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Staff information


Tom Metz

Integrative Omics
Scientist, Team Lead
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352


I received my PhD in Chemistry in the Department of Chemistry and Biochemistry at the University of South Carolina with Dr. John W. Baynes, who studied the role of the Maillard reaction in the development of diabetic complications and in aging. Originally discovered by the French scientist, Louis-Camille Maillard (1878-1936), Maillard chemistry involves non-enzymatic reactions between nucleophilic groups (e.g. a- and e-amines, thiols) of amino acids on proteins and reducing sugars and/or peroxidized lipids.

The reaction is catalyzed by heat, and products of Maillard chemistry form and accumulate in cooked food and contribute to its texture, flavor, and aroma. From its discovery until the late 1970s, the Maillard reaction remained the domain of food chemists. It was at this time that products of Maillard chemistry were identified in vivo, including in humans. After all, as John Baynes likes to say, humans are essentially low-temperature ovens with long cooking cycles. Because Maillard chemistry involves non-enzymatic modification of proteins by reducing sugars, such as glucose, individuals with chronically high levels of blood glucose (i.e. those with diabetes mellitus) accumulate Maillard products on tissue proteins to a greater extent and at a faster rate than those individuals with normal blood glucose levels. One protein modification in particular, glycated hemoglobin, is now used as a marker of long term glucose control in individuals with diabetes. The Maillard hypothesis of diabetic complications states that chronic, cumulative chemical modification of tissue proteins by glucose, and also by oxidized lipids, alters their structure, turnover, and function, ultimately leading to diabetic nephropathy, retinopathy, neuropathy, and cardiovascular disease. My PhD research in the Baynes lab focused on the quantification of Maillard reaction intermediates trapped by pyridoxamine, a vitamer of B6, in biofluids of treated, diabetic animals using liquid chromatography-mass spectrometry (LC-MS) and isotope dilution.

My post-doc was performed in the area of separations coupled with mass spectrometry under the mentorship of Dick Smith at Pacific Northwest National Laboratory (PNNL) with a major focus on metabolomics and minor focus on proteomics. At the time, metabolomics was the latest and least mature (and still is) of the systems biology sciences, and my charge was to bring metabolomics measurement capabilities to a predominately proteomics research group. I initially explored the combination of high pressure, high peak capacity capillary LC separations coupled with FTICR MS and demonstrated that many features (characterized by measured m/z and retention times) could be detected in analyses of a variety of sample types. However, the confident identification (see Sumner et al., Metabolomics, 2007 for guidelines from the Metabolomics Standards Initiative regarding metabolite identification confidence) of large numbers of metabolites in LC-MS data remained elusive, as resources such as Metlin, HMDB, etc were not yet available. For the remainder of my post-doc, I continued to apply LC-MS in metabolomics analyses, eventually also expanding to lipidomics. In additon to my work in metabolomics/lipidomics, I continued to study aspects of diabetes mellitus, including both the role of the Maillard reaction, as well as searching for novel protein or metabolite/lipid markers of both types 1 and 2 diabetes.

Currently, I am the metabolomics technical lead in the Integrative Omics group at PNNL. My research has focused on the development of both global and targeted metabolomics and lipidomics capabilities based on LC and gas chromatography (GC) coupled with mass spectrometry, both for fundamental studies of metabolism/metabolic interactions as well as for biomarker discovery. In addition, I maintain my interest in the Maillard reaction in the context of diabetic complications, and have become involved in various efforts to identify novel biomarkers of both types 1 and 2 diabetes.

Research Interests

  • Metabolomics
  • Lipidomics
  • Metabolic exchange
  • Proteomics
  • Systems Biology
  • Maillard chemistry
  • Diabetes

Education and Credentials

  • Pacific Northwest National Laboratory, Post-doctoral, Mass Spectrometry, 2003-2005
  • University of South Carolina, PhD, Chemistry, 2003
  • San Jose State University, BS, Chemistry, 1999
  • Frostburg State University, BS, Biology, 1997

Affiliations and Professional Service

  • American Diabetes Association
  • American Society for Mass Spectrometry
  • International Maillard Reaction Society
  • Metabolomics Society
  • Adjunct Faculty - Oregon State University

Awards and Recognitions

  • Membership Committee - International Maillard Reaction Society (2010)
  • Environmental Molecular Sciences Laboratory Outstanding Performance Award
  • Fundamental and Computational Sciences Directorate Outstanding Performance Award (3)
  • National Security Directorate Outstanding Performance Award

