Senior Scientist
Senior Scientist


Thomas O. Metz is a principal investigator in the Integrative Omics group within the Biological Sciences Division where his research focuses on development and applications of high throughput metabolomics and lipidomics methods, in conjunction with proteomics, to answer various biological questions. His work has resulted in more than 180 publications to date.

Currently, he is the director of the Pacific Northwest Advanced Compound Identification Core within the NIH Common Fund Metabolomics Program, co-PI of the Proteomics Laboratory for The Environmental Determinants of Diabetes in the Young consortium, Lead of the PNNL m/q Initiative, and an adjunct faculty member in the Department of Biochemistry and Biophysics at Oregon State University.

Disciplines and Skills

  • Experimental study design and incorporation of advanced statistical methods for monitoring the quality of and interpreting mass spectrometry-based ‘omics data
  • Development and application of mass spectrometry-based metabolomics and lipidomics capabilities in studies of biological systems, particularly microbial communities
  • Advancing metabolite and lipid identification through development and application of advanced computational approaches


  • BS in Biology, Frostburg State University
  • BS in Chemistry, San Jose State University
  • PhD in Chemistry, University of South Carolina

Affiliations and Professional Service

  • American Chemical Society
  • American Society for Mass Spectrometry
  • Metabolomics Association of North America
  • Metabolomics Society
  • Adjunct Faculty, Oregon State University
  • President, Metabolomics Association of North America
  • Scientific Organizing Committee, 19th Annual Conference of the Metabolomics Society
  • Co-Lead, MANA Microbiome Interest Group (2020-2022)
  • Observational Safety Monitoring Board (OSMB), Chronic Kidney Diseases of Uncertain Etiology (CKDu) in Agricultural Communities (CURE) Research Consortium Study
  • Scientific Advisory Board, Mass Spectrometry Facility, Oregon State University
  • Local Organizing Committee, 14th Annual Conference of the Metabolomics Society
  • Scientific Organizing Committee, 1st Annual MANA Meeting
  • Board Member, Metabolomics Association of North America (2019-Present)
  • Co-Chair, Metabolomics Working Group, Undiagnosed Diseases Network (2015-2018)
  • Member, Steering Committee, Undiagnosed Diseases Network (2015-2018)
  • Member, Steering Committee, NIH Common Fund Metabolomics Program Phase II (2018 – Present)
  • Chair, Compound Identification Development Cores Sub-Committee, NIH Common Fund Metabolomics Program Phase II (2018 – Present)

Awards and Recognitions

  • 2022    Pathways to Excellence Award, PNNL
  • 2021    Paper of the Year Award, Biological Sciences Division (BSD), PNNL
  • 2019    Paper of the Year Award, BSD, PNNL
  • 2018    Major Proposal Award, PNNL
  • 2017    Paper of the Year Award, BSD, PNNL
  • 2017    Major Proposal Award, PNNL
  • 2017    Nominated for election to Metabolomics Society Board of Directors
  • 2017    Keynote Speaker, Metabolomics in Health and Disease II, 13th Annual Conference of the Metabolomics Society
  • 2016    Patent Award, PNNL
  • 2014    Patent Award, PNNL
  • 2014    Software Creator Award, PNNL
  • 2012    Outstanding Performance Award, Environmental Molecular Sciences Laboratory, PNNL
  • 2010    Selected to Membership Committee of International Maillard Reaction Society
  • 2008    Outstanding Performance Award (2), Fundamental and Computational Sciences Directorate, PNNL
  • 2007    Outstanding Performance Award, Fundamental and Computational Sciences Directorate, PNNL
  • 2006    Outstanding Performance Award, National Security Directorate, PNNL



  • Couvillion SP*, Mostoller KE, Williams JE, Pace RM, Stohel IL, Peterson HK, Nicora CD, Nakayasu ES, Webb-Robertson BM, McGuire MA, McGuire MK, Metz TO*. Interrogating the role of the milk microbiome in mastitis in the multi-omics era. Front Microbiol. 2023, 14:1105675.
  • Nielson FF, Kay B, Young SJ, Colby SM, Renslow RS, Metz TO*. Similarity Downselection: Finding the n Most Dissimilar Molecular Conformers for Reference-Free Metabolomics. Metabolites. 2023, 9;13(1):105.


  • Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project 500 (EMP500) Consortium. Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nat Microbiol. 2022, 7(12):2128-2150.
  • Langley BO, Ryan JJ, Phipps J, Buttolph L, Bray B, Aslan JE, Metz TO, Stevens JF, Bradley R. Xanthohumol microbiome and signature in adults with Crohn's disease (the XMaS trial): a protocol for a phase II triple-masked, placebo-controlled clinical trial. Trials. 2022, 23(1):885.
  • Yesiltepe Y, Govind N, Metz TO, Renslow RS. An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts. J Cheminform. 2022, 14(1):64.
  • RoyChowdhury T, Bramer LM, Brown J, Kim YM, Zink E, Metz TO, McCue LA, Diefenderfer HL, Bailey V. Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland. Microorganisms. 2022, 10(8):1653.
  • Farley SE, Kyle JE, Leier HC, Bramer LM, Weinstein JB, Bates TA, Lee JY, Metz TO, Schultz C, Tafesse FG. A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants. Nat Commun. 2022, 13(1):3487.
  • Kyle JE, Bramer LM, Claborne D, Stratton KG, Bloodsworth KJ, Teeguarden JG, Gaddameedhi S, Metz TO, Van Dongen HPA. Simulated Night-Shift Schedule Disrupts the Plasma Lipidome and Reveals Early Markers of Cardiovascular Disease Risk. Nat Sci Sleep. 2022, 14:981-994.o
  • Wang F, Allen D, Tian S, Oler E, Gautam V, Greiner R, Metz TO, Wishart DS. CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. Nucleic Acids Res. 2022, 50(W1):W165-74.
  • Wishart DS, Tian S, Allen D, Oler E, Peters H, Lui VW, Gautam V, Djoumbou-Feunang Y, Greiner R, Metz TO. BioTransformer 3.0-a web server for accurately predicting metabolic transformation products. Nucleic Acids Res. 2022, 50(W1):W115-W123.
  • Webb-Robertson BM, Nakayasu ES, Frohnert BI, Bramer LM, Akers SM, Norris JM, Vehik K, Ziegler AG, Metz TO, Rich SS, Rewers MJ. Integration of Infant Metabolite, Genetic and Islet Autoimmunity Signatures to Predict Type 1 Diabetes by 6 Years of Age. J Clin Endocrinol Metab. 2022, dgac225.
  • Colby SM, Chang CH, Bade JL, Nunez JR, Blumer MR, Orton DJ, Bloodsworth KJ, Nakayasu ES, Smith RD, Ibrahim YM, Renslow RS*, Metz TO*. DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data. Anal Chem. 2022, 94(16):6130-6138.
  • Sarkar S, Melchior JT, Henry HR, Syed F, Mirmira RG*, Nakayasu ES*, Metz TO*. GDF15: a potential therapeutic target for type 1 diabetes. Expert Opin Ther Targets. 2022, 26(1):57-67.


  • Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL 2nd, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol. 2021, 39(2):169-173.
  • Webb-Robertson BM, Bramer LM, Stanfill BA, Reehl SM, Nakayasu ES, Metz TO, Frohnert BI, Norris JM, Johnson RK, Rich SS, Rewers MJ. Prediction of the development of islet autoantibodies through integration of environmental, genetic, and metabolic markers. J Diabetes. 2021, 13(2):143-153.
  • Blumer MR, Chang CH, Brayfindley E, Nunez JR, Colby SM, Renslow RS*, Metz TO*. Mass Spectrometry Adduct Calculator. J Chem Inf Model. 2021, 61(12):5721-5725.
  • Quinn RA, Hagiwara KA, Liu K, Goudarzi M, Pathmasiri W, Sumner LW, Metz TO. Bridging the Gap between Analytical and Microbial Sciences in Microbiome Research. mSystems. 2021, 6(5):e0058521.
  • Anderson-Baucum E, Piñeros AR, Kulkarni A, Webb-Robertson BJ, Maier B, Anderson RM, Wu W, Tersey SA, Mastracci TL, Casimiro I, Scheuner D, Metz TO, Nakayasu ES, Evans-Molina C, Mirmira RG. Deoxyhypusine synthase promotes a pro-inflammatory macrophage phenotype. Cell Metab. 2021, 33(9):1883-1893.e7.
  • Sims AC, Mitchell HD, Gralinski LE, Kyle JE, Burnum-Johnson KE, Lam M, Fulcher ML, West A, Smith RD, Randell SH, Metz TO, Sheahan TP, Waters KM, Baric RS. Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury. mBio. 2021, 12(4):e0157221.
  • Nakayasu ES*, Gritsenko M, Piehowski PD, Gao Y, Orton DJ, Schepmoes AA, Fillmore TL, Frohnert BI, Rewers M, Krischer JP, Ansong C, Suchy-Dicey AM, Evans-Molina C, Qian WJ, Webb-Robertson BM, Metz TO*. Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat Protoc. 2021, 16(8):3737-3760.
  • Lee JY*, Bilbao A*, Conant CR, Bloodsworth KJ, Orton DJ, Zhou M, Wilson JW, Zheng X, Webb IK, Li A, Hixson KK, Fjeldsted JC, Ibrahim YM, Payne SH, Jansson C, Smith RD, Metz TO*. AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry. Bioinformatics. 2021, btab429.
  • Xu C, Couvillion SP, Sontag RL, Isern NG, Maezato Y, Lindemann SR, Roy Chowdhury T, Zhao R, Morton BR, Chu RK, Moore RJ, Jansson JK, Bailey VL, Mouser PJ, Romine MF, Fredrickson JF, Metz TO*. MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments. mSystems. 2021, 6(3):e0105820.
  • Borges RM, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM Jr, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum chemistry calculations for metabolomics. Chem Rev. 2021, 121(10):5633-5670.
  • Kyle JE, Stratton KG, Zink EM, Kim YM, Bloodsworth KJ, Monroe ME; Undiagnosed Diseases Network, Waters KM, Webb-Robertson BM, Koeller DM*, Metz TO*. A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases. Sci Data. 2021, 8(1):114.
  • Langley BO, Ryan JJ, Hanes D, Phipps J, Stack E, Metz TO, Stevens JF, Bradley R. Xanthohumol Microbiome and Signature in Healthy Adults (the XMaS Trial): Safety and Tolerability Results of a Phase I Triple-Masked, Placebo-Controlled Clinical Trial. Mol Nutr Food Res. 2021, 65(8):e2001170.
  • Nielson FF, Colby SM, Thomas DG, Renslow RS*, Metz TO*. Exploring the Impacts of Conformer Selection Methods on Ion Mobility Collision Cross Section Predictions. Anal Chem. 2021, 93(8):3830-3838.
  • Barklis E, Alfadhli A, Kyle JE, Bramer LM, Bloodsworth KJ, Barklis RL, Leier HC, Petty RM, Zelnik ID, Metz TO, Futerman AH, Tafesse FG. Ceramide synthase 2 deletion decreases the infectivity of HIV-1. J Biol Chem. 2021, 296:100340.
  • Nyavor Y, Brands CR, Nicholson J, Kuther S, Cox KK, May G, Miller C, Yasuda A, Potter F, Cady J, Heyman HM, Metz TO, Stark TD, Hofmann T, Balemba OB. Supernatants of intestinal luminal contents from mice fed high-fat diet impair intestinal motility by injuring enteric neurons and smooth muscle cells. Neurogastroenterol Motil. 2021, 33(1):e13990.


