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National Institute of Environmental Health Sciences

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Your Environment. Your Health.

Person Details: Erin S. Baker

Superfund Research Program

Erin S. Baker

University of North Carolina-Chapel Hill
131 South Road, CB#3290
Caudill Laboratory, 017
Chapel Hill, North Carolina 27514
Phone: 919-445-1189
Email: erinmsb@unc.edu

Projects

Publications

2024

  • Gentry E, Collins S, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu H, Zuffa S, Yan T, Avila-Pacheco J, Plichta D, Aron A, Wang M, Jarmusch A, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish C, Xavier R, Chu H, Baker ES, Patterson A, Knight R, Siegel D, Dorrestein PC. 2024. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626(7998):419-426. doi:10.1038/s41586-023-06906-8 PMID:38052229
  • Odenkirk MT, Zheng X, Kyle JE, Stratton KG, Nicora CD, Bloodsworth KJ, Mclean C, Masters C, Monroe ME, Doecke J, Smith RD, Burnum-Johnson KE, Roberts BR, Baker ES. 2024. Deciphering ApoE genotype-driven proteomic and lipidomic alterations in Alzheimer's disease across distinct brain regions. J Proteome Res doi:10.1021/acs.jproteome.3c00604 PMID:38236019

2023

  • Baker ES. 2023. Assessing how chemical exposures affect human health. LC GC Eur 36:7-10. PMID:37900911 PMCID:PMC10611144
  • Baker ES, Hoang C, Uritboonthai W, Heyman HM, Pratt BS, MacCoss MJ, MacLean BX, Plumb R, Aisporna A, Siuzdak G. 2023. METLIN-CCS: an ion mobility spectrometry collision cross section database. Nat Methods doi:10.1038/s41592-023-02078-5 PMID:37932399
  • Chappel JR, King ME, Fleming J, Eberlin LS, Reif DM, Baker ES. 2023. Aggregated molecular phenotype scores: Enhancing assessment and visualization of mass spectrometry imaging data for tissue-based diagnostics. Anal Chem 95(34):12913-12922. doi:10.1021/acs.analchem.3c02389 PMID:37579019
  • Chappel JR, Kirkwood-Donelson KI, Reif DM, Baker ES. 2023. From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome. Anal Bioanal Chem doi:10.1007/s00216-023-04991-2 PMID:37875675
  • Cordova AC, Klaren WD, Ford L, Grimm FA, Baker ES, Zhou Y, Wright FA, Rusyn I. 2023. Integrative chemical-biological grouping of complex high production volume substances from lower olefin manufacturing streams. Toxics 11(7):586. doi:10.3390/toxics11070586 PMID:37505552 PMCID:PMC10385386
  • Foley MH, Walker ME, Stewart AK, O'Flaherty S, Gentry E, Patel S, Beaty VV, Allen G, Pan M, Simpson JB, Perkins C, Vanhoy ME, Dougherty MK, McGill SK, Gulati AS, Dorrestein PC, Baker ES, Redinbo MR, Barrangou R, Theriot CM. 2023. Bile salt hydrolases shape the bile acid landscape and restrict clostridioides difficile growth in the murine gut. Nat Microbiol doi:10.1038/s41564-023-01337-7 PMID:36914755 PMCID:PMC10066039
  • Kirkwood-Donelson KI, Dodds J, Schnetzer A, Hall N, Baker ES. 2023. Uncovering per- and polyfluoroalkyl substances (PFAS) with nontargeted ion mobility spectrometry-mass spectrometry analyses. Sci Adv 9(43):eadj7048. doi:10.1126/sciadv.adj7048 PMID:37878714 PMCID:PMC10599621
  • Stewart AK, Foley MH, Dougherty MK, McGill SK, Gulati AS, Gentry E, Hagey LR, Dorrestein PC, Theriot CM, Dodds J, Baker ES. 2023. Using multidimensional separations to distinguish isomeric amino acid-bile acid conjugates and assess their presence and perturbations in model systems. Anal Chem 95(41):15357-15366. doi:10.1021/acs.analchem.3c03057 PMID:37796494