PNNL Publications


  • Menachery VD, A Schafer, KE Burnum-Johnson, HD Mitchell, AJ Eisfeld-Fenney, KB Walters, CD Nicora, SO Purvine, CP Casey, ME Monroe, KK Weitz, KG Stratton, BJM Webb-Robertson, L Gralinski, TO Metz, RD Smith, KM Waters, AC Sims, Y Kawaoka, and R Baric. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115(5):E1012-E1021.  doi:10.1073/pnas.1706928115


  • Burnum-Johnson KE, EM Baker, and TO Metz. 2017. "Characterizing the Lipid and Metabolite Changes Associated with Placental Function and Pregnancy Complications Using Ion Mobility Spectrometry-Mass Spectrometry and Mass Spectrometry Imaging." Placenta 60(Supplement 1):S67-S72.  doi:10.1016/j.placenta.2017.03.016
  • Burnum-Johnson KE, JE Kyle, AJ Eisfeld, CP Casey, KG Stratton, JF Gonzalez, F Habyarimana, NM Negretti, AC Sims, S Chauhan, LB Thackray, P Halfmann, KB Walters, YM Kim, EM Zink, CD Nicora, KK Weitz, BJM Webb-Robertson, ES Nakayasu, B Ahmer, M Konkel, VL Motin, R Baric, MS Diamond, Y Kawaoka, KM Waters, RD Smith, and TO Metz. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142(3):442-448.  doi:10.1039/c6an02486f
  • Romine MF, DA Rodionov, Y Maezato, LN Anderson, P Nandhikonda, IA Rodionova, A Carre, X Li, C Xu, TRW Clauss, YM Kim, TO Metz, and AT Wright. 2017. "Elucidation of new roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism." Proceedings of the National Academy of Sciences of the United States of America 114(7):E1205-E1214.  doi:10.1073/pnas.1612360114
  • Bryant A, MJ Aldape, CR Bayer, EJ Katahira, L Bond, CD Nicora, TL Fillmore, TRW Clauss, TO Metz, BJM Webb-Robertson, and DL Stevens. 2017. "Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study." PLoS One 12(12):Article No. e0172486.  doi:10.1371/journal.pone.0172486
  • Dautel SE, JE Kyle, GCD Clair, RL Sontag, KK Weitz, AK Shukla, SN Nguyen, YM Kim, EM Zink, T Luders, C Frevert, SA Gharib, J Laskin, JP Carson, TO Metz, RA Corley, and CK Ansong. 2017. "Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung." Scientific Reports 7:Article No. 40555.  doi:10.1038/srep40555
  • Eisfeld AJ, P Halfmann, JP Wendler, JE Kyle, KE Burnum-Johnson, Z Peralta, T Maemura, KB Walters, T Watanabe, S Fukuyama, M Yamashita, JM Jacobs, YM Kim, CP Casey, KG Stratton, BJM Webb-Robertson, MA Gritsenko, ME Monroe, KK Weitz, AK Shukla, M Tian, G Neumann, JL Reed, H van Bakel, TO Metz, RD Smith, KM Waters, A N'jai, F Sahr, and Y Kawaoka. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22(6):817-829.  doi:10.1016/j.chom.2017.10.011
  • Kerkhoven EJ, YM Kim, S Wei, CD Nicora, TL Fillmore, SO Purvine, BJM Webb-Robertson, RD Smith, SE Baker, TO Metz, and JB Nielsen. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8(3):Article No. e00857-17.  doi:10.1128/mBio.00857-17
  • Kyle JE, KL Crowell, CP Casey, GM Fujimoto, S Kim, SE Dautel, RD Smith, SH Payne, and TO Metz. 2017. "LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data." Bioinformatics 33(11):1744-1746.  doi:10.1093/bioinformatics/btx046
  • Ma J, CP Casey, X Zheng, YM Ibrahim, CS Wilkins, RS Renslow, DG Thomas, SH Payne, ME Monroe, RD Smith, JG Teeguarden, EM Baker, and TO Metz. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33(17):2715-2722.  doi:10.1093/bioinformatics/btx305
  • Metz TO, EM Baker, EL Schymanski, RS Renslow, DG Thomas, TJ Causon, IK Webb, S Hann, RD Smith, and JG Teeguarden. 2017. "Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go?" Bioanalysis 9(1):81-98.  doi:10.4155/bio-2016-0244
  • Muralimanoharan S, C Li, ES Nakayasu, CP Casey, TO Metz, PW Nathanielsz, and A Maloyan. 2017. "Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction." Journal of Molecular and Cellular Cardiology 108:181-193.  doi:10.1016/j.yjmcc.2017.06.006
  • Snijders AM, SA Langley, YM Kim, CJ Brislawn, C Noecker, EM Zink, SJ Fansler, CP Casey, D Miller, Y Huang, GH Karpen , SE Celniker, JB Brown, EA Borenstein, JK Jansson, TO Metz, and JH Mao. 2017. "Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome." Nature Microbiology 2(2):Article No. 16221.  doi:10.1038/nmicrobiol.2016.221