  • Couvillion SP, Agrawal N, Colby SM, Brandvold KR, Metz TO*. Who Is metabolizing what? Discovering novel biomolecules in the microbiome and the organisms who make them. Front Cell Infect Microbiol. 2020, 10:388.
  • Leier HC, Weinstein JB, Kyle JE, Lee JY, Bramer LM, Stratton KG, Kempthorne D, Navratil AR, Tafesse EG, Hornemann T, Messer WB, Dennis EA, Metz TO, Barklis E, Tafesse FG. A global lipid map defines a network essential for Zika virus replication. Nat Comm. 2020, 11(1):3652.
  • McClure RS, Lee JY, Chowdhury TR, Bottos EM, White RA 3rd, Kim YM, Nicora CD, Metz TO, Hofmockel KS, Jansson JK, Song HS. Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. Sci Rep. 2020, 10(1):10882.
  • Blanco-Sanchez B, Clement A, Stednitz SJ, Kyle JE, Peirce JL, McFadden M, Wegner J, Phillips JB, Macnamara E, Huang Y, Adams DR, Toro C, Gahl WA, Malicdan MCV, Tifft CJ, Zink EM, Bloodsworth KJ, Stratton KG, Koeller D, Metz TO, Washbourne P, Westerfield M. yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development. PLoS Gent. 2020, 16(6):e1008841.
  • Colli ML, Ramos-Rodríguez M, Nakayasu ES, Alvelos MI, Lopes M, Hill JLE, Turatsinze JV, Coomans de Brachène A, Russell MA, Raurell-Vila H, Castela A, Juan-Mateu J, Webb-Robertson BM, Krogvold L, Dahl-Jorgensen K, Marselli L, Marchetti P, Richardson SJ, Morgan NG, Metz TO, Pasquali L, Eizirik DL. An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells. Nat Comm., 2020, 11(1):2584.
  • Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Genetic and metabolic links between the murine microbiome and memory. Microbiome, 2020, 8(1):53.
  • Khare S, DeLoid GM, Molina RM, Gokulan K, Couvillion SP, Bloodsworth KJ, Eder EK, Wong AR, Hoyt DW, Bramer LM, Metz TO, Thrall BD, Brain JD, Demokritou P. Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats. NanoImpact, 2020, 18. pii: 100216.
  • Ilhan ZE, DiBaise JK, Dautel SE, Isern NG, Kim YM, Hoyt DW, Schepmoes AA, Brewer HM, Weitz KK, Metz TO, Crowell MD, Kang DW, Rittmann BE, Krajmalnik-Brown R. Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery. NPJ Biofilms Microbiomes, 2020 6(1):12.
  • Nuñez JR, Mcgrady M, Yesiltepe Y, Renslow RS*, Metz TO*. Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets. J Chem Inf Model. 2020, 60(12):6251-6257.
  • Nakayasu ES, Metz TO, Mirmira RG. Probing islet stress in type 1 diabetes. Aging. 2020, 12(19):18795-18796.
  • Bradley R, Langley BO, Ryan JJ, Phipps J, Hanes DA, Stack E, Jansson JK, Metz TO, Stevens JF. Xanthohumol microbiome and signature in healthy adults (the XMaS trial): a phase I triple-masked, placebo-controlled clinical trial. Trials. 2020, 21(1):835
  • Nakayasu ES, Syed F, Tersey SA, Gritsenko MA, Mitchell HD, Chan CY, Dirice E, Turatsinze JV, Cui Y, Kulkarni RN, Eizirik DL, Qian WJ, Webb-Robertson BM, Evans-Molina C, Mirmira RG, Metz TO. Comprehensive Proteomics Analysis of Stressed Human Islets Identifies GDF15 as a Target for Type 1 Diabetes Intervention. Cell Metab. 2020, 31(2):363-374.e6.
  • Nicora CD, Sims AC, Bloodsworth KJ, Kim YM, Moore RJ, Kyle JE, Nakayasu ES, Metz TO. Metabolite, Protein, and Lipid Extraction (MPLEx): A Method that Simultaneously Inactivates Middle East Respiratory Syndrome Coronavirus and Allows Analysis of Multiple Host Cell Components Following Infection. Methods Mol Biol. 2020, 2099:173-194.
  • Webb-Robertson BM, Stratton KG, Kyle JE, Kim YM, Bramer LM, Waters KM, Koeller DM, Metz TO. Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network. Anal Chem. 2020, 92(2):1796-1803.


  • Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends Analyt Chem. 2019, 116:292-299.
  • Fudyma JD, Lyon J, AminiTabrizi R, Gieschen H, Chu RK, Hoyt DW, Kyle JE, Toyoda J, Tolic N, Heyman HM, Hess NJ, Metz TO, Tfaily MM. Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites. Plant Direct. 2019, 3(11):e00179.
  • Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci. 2019, 6:108.
  • Ramos-Rodríguez M, Raurell-Vila H, Colli ML, Alvelos MI, Subirana-Granés M, Juan-Mateu J, Norris R, Turatsinze JV, Nakayasu ES, Webb-Robertson BM, Inshaw JRJ, Marchetti P, Piemonti L, Esteller M, Todd JA, Metz TO, Eizirik DL, Pasquali L. The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes. Nat Genet. 2019, 51(11):1588-1595.
  • Wojcik R, Nagy G, Attah IK, Webb IK, Garimella SVB, Weitz KK, Hollerbach A, Monroe ME, Ligare MR, Nielson FF, Norheim RV, Renslow RS, Metz TO, Ibrahim YM, Smith RD. SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes. Anal Chem. 2019, 91(18):11952-11962.
  • Nuñez JR, Colby SM, Thomas DG, Tfaily MM, Tolic N, Ulrich EM, Sobus JR, Metz TO, Teeguarden JG, Renslow RS. Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. J Chem Inf Model. 2019, 59(9):4052-4060.
  • Stanfill B, Reehl S, Bramer L, Nakayasu ES, Rich SS, Metz TO, Rewers M, Webb-Robertson BJ; TEDDY Study Group. Extending Classification Algorithms to Case-Control Studies. Biomed Eng Comput Biol. 2019, 10:1179597219858954.
  • Evans MV, Getzinger G, Luek JL, Hanson AJ, McLaughlin MC, Blotevogel J, Welch SA, Nicora CD, Purvine SO, Xu C, Cole DR, Darrah TH, Hoyt DW, Metz TO, Lee Ferguson P, Lipton MS, Wilkins MJ, Mouser PJ. In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing. ISME J. 2019, 13(11):2690-2700.
  • Nakayasu ES, Qian WJ, Evans-Molina C, Mirmira RG, Eizirik DL, Metz TO. The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes. Expert Rev Proteomics. 2019, 16(7):569-582.
  • Roy Chowdhury T, Lee JY, Bottos EM, Brislawn CJ, White RA 3rd, Bramer LM, Brown J, Zucker JD, Kim YM, Jumpponen A, Rice CW, Fansler SJ, Metz TO, McCue LA, Callister SJ, Song HS, Jansson JK. Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations. mSystems. 2019, 4(4). pii: e00061-19.
  • Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell. 2019, 177(6):1600-1618.e17.
  • Kyle JE, Burnum-Johnson KE, Wendler JP, Eisfeld AJ, Halfmann PJ, Watanabe T, Sahr F, Smith RD, Kawaoka Y, Waters KM, Metz TO. Plasma lipidome reveals critical illness and recovery from human Ebola virus disease. Proc Natl Acad Sci U S A. 2019, 116(9):3919-3928.
  • Colby SM, Thomas DG, Nuñez JR, Baxter DJ, Glaesemann KR, Brown JM, Pirrung MA, Govind N, Teeguarden JG, Metz TO, Renslow RS. ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries. Anal Chem. 2019, 91(7):4346-4356.
  • Bramer LM, Stratton KG, White AM, Bleeker AH, Kobold MA, Waters KM, Metz TO, Rodland KD, Webb-Robertson BM. P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data. J Proteome Res. 2019, 18(3):1426-1432.
  • Gibbons BC, Fillmore TL, Gao Y, Moore RJ, Liu T, Nakayasu ES, Metz TO, Payne SH. Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards. J Proteome Res. 2019, 18(2):694-699.
  • Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst. 2019, 144(3):794-807.


  • Yesiltepe Y, Nuñez JR, Colby SM, Thomas DG, Borkum MI, Reardon PN, Washton NM, Metz TO, Teeguarden JG, Govind N, Renslow RS. An automated framework for NMR chemical shift calculations of small organic molecules. J Cheminform. 2018, 10(1):52.
  • Splinter K, Adams DR, Bacino CA, Bellen HJ, Bernstein JA, Cheatle-Jarvela AM, Eng CM, Esteves C, Gahl WA, Hamid R, Jacob HJ, Kikani B, Koeller DM, Kohane IS, Lee BH, Loscalzo J, Luo X, McCray AT, Metz TO, Mulvihill JJ, Nelson SF, Palmer CGS, Phillips JA 3rd, Pick L, Postlethwait JH, Reuter C, Shashi V, Sweetser DA, Tifft CJ, Walley NM, Wangler MF, Westerfield M, Wheeler MT, Wise AL, Worthey EA, Yamamoto S, Ashley EA; Undiagnosed Diseases Network. Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. N Engl J Med. 2018 [Epub ahead of print]
  • Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White RA 3rd, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES. The MPLEx Protocol for Multi-omic Analyses of Soil Samples. J Vis Exp. 2018, (135).
  • Stanfill BA, Nakayasu ES, Bramer LM, Thompson AM, Ansong CK, Clauss T, Gritsenko MA, Monroe ME, Moore RJ, Orton DJ, Piehowski PD, Schepmoes AA, Smith RD, Webb-Robertson BJ, Metz TO, TEDDY Study Group. QC-ART: A tool for real-time quality control assessment of mass spectrometry-based proteomics data. Mol Cell Proteomics. 2018, 17(9):1824-1836.
  • Cole JK, Morton BR, Cardamone HC, Lake HRR, Dohnalkova AC, Kim YM, Kyle JE, Maezato Y, Dana KL, Metz TO, Romine MF, Nelson WC, Lindemann SR. Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae. Int J Syst Evol Microbiol. 2018, 68(5):1591-1598.
  • Moghieb A, Clair G, Mitchell H, Kitzmiller JA, Zink EM, Kim YM, Petyuk V, Shukla AK, Moore RJ, Metz TO, Carson JP, McDermott JE, Corley RA, Whitsett JA, Ansong C. Time-resolved Proteome Profiling of Normal Lung Development. Am J Physiol Lung Cell Mol Physiol. 2018, 315(1):L11-L24.
  • Wu J, Sabag-Daigle A, Borton MA, Kop LFM, Szkoda BE, Deatherage Kaiser BL, Lindemann SR, Renslow RS, Wei S, Nicora CD, Weitz KK, Kim YM, Adkins JN, Metz TO, Boyaka P, Gopalan V, Wrighton KC, Wysocki VH, Ahmer BMM. Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut. Infect Immun. 2018, pii: IAI.00945-17.
  • Oláhová M, Yoon WH, Thompson K, Jangam S, Fernandez L, Davidson JM, Kyle JE, Grove ME, Fisk DG, Kohler JN, Holmes M, Dries AM, Huang Y, Zhao C, Contrepois K, Zappala Z, Frésard L, Waggott D, Zink EM, Kim YM, Heyman HM, Stratton KG, Webb-Robertson BM; Undiagnosed Diseases Network, Snyder M, Merker JD, Montgomery SB, Fisher PG, Feichtinger RG, Mayr JA, Hall J, Barbosa IA, Simpson MA, Deshpande C, Waters KM, Koeller DM, Metz TO, Morris AA, Schelley S, Cowan T, Friederich MW, McFarland R, Van Hove JLK, Enns GM, Yamamoto S, Ashley EA, Wangler MF, Taylor RW, Bellen HJ, Bernstein JA, Wheeler MT. Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. Am J Hum Genet. 2018, 102(3):494-504.
  • Menachery VD, Schäfer A, Burnum-Johnson KE, Mitchell HD, Eisfeld AJ, Walters KB, Nicora CD, Purvine SO, Casey CP, Monroe ME, Weitz KK, Stratton KG, Webb-Robertson BM, Gralinski LE, Metz TO, Smith RD, Waters KM, Sims AC, Kawaoka Y, Baric RS. MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proc Natl Acad Sci U S A. 2018, 115(5):E1012-E1021.
  • Wu J, Sabag-Daigle A, Metz TO, Deatherage Kaiser BL, Gopalan V, Behrman EJ, Wysocki VH, Ahmer BMM. Measurement of Fructose-Asparagine Concentrations in Human and Animal Foods. J Agric Food Chem. 2018, 66(1):212-217


