul, H. B. (2022, September 8). NEUROENDOCRINOLOGY, Vol. 9.

Introducing the Lipidomics Minimal Reporting Checklist

McDonald, J. G., Ejsing, C. S., Kopczynski, D., Holcapek, M., Aoki, J., Arita, M., … Ekroos, K. (2022, August 8). NATURE METABOLISM, Vol. 8.

Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry

Kostelic, M. M., Ryan, J. P., Brown, L. S., Jackson, T. W., Hsieh, C.-C., Zak, C. K., … Marty, M. T. (2022, August 18). ANALYTICAL CHEMISTRY, Vol. 8.

Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 33(6), 1031–1037.

Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight

MARINE POLLUTION BULLETIN, 185.

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.

Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS)

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 56(6), 3441–3451.

Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions

Kirkwood, K. I., Pratt, B. S., Shulman, N., Tamura, K., MacCoss, M. J., MacLean, B. X., & Baker, E. S. (2022, July 13). NATURE PROTOCOLS, Vol. 7.

A Comparative Analysis of Analytical Techniques for Rapid Oil Spill Identification

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 40(4), 1034–1049.

Data Processing Workflow to Identify Structurally Related Compounds in Petroleum Substances Using Ion Mobility Spectrometry-Mass Spectrometry

ENERGY & FUELS, 35(13), 10529–10539.

Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity

Kirkwood, K. I., Christopher, M. W., Burgess, J. L., Littau, S. R., Foster, K., Richey, K., … Baker, E. S. (2021, December 7). JOURNAL OF PROTEOME RESEARCH, Vol. 12.

From Pesticides to Per- and Polyfluoroalkyl Substances: An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics

[Review of ]. ANALYTICAL CHEMISTRY, 93(1), 641–656.

From Plants to Ants: Fungal Modification of Leaf Lipids for Nutrition and Communication in the Leaf-Cutter Ant Fungal Garden Ecosystem

MSYSTEMS, 6(2).

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions

BIOMOLECULES, 11(1).

Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry-Mass Spectrometry

ANALYTICAL CHEMISTRY, 93(51), 17094–17102.

In situ imaging reveals disparity between prostaglandin localization and abundance of prostaglandin synthases

COMMUNICATIONS BIOLOGY, 4(1).

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.

Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments

ANALYTICAL CHEMISTRY, 93(22), 7763–7773.

Per- and polyfluoroalkyl substances (PFAS)-contaminants of emerging concern

Baker, E. S., & Knappe, D. R. U. (2021, December 2). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 12.

Recommendations for good practice in MS-based lipidomics

[Review of ]. JOURNAL OF LIPID RESEARCH, 62.

Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes

FOOD AND CHEMICAL TOXICOLOGY, 149.

Spatial Distribution of Polycyclic Aromatic Hydrocarbon Contaminants after Hurricane Harvey in a Houston Neighborhood.

Journal of Health & Pollution.

Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase

FRONTIERS IN CHEMISTRY, 9.

Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites

Aly, N. A., Dodds, J. N., Luo, Y.-S., Grimm, F. A., Foster, M. K., Rusyn, I., & Baker, E. S. (2021, October 20). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 10.

Utilizing liquid chromatography, ion mobility spectrometry, and mass spectrometry to assess INLIGHT (TM) derivatized N-linked glycans in biological samples

Butler, K. E., Kalmar, J. G., Muddiman, D. C., & Baker, E. S. (2021, August 4). ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 8.

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.

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.

Metabolite collision cross section prediction without energy-minimized structures

The Analyst, 145(16), 5414–5418.

Proteomic assessment of serum biomarkers of longevity in older men

AGING CELL, 19(11).

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.

Rapid Characterization of Per- and Polyfluoroalkyl Substances (PFAS) by Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)

Analytical Chemistry, 92(6), 4427–4435.

Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

ANALYST, 145(22), 7197–7209.

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.

Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools

MOLECULAR OMICS, 16(6).

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.