  • Heyman HM, X Zhang, K Tang, ES Baker, and TO Metz. 2016. "Conventional and Advanced Separations in Mass Spectrometry-Based Metabolomics: Methodologies and Applications." In Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, ed. Reedijk, J.  Elsevier, Amsterdam, , Netherlands.  doi:10.1016/B978-0-12-409547-2.12132-8
  • Kyle JE, X Zhang, KK Weitz, ME Monroe, YM Ibrahim, RJ Moore, J Cha, X Sun, ES Lovelace, J Wagoner, S Polyak, TO Metz, SK Dey, RD Smith, KE Burnum-Johnson, and ES Baker. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst 141(5):1649-1659.  doi:10.1039/C5AN02062J
  • Nakayasu ES, CD Nicora, AC Sims, KE Burnum-Johnson, YM Kim, JE Kyle, MM Matzke, AK Shukla, RK Chu, AA Schepmoes, JM Jacobs, R Baric, BJM Webb-Robertson, RD Smith, and TO Metz. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1(3):e00043-16.  doi:10.1128/mSystems.00043-16
  • Pomraning KR, YM Kim, CD Nicora, RK Chu, EL Bredeweg, SO Purvine, D Hu, TO Metz, and SE Baker. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17(138):1-18.  doi:10.1186/s12864-016-2471-2
  • Tisoncik-Go J, DJ Gasper, JE Kyle, AJ Eisfeld, C Selinger, M Hatta, J Morrison, MJ Korth, EM Zink, YM Kim, AA Schepmoes, CD Nicora, SO Purvine, KK Weitz, X Peng, R Green, SC Tilton, BJM Webb-Robertson, KM Waters, TO Metz, RD Smith, Y Kawaoka, M Suresh, L Josset, and MG Katze. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19(2):254-66.  doi:10.1016/j.chom.2016.01.002
  • Wang M, JJ Carver, VV Phelan, LM Sanchez, N Garg, Y Peng, DD Nguyen, JD Watrous, CA Kapono, T Luzzatto-Knaan, C Porto, A Bouslimani, AV Melnik, MJ Meehan, WT Liu, M Crusemann, PD Boudreau, E Esquenazi, M Sandoval-Calderon, R Kersten, LA Pace, RA Quinn, KR Duncan, CC Hsu, DJ Floros, RG Gavilan, K Kleigrewe, TR Northen, RJ Dutton, D Parrot, EE Carlson, B Aigle, CF Michelsen, L Jelsbak, C Sohlenkamp, PA Pevzner, A Edlund, JS Mclean, J Piel, BT Murphy, L Gerwick, CC Liaw, YL Yang, HU Humpf, M Maansson, RA Keyzers, AC Sims, A Johnson, AM Sidebottom, BE Sedio, A Klitgaard, CB Larson, CA Boya P, D Torres-Mendoza, D Gonzalez, JR, DB Silva, LM Marques, DP Demarque, E Pociute, EC O'Neill, E Briand, EJ Helfrich, EA Granatosky, E Glukhov, F Ryffel, H Houson, H Mohimani, JJ Kharbush, Y Zeng, JA Vorholt, KL Kurita, P Charusanti, KL McPhail, KF Nielsen, L Vuong, M Elfeki, MF Traxler, N Engene, N Koyama, OB Vining, R Baric, RR Silva, SJ Mascuch, S Tomasi, S Jenkins, V Macherla, T Hoffman, V Agarwal, PG Williams, J Dai, R Neupane, J Gurr, AM Rodriguez, A Lamsa, C Zhang, K Dorrestein, BM Duggan, J Almaliti, PM Allard, P Phapale, LF Nothias, T Alexandrov, M Litaudon, JL Wolfender, JE Kyle, TO Metz, T Peryea, DT Nguyen, D VanLeer, P Shinn, A Jadhav, R Muller, KM Waters, W Shi, X Liu, L Zhang, R Knight, PR Jensen, BO Palsson, K Pogliano, RG Linington, M Gutierrez, NP Lopes, WH Gerwick, BS Moore, PC Dorrestein, and N Bandeira. 2016. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature Biotechnology 34(8):828-837.  doi:10.1038/nbt.3597
  • Webb-Robertson BJM, LM Bramer, SM Reehl, TO Metz, Q Zhang, M Rewers, and B Frohnert. 2016. "ROFI - The use of Repeated Optimization for Feature Interpretation." In International Conference on Computational Science and Computational Intelligence (CSCI 2016), December 15-17, 206, Las Vegas, Nevada, ed. HR Arabnia, L Deligiannidis and M Yang.  IEEE, PISCATAWAY, NJ.  doi:10.1109/CSCI.2016.0013
  • Zhang X, MV Romm, X Zheng, EM Zink, YM Kim, KE Burnum-Johnson, DJ Orton, A Apffel, YM Ibrahim, ME Monroe, RJ Moore, JN Smith, J Ma, RS Renslow, DG Thomas, A Blackwell, G Swinford, J Sausen, RT Kurulugama Lekamlage, N Eno, E Darland, G Stafford, JC Fjeldsted, TO Metz, JG Teeguarden, RD Smith, and ES Baker. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2:1-10.  doi:10.1016/j.clinms.2016.11.002