2022

  • Bilbao A, Gibbons BC, Stow SM, Kyle AD, Bloodsworth KJ, Payne SH, Smith RD, Ibrahim YM, Baker ES, Fjeldsted JC. 2022. A preprocessing tool for enhanced ion mobility-mass spectrometry-based omics workflows. J Proteome Res 21:798-807. doi:10.1021/acs.jproteome.1c00425 PMID:34382401 PMCID:PMC8837709
  • Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz KK, Burnet MC, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim Y, Apffel A, Magnuson JK, Burnum-Johnson KE. 2022. PeakDecoder: A machine learning-based identification algorithm for multidimensional mass spectrometry measurements and its application for synthetic biology. Nat Commun
  • Butler KE, Baker ES. 2022. A high-throughput ion mobility spectrometry-mass spectrometry screening method for opioid profiling. J Am Soc Mass Spectrom 33(10):1904-1913. doi:10.1021/jasms.2c00186 PMID:36136315
  • Butler KE, Dodds J, Flick T, Campuzano ID, Baker ES. 2022. High-resolution demultiplexing (HRdm) ion mobility spectrometry-mass spectrometry for aspartic and isoaspartic acid determination and screening. Anal Chem doi:10.1021/acs.analchem.1c05533 PMID:35421308
  • Dodds J, Wang L, Patti GJ, Baker ES. 2022. Combining isotopologue workflows and simultaneous multidimensional separations to detect, identify, and validate metabolites in untargeted analyses. Anal Chem doi:10.1021/acs.analchem.1c04430 PMID:35089687 PMCID:PMC8934380
  • Doyle MG, Odenkirk MT, Stewart AK, Nelson JP, Baker ES, De La Cruz F. 2022. Assessing the fate of dissolved organic compounds in landfill leachate and wastewater treatment systems. ACS ES&T Wat doi:10.1021/acsestwater.2c00320
  • Foster MR, Rainey M, Watson C, Dodds J, Kirkwood KI, Fernandez FM, Baker ES. 2022. Uncovering PFAS and other xenobiotics in the dark metabolome using ion mobility spectrometry, mass defect analysis, and machine learning. Environ Sci Technol 56:doi:10.1021/acs.est.2c00201 PMID:35653285 PMCID:PMC9474714
  • Gentry E, Collins S, Panitchpakdi M, Belda-Ferre P, Stewart AK, Wang M, Jarmusch A, Avila-Pacheco J, Plichta D, Aron A, Vlamakis H, Ananthakrishnan AN, Clish C, Xavier R, Baker ES, Patterson A, Knight R, Siegel D. 2022. Synthesis-based reverse metabolomics approach for the discovery of chemical structures from humans and animals. Nature PMID:38052229
  • Kirkwood KI, Dodds J, Baker ES. 2022. An investigation into the presence and migration of perfluoroalkyl substances in nonstick cookware advertised as PFAS-free. Environ Sci Technol
  • Kirkwood KI, Fleming J, Nguyen H, Reif DM, Baker ES, Belcher SM. 2022. Utilizing pine needles to temporally and spatially profile per- and polyfluoroalkyl substances (PFAS). Environ Sci Technol 56:3441-3451. doi:10.1021/acs.est.1c06483 PMID:35175744
  • Kirkwood KI, Pratt BS, Shulman N, Tamura K, MacCoss MJ, MacLean BX, Baker ES. 2022. Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions. Nat Protoc doi:10.1038/s41596-022-00714-6 PMID:35831612
  • Odenkirk MT, Horman BM, Dodds J, Patisaul HB, Baker ES. 2022. Combining micropunch histology and multidimensional lipidomic measurements for in-depth tissue mapping. ACS Meas Sci Au 2(1):67-75. doi:10.1021/acsmeasuresciau.1c00035 PMID:35647605 PMCID:PMC9139744
  • Rainey M, Watson C, Asef CK, Foster MR, Baker ES, Fernandez FM. 2022. CCS predictor 2.0: an open-source Jupyter notebook tool for filtering out false positives in metabolomics. Anal Chem 94(50):17456-17466. doi:10.1021/acs.analchem.2c03491 PMID:36473057 PMCID:PMC9772062
  • Roman-Hubers AT, Aeppli C, Dodds J, Baker ES, McFarlin KM, Letinski DJ, Zhao L, Mitchell DA, Parkerton TF, Prince RC, Nedwed T, Rusyn I. 2022. Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight. Mar Pollut Bull 185:114360. doi:10.1016/j.marpolbul.2022.114360 PMID:36413931
  • Roman-Hubers AT, Cordova AC, Rohde A, Chiu WA, McDonald TJ, Wright FA, Dodds J, Baker ES, Rusyn I. 2022. Characterization of compositional variability in petroleum substances. Fuel 317:doi:10.1016/j.fuel.2022.123547 PMID:35250041 PMCID:PMC8896784
  • Valdiviezo A, Kato Y, Baker ES, Chiu WA, Rusyn I. 2022. Evaluation of metabolism of a defined pesticide mixture through multiple in vitro liver models. Toxics 10(10):566. doi:10.3390/toxics10100566 PMID:36287846 PMCID:PMC9609317
  • Witchey SK, Doyle MG, Fredenburg JD, Armour GS, Horman BM, Odenkirk MT, Aylor DL, Baker ES, Patisaul HB. 2022. Impacts of gestational FireMaster 550 (FM 550) exposure on the neonatal cortex are sex specific and largely attributable to the organophosphate esters. Neuroendocrinology doi:10.1159/000526959 PMID:36075192