Challenges in Identifying the Dark Molecules of Life

ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 12, Vol. 12, pp. 177–199.

Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry

ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 411(19), 4673–4682.

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.

Ion Mobility Spectrometry: Fundamental Concepts, Instrumentation, Applications, and the Road Ahead

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 30(11), 2185–2195.

Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses

In Comprehensive Analytical Chemistry (Vol. 83, pp. 123–159).

Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples

[Review of ]. TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 116, 292–299.

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.

Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS

ANALYTICAL CHEMISTRY, 91(8), 5191–5199.

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.

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.

Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis

Tuberculosis, 112, 52–61.

Cell type-resolved human lung lipidome reveals cellular cooperation in lung function

Scientific Reports, 8(1).

Comparing residential contamination in a Houston environmental justice neighborhood before and after Hurricane Harvey

PLoS ONE, 13(2).

Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations

Electrophoresis, 39(24), 3148–3155.

Editorial overview: Omics

Current Opinion in Chemical Biology, 42, A1–A2.

Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry

Bioanalysis, 10(5), 279–289.

Guest editor's personal foreward

International Journal of Mass Spectrometry, 427, 1–3.

High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men

Aging Cell, 17(2).

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.

Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism

Online Ozonolysis Combined with Ion Mobility-Mass Spectrometry Provides a New Platform for Lipid Isomer Analyses

Analytical Chemistry, 90(2), 1292–1300.

Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations

Analytical Chemistry, 90(18), 11086–11091.

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.

The MPLEx protocol for multi-omic analyses of soil samples

Journal of Visualized Experiments, 2018(135).

Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS

Journal of the American Society for Mass Spectrometry, 29(5), 817–826.

Unraveling the isomeric heterogeneity of glycans: Ion mobility separations in structures for lossless ion manipulations

Chemical Communications, 54(83), 11701–11704.

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.

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.

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.

An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements

Analytical Chemistry, 89(17), 9048–9055.

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.

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.

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.

Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications

In Encyclopedia of Spectroscopy and Spectrometry (pp. 376–384).

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).

Distinguishing D- and L-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry

Chemical Communications, 53(56), 7913–7916.

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.

Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics

Journal of Bone and Mineral Research, 32(7), 1559–1567.

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.

Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

Chemical Communications, 53(53), 7389–7392.

Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations

International Journal of Molecular Sciences, 18(1).

New frontiers for mass spectrometry based upon structures for lossless ion manipulations

Analyst, 142(7), 1010–1021.

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.

Profiling microbial lignocellulose degradation and utilization by emergent omics technologies

Critical Reviews in Biotechnology, 37(5), 626–640.

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.

Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry

Journal of Physical Chemistry Letters, 8(7), 1381–1388.

A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation

Journal of the American Society For Mass Spectrometry, 27(7), 1285–1288.

A multi-omic future for microbiome studies

Nature Microbiology, 1(5).

Achieving High Resolution Ion Mobility Separations Using Traveling Waves in Compact Multiturn Structures for Lossless Ion Manipulations

Analytical Chemistry, 88(18), 8949–8956.

Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform

Analytical Chemistry, 88(24), 12152–12160.

Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations

Analytical Chemistry, 88(20), 10143–10150.

Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry

Chemistryselect, 1(10), 2396–2399.

Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform

Lab on a Chip, 16(9), 1544–1548.

Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations

Analytical Chemistry, 88(3), 1728–1733.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

Clinical Mass Spectrometry, 2, 1–10.

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry

Molecular &Amp; Cellular Proteomics, 15(12), 3694–3705.

Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry

Journal of the American Society For Mass Spectrometry, 27(6), 1128–1135.

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.

Surprising impact of remote groups on the folding-unfolding and dimer-chain equilibria of bifunctional H-bonding unimers

Chemical Communications, 52(19), 3773–3776.

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.

The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates

Molecular Ecology, 25(22), 5795–5805.

The past, present and future of microbiome analyses

Nature Protocols, 11(11), 4–8.

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.

Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry

Analyst, 141(5), 1649–1659.