  • Kebaabetswe LP, AK Haick, MA Gritsenko, TL Fillmore, RK Chu, SO Purvine, BJM Webb-Robertson, MM Matzke, RD Smith, KM Waters, TO Metz, and TA Miura. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438:96-107.  doi:10.1016/j.virol.2015.03.045
  • Kim YM, S Nowack, M Olsen, E Becraft, JM Wood, V Thiel, I Klapper, M Kuhl, JK Fredrickson, DA Bryant, DM Ward, and TO Metz. 2015. "Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms." Frontiers in Microbiology 6:Article 209.  doi:10.3389/fmicb.2015.00209
  • Lovelace ES, J Wagoner, J MacDonald, T Bammler, J Bruckner, J Brownell, R Beyer, EM Zink, YM Kim, JE Kyle, BJM Webb-Robertson, KM Waters, TO Metz, F Farin, NH Oberlies, and S Polyak. 2015. "Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling." Journal of Natural Products 78(8):1990-2000.  doi:10.1021/acs.jnatprod.5b00288
  • Pomraning KR, S Wei, SA Karagiosis, YM Kim, A Dohnalkova, BW Arey, EL Bredeweg, G Orr, TO Metz, and SE Baker. 2015. "Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis." PLoS One 10(4):e0123188.  doi:10.1371/journal.pone.0123188
  • Suh MJ, A Tovchigrechko, V Thovari, MA Rolfe, M Torralba, J Wang, JN Adkins, BJM Webb-Robertson, W Osborne, F Cogen, P Kaplowitz, TO Metz, KE Nelson, R Madupu, and R Pieper. 2015. "Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes." Journal of Proteome Research 14(8):3123-3135.  doi:10.1021/acs.jproteome.5b00052
  • Touchette MH, GR Bommineni, RJ Delle Bovi, J Gadbery, CD Nicora, AK Shukla, JE Kyle, TO Metz, DW Martin, NS Sampson, WT Miller, PJ Tonge, and JC Seeliger. 2015. "Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl ß-Diol Lipids." Biochemistry 54(35):5457-5468.  doi:10.1021/acs.biochem.5b00455
  • Webb-Robertson BJM, HK Wiberg, MM Matzke, JN Brown, J Wang, JE McDermott, RD Smith, KD Rodland, TO Metz, JG Pounds, and KM Waters. 2015. "Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics." Journal of Proteome Research 14(5):1993-2001.  doi:10.1021/pr501138h