2021

  • Aly NA, Dodds J, Luo Y, Grimm FA, Foster MR, Rusyn I, Baker ES. 2021. Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites. Anal Bioanal Chem 414(3):doi:10.1007/s00216-021-03686-w PMID:34668045 (ahead of print)
  • Butler KE, Takinami Y, Rainczuk A, Baker ES, Roberts BR. 2021. Utilizing ion mobility-mass spectrometry to investigate the unfolding pathway of Cu/Zn superoxide dismutase. Front Chem 9:614595. doi:10.3389/fchem.2021.614595 PMID:33634076 PMCID:PMC7900566
  • Dodds J, Alexander NL, Kirkwood KI, Foster MR, Hopkins ZR, Knappe D, Baker ES. 2021. From Pesticides to Per- and Polyfluoroalkyl Substances: An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics. Anal Chem 93:641-656. doi:10.1021/acs.analchem.0c04359 PMID:33136371
  • Dodds J, Baker ES. 2021. Improving the speed and selectivity of newborn screening using ion mobility spectrometry-mass spectrometry. Anal Chem 93:17094-17102. doi:10.1021/acs.analchem.1c04267 PMID:34851605 PMCID:PMC8730783
  • Khadempour L, Kyle JE, Webb-Robertson B, Nicora CD, Smith FB, Smith RD, Lipton MS, Currie CR, Baker ES, Burnum-Johnson KE. 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):e013070-20. doi:10.1128/mSystems.01307-20 PMID:33758033 PMCID:PMC8547007
  • Kirkwood KI, Christopher MW, Burgess JL, Littau S, Foster K, Richey K, Pratt BS, Shulman N, Tamura K, MacCoss MJ, MacLean BX, Baker ES. 2021. Development and application of multidimensional lipid libraries to investigate lipidomic dysregulation related to smoke inhalation injury severity. J Proteome Res doi:10.1021/acs.jproteome.1c00820 PMID:34874736 PMCID:PMC8741653
  • Kofeler HC, Ahrends R, Baker ES, Ekroos K, Han X, Hoffmann N, Holcapek M, Wenk MR, Liebisch G. 2021. Recommendations for good practice in MS-based lipidomics. J Lipid Res 62:doi:10.1016/j.jlr.2021.100138 PMID:34662536 PMCID:PMC8585648
  • Luo Y, Chen Z, Blanchette A, Zhou Y, Wright FA, Baker ES, Chiu WA, Rusyn I. 2021. Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-derived cardiomyocytes. Food Chem Toxicol doi:10.1016/j.fct.2021.111979 PMID:33450301
  • Odenkirk MT, Reif DM, Baker ES. 2021. Multiomic big data analysis challenges: Increasing confidence in the interpretation of artificial intelligence assessments. Anal Chem 93(22):7763-7773. doi:10.1021/acs.analchem.0c04850 PMID:34029068
  • Roman-Hubers AT, Cordova AC, Aly NA, McDonald TJ, Lloyd D, Wright FA, Baker ES, Chiu WA, Rusyn I. 2021. Data processing workflow to identify structurally related compounds in petroleum substances using ion mobility spectrometry-mass spectrometry. Energy Fuels 35:10529-10539. doi:10.1021/acs.energyfuels.1c00892 PMID:34366560 PMCID:PMC8341389
  • Roman-Hubers AT, McDonald TJ, Baker ES, Chiu WA, Rusyn I. 2021. A comparative analysis of analytical techniques for rapid oil spill identification. Environ Toxicol Chem 40(4):1034-1049. doi:10.1002/etc.4961 PMID:33315271 PMCID:PMC8104454