  • Eisfeld AJ, Halfmann PJ, Wendler JP, Kyle JE, Burnum-Johnson KE, Peralta Z, Maemura T, Walters KB, Watanabe T, Fukuyama M, Jacobs JM, Kim YM, Casey CP, Stratton KG, Webb-Robertson BJ, Gritsenko MA, Monroe ME, Weitz KK, Shukla AK, Tian M, Neumann G, Reed JL, van Bakel H, Metz TO, Smith RD, Waters KM, N’jai A, Sahr F, Kawaoka Y. Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell Host Microbe. 2017, 22(6):817-829.e8.
  • Muralimanoharan S, Li C, Nakayasu ES, Casey CP, Metz TO, Nathanielsz PW, Maloyan A. Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction. J Mol Cell Cardiol. 2017, 108:181-193
  • Kerkhoven EJ, Kim YM, Wei S, Nicora CD, Fillmore TL, Purvine SO, Webb-Robertson BJ, Smith RD, Baker SE, Metz TO, Nielsen J. Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica. MBio. 2017, 8(3). pii: e00857-17
  • Ma J, Casey CP, Zheng X, Ibrahim YM, Wilkins CS, Renslow RS, Thomas DG, Payne SH, Monroe ME, Smith RD, Teeguarden JG, Baker ES, Metz TO. PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association. Bioinformatics. 2017, doi: 10.1093/bioinformatics/btx305. [Epub ahead of print]
  • Burnum-Johnson KE, Baker ES, Metz TO. Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging. Placenta. 2017, pii: S0143-4004(17)30217-5
  • Bryant AE, Aldape MJ, Bayer CR, Katahira EJ, Bond L, Nicora CD, Fillmore TL, Clauss TR, Metz TO, Webb-Robertson BJ, Stevens DL. Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study. PLoS One. 2017, 12(2):e0172486
  • Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics. 2017, 33(11):1744-1746
  • Dautel SE, Kyle JE, Clair G, Sontag RL, Weitz KK, Shukla AK, Nguyen SN, Kim YM, Zink EM, Luders T, Frevert CW, Gharib SA, Laskin J, Carson JP, Metz TO, Corley RA, Ansong C. Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung. Sci Rep. 2017, 7:40555
  • Romine MF, Rodionov DA, Maezato Y, Anderson LN, Nandhikonda P, Rodionova IA, Carre A, Li X, Xu C, Clauss TR, Kim YM, Metz TO, Wright AT. Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism. Proc Natl Acad Sci U S A. 2017, 114(7):E1205-E1214
  • Burnum-Johnson KE, Kyle JE, Eisfeld AJ, Casey CP, Stratton KG, Gonzalez JF, Habyarimana F, Negretti NM, Sims AC, Chauhan S, Thackray LB, Halfmann PJ, Walters KB, Kim YM, Zink EM, Nicora CD, Weitz KK, Webb-Robertson BM, Nakayasu ES, Ahmer B, Konkel ME, Motin V, Baric RS, Diamond MS, Kawaoka Y, Waters KM, Smith RD, Metz TO. MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. Analyst. 2017, 142(3):442-448
  • Metz TO, Baker ES, Schymanski EL, Renslow RS, Thomas DG, Causon TJ, Webb IK, Hann S, Smith RD, Teeguarden JG. Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go? Bioanalysis. 2017, 9(1):81-98.


  • Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker SE, Brown JB, Borenstein E, Jansson JK, Metz TO, Mao JH. Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nat Microbiol. 2016, 2:16221
  • Zhang X, Romm M, Zheng X, Zink EM, Kim YM, Burnum-Johnson KE, Orton DJ, Apffel A, Ibrahim YM, Monroe ME, Moore RJ, Smith JN, Ma J, Renslow RS, Thomas DG, Blackwell AE, Swinford G, Sausen J, Kurulugama RT, Eno N, Darland E, Stafford G, Fjeldsted J, Metz TO, Teeguarden JG, Smith RD, Baker ES. SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. Clin Mass Spectrom. 2016, 2:1-10.
  • Nakayasu ES, Nicora CD, Sims AC, Burnum-Johnson KE, Kim YM, Kyle JE, Matzke MM, Shukla AK, Chu RK, Schepmoes AA, Jacobs JM, Baric RS, Webb-Robertson BJ, Smith RD, Metz TO. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. mSystems. 2016, 1(3). pii: e00043-16
  • Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016, 34(8):828-837
  • Pomraning KR, Kim YM, Nicora CD, Chu RK, Bredeweg EL, Purvine SO, Hu D, Metz TO, Baker SE. Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. BMC Genomics. 2016, 17:138.
  • Tisoncik-Go J, Gasper DJ, Kyle JE, Eisfeld AJ, Selinger C, Hatta M, Morrison J, Korth MJ, Zink EM, Kim YM, Schepmoes AA, Nicora CD, Purvine SO, Weitz KK, Peng X, Green RR, Tilton SC, Webb-Robertson BJ, Waters KM, Metz TO, Smith RD, Kawaoka Y, Suresh M, Josset L, Katze MG. Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell Host Microbe. 2016, 19(2):254-66.
  • Kyle JE, Zhang X, Weitz KK, Monroe ME, Ibrahim YM, Moore RJ, Cha J, Sun X, Lovelace ES, Wagoner J, Polyak SJ, Metz TO, Dey SK, Smith RD, Burnum-Johnson KE, Baker ES. Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. Analyst. 2016, 141(5):1649-59.


