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Project Publications: North Carolina State University: Core of Advanced Platform Technologies Used for Remediation and Exploration (CAPTURE)

Superfund Research Program

Core of Advanced Platform Technologies Used for Remediation and Exploration (CAPTURE)

Co-Investigator: Erin S. Baker (University of North Carolina-Chapel Hill)
Grant Number: P42ES031009
Funding Period: 2020-2025
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

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  • 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


  • 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. 2023. PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements. Nat Commun 14(1):doi:10.1038/s41467-023-37031-9
  • 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
  • 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


  • 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
  • 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
  • Enders J, Weed RA, Griffith EH, Muddiman DC. 2022. Development and validation of a high resolving power absolute quantitative per- and polyfluoroalkyl substances method incorporating Skyline data processing. Rapid Commun Mass Spectrom 36:e9295. doi:10.1002/rcm.9295 PMID:35275435
  • 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
  • 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
  • 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


  • 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
  • Enders J, O' Neill G, Whitten JL, Muddiman DC. 2021. Understanding the electrospray ionization response factors of per- and poly-fluoroalkyl substances (PFAS). Anal Bioanal Chem doi:10.1007/s00216-021-03545-8 PMID:34291300
  • 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
  • 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


  • 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, 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
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