  • Sansom G, Kirsch KR, Casillas GA, Camargo K, Wade TL, Knap A, Baker ES, Horney JA. 2021. Spatial distribution of polycyclic aromatic hydrocarbon contaminants after Hurricane Harvey in a Houston neighborhood. J Health Pollut 11(29):doi:10.5696/2156-9614-11.29.210308 PMID:33815906 PMCID:PMC8009646
  • Valdiviezo A, Aly NA, Luo Y, Cordova AC, Casillas GA, Foster MR, Baker ES, Rusyn I. 2021. 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. J Environ Sci (China) 115:350-362. doi:10.1016/j.jes.2021.08.004 PMID:34969462 PMCID:PMC8724578
  • Zamith-Miranda D, Heyman HM, Burnet MC, Couvillion SP, Zheng X, Munoz N, Nelson WC, Kyle JE, Zink EM, Weitz KK, Bloodsworth KJ, Clair G, Zucker JD, Teuton JR, Payne SH, Kim Y, Gil MR, Baker ES, Bredeweg EL, Nosanchuk JD, Nakayasu ES. 2021. A histoplasma capsulatum lipid metabolic map identifies antifungal targets. MBio 12(6):e0297221. doi:10.1128/mBio.02972-21 PMID:34809453 PMCID:PMC8609360

2020

  • Aly NA, Luo Y, Liu Y, Casillas GA, McDonald TJ, Kaihatu JM, Jun M, Ellis N, Gossett S, Dodds J, Baker ES, Bhandari S, Chiu WA, 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. Environ Pollut 265:115009. doi:10.1016/j.envpol.2020.115009 PMID:32574947 PMCID:PMC7857671
  • Dodds J, Hopkins ZR, Knappe D, Baker ES. 2020. Rapid characterization of per- and polyfluoroalkyl substances (PFAS) by ion mobility spectrometry-mass spectrometry (IMS-MS). Anal Chem 92:4427-4435. doi:10.1021/acs.analchem.9b05364 PMID:32011866 PMCID:PMC7173758
  • Ekelof M, Dodds J, Khodjaniyazova S, Garrard K, Baker ES, Muddiman DC. 2020. Coupling IR-MALDESI with Drift Tube Ion Mobility-Mass Spectrometry for High-Throughput Screening and Imaging Applications. J Am Soc Mass Spectrom 31:doi:10.1021/jasms.9b00081 PMID:31971795 PMCID:PMC7263366
  • Luo Y, Aly NA, McCord JP, Strynar M, Chiu WA, Dodds J, Baker ES, Rusyn I. 2020. Rapid characterization of emerging per- and polyfluoroalkyl substances in aqueous film-forming foams using ion mobility spectrometry-mass spectrometry. Environ Sci Technol 54(23):15024-15034. doi:10.1021/acs.est.0c04798 PMID:33176098 PMCID:PMC7719402
  • Odenkirk MT, Stratton KG, Bramer LM, Webb-Robertson B, Bloodsworth KJ, Monroe ME, Burnum-Johnson KE, Baker ES. 2020. From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions. Biomolecules 11(1):40. doi:10.3390/biom11010040 PMID:33396843 PMCID:PMC7824308
  • Odenkirk MT, Stratton KG, Gritsenko MA, Bramer LM, Webb-Robertson B, Bloodsworth KJ, Weitz KK, Lipton AK, Monroe ME, Ash J, Fourches D, Taylor BD, Burnum-Johnson KE, Baker ES. 2020. Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools. Mol Omics 16(6):doi:10.1039/d0mo00074d PMID:32966491 (ahead of print)
  • Odenkirk MT, Zin PK, Ash J, Reif DM, Fourches D, Baker ES. 2020. Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems. Analyst 145:7197-7209. doi:10.1039/d0an01638a PMID:33094747 PMCID:PMC769503
  • Soper-Hopper M, Vandegrift J, Baker ES, Fernandez FM. 2020. Metabolite collision cross section prediction without energy-minimized structures. Analyst 16:doi:10.1039/d0an00198h PMID:32583823 PMCID:PMC7423765