  • Touchette MH, Bommineni GR, Delle Bovi RJ, Gadbery JE, Nicora CD, Shukla AK, Kyle JE, Metz TO, Martin DW, Sampson NS, Miller WT, Tonge PJ, Seeliger JC. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids. Biochemistry. 2015, 54(35):5457-68.
  • Lovelace ES, Wagoner J, MacDonald J, Bammler T, Bruckner J, Brownell J, Beyer RP, Zink EM, Kim YM, Kyle JE, Webb-Robertson BJ, Waters KM, Metz TO, Farin F, Oberlies NH, Polyak SJ. Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling. J Nat Prod. 2015, 78(8):1990-2000.
  • Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJ, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R. Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes. J Proteome Res. 2015, 14(8):3123-35.
  • Kebaabetswe LP, Haick AK, Gritsenko MA, Fillmore TL, Chu RK, Purvine SO, Webb-Robertson BJ, Matzke MM, Smith RD, Waters KM, Metz TO, Miura TA. Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus. Virology. 2015, 483:96-107.
  • Kim YM, Nowack S, Olsen MT, Becraft ED, Wood JM, Thiel V, Klapper I, Kühl M, Fredrickson JK, Bryant DA, Ward DM, Metz TO. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Front Microbiol. 2015, 6:209.
  • Pomraning KR, Wei S, Karagiosis SA, Kim YM, Dohnalkova AC, Arey BW, Bredeweg EL, Orr G, Metz TO, Baker SE. Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis. PLoS One. 2015, 10(4):e0123188.
  • Webb-Robertson BJ, Wiberg HK, Matzke MM, Brown JN, Wang J, McDermott JE, Smith RD, Rodland KD, Metz TO, Pounds JG, Waters KM. Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. J Proteome Res. 2015, 14(5):1993-2001.


  • Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM. Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Mol Cell Proteomics. 2014, 13(12):3639-46.
  • Webb-Robertson BJ, Kim YM, Zink EM, Hallaian KA, Zhang Q, Madupu R, Waters KM, Metz TO. A statistical analysis of the effects of urease pre-treatment on the measurement of the urinary metabolome by gas chromatography-mass spectrometry. Metabolomics 2014, 10(5):897-908.
  • Huang EL, Aylward FO, Kim YM, Webb-Robertson BJ, Nicora CD, Hu Z, Metz TO, Lipton MS, Smith RD, Currie CR, Burnum-Johnson KE. The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environ Microbiol Rep. 2014,  6(4):389-95
  • Menachery VD, Eisfeld AJ, Schäfer A, Josset L, Sims AC, Proll S, Fan S, Li C, Neumann G, Tilton SC, Chang J, Gralinski LE, Long C, Green R, Williams CM, Weiss J, Matzke MM, Webb-Robertson BJ, Schepmoes AA, Shukla AK, Metz TO, Smith RD, Waters KM, Katze MG, Kawaoka Y, Baric RS. Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. MBio. 2014, 5(3). pii: e01174-14
  • Cole JK, Hutchison JR, Renslow RS, Kim YM, Chrisler WB, Engelmann HE, Dohnalkova AC, Hu D, Metz TO, Fredrickson JK, Lindemann SR. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions. Front Microbiol. 2014, 5:109
  • Anderson JC, Wan Y, Kim YM, Pasa-Tolic L, Metz TO, Peck SC. Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae. Proc Natl Acad Sci U S A. 2014, 111(18):6846-6851.
  • Merkley ED, Metz TO, Smith RD, Baynes JW, Frizzell, N. The succinated proteome. Mass Spectrom. Rev. 2014, 33(2):98-109.


  • Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics. 2013, 29(22):2900-2908.
  • Mitchell HD, Eisfeld AJ, Sims AC, McDermott JE, Matzke MM, Webb-Robertson BJ, Tilton SC, Tchitchek N, Josset L, Li C, Ellis AL, Chang JH, Heegel RA, Luna ML, Schepmoes AA, Shukla AK, Metz TO, Neumann G, Benecke AG, Smith RD, Baric RS, Kawaoka Y, Katze MG, Waters KM. A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. PLoS One. 2013, 8(7):e69374.
  • Gralinski LE, Bankhead A 3rd, Jeng S, Menachery VD, Proll S, Belisle SE, Matzke M, Webb-Robertson BJ, Luna ML, Shukla AK, Ferris MT, Bolles M, Chang J, Aicher L, Waters KM, Smith RD, Metz TO, Law GL, Katze MG, McWeeney S, Baric RS. Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury. MBio. 2013, 4(4). e00271-13.
  • Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson BJ, Ferris MT, Totura AL, Li C, Neumann G, Metz TO, Smith RD, Waters KM, Baric R, Kawaoka Y, Katze MG. Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC Syst Biol. 2013, 7:69.
  • Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO, Brown JN, Metz TO, Smith RD, Heffron F, Adkins JN. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. PLoS One. 2013, 8(6):e67155.
  • Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst. 2013, 9(6):1522-1534.
  • Webb-Robertson BJ, Matzke MM, Metz TO, McDermott JE, Walker H, Rodland KD, Pounds JG, Waters KM. Sequential projection pursuit principal component analysis - dealing with missing data associated with new -omics technologies. Biotechniques. 2013, 54(3):165-168.
  • LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD. MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC Bioinformatics. 2013, 14:49.
  • Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schäfer A, Matzke MM, Webb-Robertson BJ, Chang J, Luna ML, Long CE, Shukla AK, Bankhead AR 3rd, Burkett SE, Zornetzer G, Tseng CT, Metz TO, Pickles R, McWeeney S, Smith RD, Katze MG, Waters KM, Baric RS. Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol. 2013, 87(7):3885-3902.
  • Zhang Q, Fillmore TL, Schepmoes AA, Clauss TR, Gritsenko MA, Mueller PW, Rewers M, Atkinson MA, Smith RD, Metz TO. Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes. J Exp Med. 2013, 210(1):191-203.
  • Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim YM, McAteer K, Deatherage Kaiser BL, Dubois JL, Brewer HM, Frank BC, McDermott JE, Metz TO, Peterson SN, Smith RD, Motin VL, Adkins JN. A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Mol Biosyst. 2013, 9(1):44-54.
  • Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson BJ. A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics. 2013, 13(3-4):493-503.
  • Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN. Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated 'Omics and Modeling. Curr Top Microbiol Immunol. 2013, 363:21-41.


  • Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol. 2012, 8:558.
  • Hu ZP, Kim YM, Sowa MB, Robinson RJ, Gao X, Metz TO, Morgan WF, Zhang Q. Metabolomic response of human skin tissue to low dose ionizing radiation. Mol Biosyst. 2012, 8(7):1979-1986.
  • Kangas LJ, Metz TO, Isaac G, Schrom BT, Ginovska-Pangovska B, Wang L, Tan L, Lewis RR, Miller JH. In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids. Bioinformatics. 2012, 28(13):1705-1713.
  • Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. J Proteome Res. 2012, 11(7):3520-3532.
  • Perera R, Riley C, Isaac G, Hopf-Jannasch AS, Moore RJ, Weitz KW, Pasa-Tolic L, Metz TO, Adamec J, Kuhn RJ. Dengue virus infection perturbs lipid homeostasis in infected mosquito cells. PLoS Pathog, 2012, 8(3):e1002584.
  • Nagai R, Murray DB, Metz TO, Baynes JW. Chelation: a fundamental mechanism of action of AGE inhibitors, AGE breakers, and other inhibitors of diabetes complications. Diabetes, 2012, 61(3):549-559.
  • Gao X, Zhang Q, Meng D, Isaac G, Zhao R, Fillmore TL, Chu RK, Zhou J, Tang K, Hu Z, Moore RJ, Smith RD, Katze MG, Metz TO. A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling. Anal Bioanal Chem, 2012, 402(9):2923-2933.


  • Shvartsburg AA, Isaac G, Leveque N, Smith RD, Metz TO. Separation and classification of lipids using differential ion mobility spectrometry. J Am Soc Mass Spectrom, 2011, 22(7):1146-1155.
  • Rasmussen AL, Diamond DL, McDermott JE, Gao X, Metz TO, Matzke MM, Carter VS, Belisle SE, Korth MJ, Waters KM, Smith RD, Katze MG. Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl-CoA delta isomerase (DCI), required for HCV replication and likely pathogenesis. J Virol, 2011, 85(22):11646-11654.
  • Kim YM, Metz TO, Hu Z, Wiedner SD, Kim JS, Smith RD, Morgan WF, Zhang Q. Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics. Rapid Commun Mass Spectrom, 2011, 25(17):2561-2564.
  • Matzke MM, Waters KM, Metz TO, Jacobs JM, Sims AC, Baric RS, Pounds JG, Webb-Robertson BJ. Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics, 2011, Epub ahead of print.
  • McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of Salmonella. Front. Microbiol, 2011, 2:121.
  • Zhang Q, Monroe ME, Schepmoes AA, Clauss TR, Gritsenko MA, Meng D, Petyuk VA, Smith RD, Metz TO.  Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects.  J Proteome Res, 2011, 10(7):3076-3088.
  • Gonzalez RM, Zhang Q, Zangar RC, Smith RD, Metz TO. Development of a fibrinogen-specific sandwich enzyme-linked immunosorbent assay microarray assay for distinguishing between blood plasma and serum samples. Anal Biochem, 2011, 414(1):99-102.


  • Webb-Robertson BJ, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, Varnum SM, Pounds JG. Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data.  J Proteome Res, 2010, 9(11):5748-5756.
  • Sorensen CM, Ding J, Zhang Q, Alquier T, Zhao R, Mueller PW, Smith RD, Metz TO.  Perturbations in the lipid profile of individuals with newly diagnosed type 1 diabetes mellitus: Lipidomics analysis of a Diabetes Antibody Standardization Program sample subset. Clin Biochem, 2010, 43(12):948-956.
  • Diamond DL, Snyder AJ, Jacobs JM, Sorensen CM, Walters KA, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R, Metz TO, Camp DG, Waters KM, Smith RD, Rice CM, Katze MG. Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics. PLoS Pathog, 2010, 6:e1000719.


  • Alquier T, Peyot ML, Latour MG, Kebede M, Sorensen CM, Gesta S, Kahn C, Smith RD, Jetton TL, Metz TO, Prentki M, Poitout V. Deletion of GPR40 impairs glucose-induced insulin secretion in vivo in mice without affecting intracellular fuel metabolism in islets. Diabetes, 2009, 58(11):2607-2615.
  • Karpievitch Y, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian WJ, Yoon H, Smith RD, Dabney AR. A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics, 2009, 25(16):2028-2034.