  • Aevermann B, BE Pickett, S Kumar, EB Klem, S Agnihothram, PS Askovich, A Bankhead, M Bolles, V Carter, JH Chang, TRW Clauss, P Dash, AH Diercks, AJ Eisfeld, AL Ellis, S Fan, MT Ferris, L Gralinski, R Green, MA Gritsenko, M Hatta, RA Heegel, JM Jacobs, S Jeng, L Josset, SM Kaiser, S Kelly, GL Law, C Li, J Li, C Long, ML Luna, MM Matzke, JE McDermott, V Menachery, TO Metz, HD Mitchell, ME Monroe, G Navarro, G Neumann, RL Podyminogin, SO Purvine, C Rosenberger, CJ Sanders, AA Schepmoes, AK Shukla, A Sims, P Sova, VC Tam, N Tchitchek, PG Thomas, SC Tilton, AL Totura, J Wang, BJM Webb-Robertson, J Wen, JM Weiss, F Yang, B Yount, Q Zhang, SK Mcweeney, RD Smith, KM Waters, Y Kawaoka, R Baric, A Aderem, MG Katze, and RH Scheuermann. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1:Article No. 140033.  doi:10.1038/sdata.2014.33
  • Anderson JC, Y Wan, YM Kim, L Pasa-Tolic, TO Metz, and SC Peck. 2014. "Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae." Proceedings of the National Academy of Sciences of the United States of America 111(18):6846-6851.  doi:10.1073/pnas.1403248111
  • Cole JK, JR Hutchison, RS Renslow, YM Kim, WB Chrisler, HE Engelmann, A Dohnalkova, D Hu, TO Metz, JK Fredrickson, and SR Lindemann. 2014. "Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions." Frontiers in Microbiology 5:Article No. 109.  doi:10.3389/fmicb.2014.00109
  • Huang EL, FO Aylward, YM Kim, BJM Webb-Robertson, CD Nicora, Z Hu, TO Metz, MS Lipton, RD Smith, CR Currie, and KE Burnum-Johnson. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6(4):389-95.  doi:10.1111/1758-2229.12163
  • Menachery V, AJ Eisfeld, A Schafer, L Josset, AC Sims, S Proll, S Fan, C Li, G Neumann, SC Tilton, JH Chang, L Gralinski, C Long, R Green, CM Williams, JM Weiss, MM Matzke, BJM Webb-Robertson, AA Schepmoes, AK Shukla, TO Metz, RD Smith, KM Waters, MG Katze, Y Kawaoka, and R Baric. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5(3):Article No. e01174-14.  doi:10.1128/mBio.01174-14
  • Merkley ED, TO Metz, RD Smith, J Baynes, and N Frizell. 2014. "The Succinated Proteome." Mass Spectrometry Reviews 33(22):98-109.  doi:10.1002/mas.21382
  • Webb-Robertson BJM, MM Matzke, S Datta, SH Payne, J Kang, LM Bramer, CD Nicora, AK Shukla, TO Metz, KD Rodland, RD Smith, MF Tardiff, JE McDermott, JG Pounds, and KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12):3639-3646.  doi:10.1074/mcp.M113.030932
  • Webb-Robertson BJM, YM Kim, EM Zink, KA Hallaian, Q Zhang, R Madupu, KM Waters, and TO Metz. 2014. "A Statistical Analysis of the Effects of Urease Pre-Treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry." Metabolomics 10(5):897-908.  doi:10.1007/s11306-014-0642-1