2019

2018

  • Horney JA, Casillas GA, Baker ES, Stone KW, Kirsch KR, Camargo K, Wade TL, McDonald TJ. 2018. Comparing residential contamination in a Houston environmental justice neighborhood before and after Hurricane Harvey. PLoS One 13(2):e0192660. doi:10.1371/journal.pone.0192660 PMID:29420658 PMCID:PMC5805347
  • MacLean BX, Prat BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. 2018. Using skyline to analyze data-containing liquid chromatography, ion mobility spectrometry, and mass spectrometry dimensions. J Am Soc Mass Spectrom 1-7. doi:10.1007/s13361-018-2028-5 PMID:30047074 PMCID:PMC6191345
  • Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White RA, Chowdhury TR, Kyle JE, Kim Y, Smith RD, Metz TO, Jansson J, Baker ES. 2018. The MPLEx protocol for multi-omic analyses of soil samples. J Vis Exp 135:e57343. doi:10.3791/57343 PMID:29912205 PMCID:PMC6101435
  • Orton DJ, Tfaily MM, Moore RJ, LaMarche BL, Zheng X, Fillmore TL, Chu RK, Weitz KK, Monroe ME, Kelly RT, Smith RD, Baker ES. 2018. A customizable flow injection system for automated, high throughput, and time sensitive ion mobility spectrometry and mass spectrometry measurements. Anal Chem 90(1):737-744. doi:10.1021/acs.analchem.7b02986 PMID:29161511 PMCID:PMC5764703
  • Zheng X, Dupuis KT, Aly NA, Zhou Y, Smith FB, Tang K, Smith RD, Baker ES. 2018. Utilizing ion mobility spectrometry and mass spectrometry for the analysis of polycyclic aromatic hydrocarbons, polychlorinated biphenyls, polybrominated diphenyl ethers and their metabolites. Anal Chim Acta 1037:265-273. doi:10.1016/j.aca.2018.02.054 PMID:30292301 PMCID:PMC6223027
  • Zheng X, Smith RD, Baker ES. 2018. Recent advances in lipid separations and structural elucidation using mass spectrometry combined with ion mobility spectrometry, ion-molecule reactions and fragmentation approaches. Curr Opin Chem Biol 42:111-118. doi:10.1016/j.cbpa.2017.11.009 PMID:29223060 PMCID:PMC5828972

2017

  • Zheng X, Aly NA, Zhou Y, Dupuis KT, Bilbao A, Paurus VL, Orton DJ, Wilson R, Payne SH, Smith RD, Baker ES. 2017. A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. Chem Sci 8(11):7724-7736. doi:10.1039/c7sc03464d PMID:29568436 PMCID:PMC5853271
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