  • Zhang Q, Ames JM, Smith RD, Baynes JW, Metz TO.  A perspective on the Maillard reaction and the analysis of protein glycation by mass spectrometry: probing the pathogenesis of chronic disease.  J Proteome Res, 2008, 8(2):754-769.
  • Zhang Q, Schepmoes AA, Brock JWC, Wu S, Moore RJ, Purvine SO, Baynes JW, Smith RD, Metz TO. Improved methods for the enrichment and analysis of glycated peptides.  Anal Chem, 2008, 80(24):9822-9829.
  • Zhang Q, Petyuk VA, Schepmoes AA, Orton DJ, Monroe ME, Yang F, Smith RD, Metz TO.  Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS3 versus multi-stage activation tandem mass spectrometry.  Rapid Commun Mass Spectrom, 2008, 22(19):3027-3034.
  • Ding J, Sorensen CM, Jaitly N, Jiang H, Orton DJ, Monroe ME, Moore RJ, Smith RD, Metz TO.  Application of the accurate mass and time tag approach in studies of the human blood lipidome.  J Chromatogr B Analyt Technol Biomed Life Sci, 2008, 871(2):243-252.
  • Zhang Q, Tang N, Schepmoes AA, Phillips LS, Smith RD, Metz TO.  Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes.  J Proteome Res, 2008, 7(5):2025-2032.
  • Metz TO, Page JS, Baker ES, Tang K, Ding J, Shen Y, Smith RD.  High-resolution separations and improved ion production and transmission in metabolomics.  Trends Analyt Chem, 2008, 27(3):205-214.
  • Petyuk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME, Dabney AR, Qian WJ, Camp DG, Smith RD.  Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content.  Anal Chem, 2008, 80(3):693-706.
  • Metz TO, Qian WJ, Jacobs JM, Gritsenko MA, Moore RJ, Polpitiya AD, Monroe ME, Camp DG, Mueller PW, Smith RD.  Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset.  J Proteome Res, 2008, 7(2):698-707.


  • Ding J, Sorensen CM, Zhang Q, Jiang H, Jaitly N, Livesay EA, Shen Y, Smith RD, Metz TO.  Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling.  Anal Chem, 2007, 79(16):6081-6093.
  • Metz TO, Zhang Q, Page JS, Shen Y, Callister SJ, Jacobs JM, Smith RD.  Future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery.  Biomarkers Med, 2007, 1(1):159-185.
  • Zhang Q, Tang N, Brock JW, Mottaz HM, Ames JM, Baynes JW, Smith RD, Metz TO.  Enrichment and analysis of nonenzymatically glycated peptides: boronate affinity chromatography coupled with electron-transfer dissociation mass spectrometry.  J Proteome Res, 2007, 6(6):2323-2330.
  • Zhang Q, Frolov A, Tang N, Hoffmann R, van de Goor T, Metz TO, Smith RD.  Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides.  Rapid Commun Mass Spectrom, 2007, 21(5):661-666.
  • Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JS, Metz TO, Adkins JN, Smith RD, Heffron F.  Targeted protein degradation by salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.  Mol Cell Proteomics, 2007, 6(4):717-727.


  • Metz TO, Jacobs JM, Gritsenko MA, Fontes G, Qian WJ, Camp DG, Poitout V, Smith RD  Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS.  J Proteome Res, 2006, 5(12):3345-3354.


  • Shen Y, Strittmatter EF, Zhang R, Metz TO, Moore RJ, Li F, Udseth HR, Smith RD, Unger KK, Kumar D, Lubda D.   Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements.  Anal Chem, 2005, 77(23):7763-7773.
  • Shen Y, Zhang R, Moore RJ, Kim J, Metz TO, Hixson KK, Zhao R, Livesay EA, Udseth HR, Smith RD.  Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics.  Anal Chem, 2005, 77(10):3090-3100.


  • Cotham WE, Metz TO, Ferguson PL, Brock JWC, Hinton DJS, Thorpe SR, Baynes JW, Ames JM.  Proteomic analysis of arginine adducts on glyoxal-modified ribonuclease.   Mol Cell Proteomics, 2004, 3(12):1145-1153.
  • Alderson NL, Chachich ME, Frizzell N, Canning P, Metz TO, Januszewski AS, Youssef NN, Stitt AW, Baynes JW, Thorpe SR.  Effect of Antioxidants and ACE-inhibition on Chemical Modification of Proteins and Progression of Nephropathy in the STZ-Diabetic Rat.  Diabetologia, 2004, 47(8): 1385-1395.


  • Metz TO, Alderson NL, Chachich ME, Thorpe SR, Baynes JW.  Pyridoxamine traps intermediates in lipid peroxidation reactions in vivo: evidence on the role of lipids in chemical modification of protein and development of diabetic complications.  J Biol Chem, 2003, 278(43):42012-42019.
  • Metz TO, Alderson NL, Thorpe SR, Baynes JW.  Pyridoxamine, an inhibitor of advanced glycation and lipoxidation reactions: a novel therapy for treatment of diabetic complications.  Arch Biochem Biophys, 2003, 419(1):41-49.
  • Januszewski AS, Alderson NL, Metz TO, Thorpe SR, Baynes JW.  Role of lipids in chemical modification of proteins and development of complications in diabetes.  Biochem Soc Trans, 2003, 31(Pt 6):1413-1416.
  • Brock JWC, Hinton DJS, Cotham WE, Metz TO, Thorpe SR, Baynes JW, Ames JM.  Proteomic analysis of the site specificity of glycation and carboxymethylation of ribonuclease.  J Proteome Res, 2003, 2(5):506-513.
  • Cotham WE, Hinton DJS, Metz TO, Brock JWC, Thorpe SR, Baynes JW, Ames JM.  Mass spectrometric analysis of glucose-modified ribonuclease.  Biochem Soc Trans, 2003, 31(6):1426-1427.


  • Voziyan PA, Metz TO, Baynes JW, Hudson BG.  A post-Amadori inhibitor, pyridoxamine, also inhibits chemical modification of proteins by scavenging carbonyl intermediates of carbohydrate and lipid degradation.  J Biol Chem, 2002, 277(5):3397-3403.