  • Ansong C, AC Rutledge, HD Mitchell, S Chauhan, MB Jones, YM Kim, K Mcateer, BL Deatherage, JL DuBois, HM Brewer, BC Frank, JE McDermott, TO Metz, SN Peterson, RD Smith, VL Motin, and JN Adkins. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9(1):44-54.  doi:10.1039/C2MB25287B
  • Gralinski L, A Bankhead, S Jeng, V Menachery, S Proll, S Belisle, MM Matzke, BJM Webb-Robertson, ML Luna, AK Shukla, MT Ferris, M Bolles, JH Chang, LD Aicher, KM Waters, RD Smith, TO Metz, GL Law, MG Katze, SK Mcweeney, and R Baric. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4(4):Article No. e00271-13.  doi:10.1128/mBio.00271-13
  • Kaiser BLD, J Li, JA Sanford, YM Kim, SR Kronewitter, MB Jones, C Peterson, SN Peterson, BC Frank, SO Purvine, JN Brown, TO Metz, RD Smith, F Heffron, and JN Adkins. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8(6):Article No. e67155.  doi:10.1371/journal.pone.0067155
  • Kim YM, B Schmidt, AS Kidwai, MB Jones, BL Deatherage, HM Brewer, HD Mitchell, BO Palsson, JE McDermott, F Heffron, RD Smith, SN Peterson, C Ansong, DR Hyduke, TO Metz, and JN Adkins. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9(6):1522-1534.  doi:10.1039/C3MB25598K
  • Lamarche BL, KL Crowell, N Jaitly, VA Petyuk, AR Shah, AD Polpitiya, JD Sandoval, GR Kiebel, ME Monroe, SJ Callister, TO Metz, GA Anderson, and RD Smith. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14:Article No. 49.  doi:10.1186/1471-2105-14-49
  • Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJM Webb-Robertson. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13(3-4):493-503.  doi:10.1002/pmic.201200269
  • Mitchell HD, AJ Eisfeld, A Sims, JE McDermott, MM Matzke, BJM Webb-Robertson, SC Tilton, N Tchitchek, L Josset, C Li, AL Ellis, JH Chang, RA Heegel, ML Luna, AA Schepmoes, AK Shukla, TO Metz, G Neumann, A Benecke, RD Smith, R Baric, Y Kawaoka, MG Katze, and KM Waters. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8(7):e69374.  doi:10.1371/journal.pone.0069374
  • Schmidt B, A Ebrahim, TO Metz, JN Adkins, BO Palsson, and DR Hyduke. 2013. "GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data." Bioinformatics 29(22):2900-2908.  doi:10.1093/bioinformatics/btt493
  • Sims AC, SC Tilton, V Menachery, L Gralinski, A Schafer, MM Matzke, BJM Webb-Robertson, JH Chang, ML Luna, C Long, AK Shukla, A Bankhead, S Burkett, G Zornester, CK Tseng, TO Metz, R Pickles, SK Mcweeney, RD Smith, MG Katze, KM Waters, and R Baric. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87(7):3885-902.  doi:10.1128/JVI.02520-12
  • Tchitchek N, AJ Eisfeld, J Tisoncik-Go, L Josset, L Gralinski, C Becavin, SC Tilton, BJM Webb-Robertson, MT Ferris, AL Totura, C Li, G Neumann, TO Metz, RD Smith, KM Waters, R Baric, Y Kawaoka, and MG Katze. 2013. "Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice." BMC Systems Biology 7:Article No. 69.  doi:10.1186/1752-0509-7-69
  • Webb-Robertson BJM, MM Matzke, TO Metz, JE McDermott, J Walker, KD Rodland, JG Pounds, and KM Waters. 2013. "Sequential Projection Pursuit Principal Component Analysis - Dealing with Missing Data Associated with New -Omics Technologies." BioTechniques 54(3):165-168. 
  • Zhang Q, TL Fillmore, AA Schepmoes, TRW Clauss, MA Gritsenko, PW Mueller, M Rewers, MA Atkinson, RD Smith, and TO Metz. 2013. "Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes." The Journal of Experimental Medicine 210(1):191-203.  doi:10.1084/jem.20111843


  • Bordbar A, ML Mo, ES Nakayasu, AC Rutledge, YM Kim, TO Metz, MB Jones, BC Frank, RD Smith, SN Peterson, DR Hyduke, JN Adkins, and BO Palsson. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8:Article No. 558.  doi:10.1038/msb.2012.21
  • Gao X, Q Zhang, D Meng, G Isaac, R Zhao, TL Fillmore, RK Chu, J Zhou, K Tang, Z Hu, RJ Moore, RD Smith, MG Katze, and TO Metz. 2012. "A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling." Analytical and Bioanalytical Chemistry 402(9):2923-2933. 
  • Hu Z, YM Kim, MB Sowa, RJ Robinson, X Gao, TO Metz, WF Morgan, and Q Zhang. 2012. "Metabolomic Response of Human Skin Tissue to Low Dose Ionizing Radiation." Molecular Biosystems 8(7):1979-1986.  doi:10.1039/C2MB25061F
  • Kangas LJ, TO Metz, G Isaac, BT Schrom, B Ginovska-Pangovska, L Wang, L Tan, RR Lewis, and JH Miller. 2012. "In Silico Identification Software (ISIS): A Machine Learning Approach to Tandem Mass Spectral Identification of Lipids." Bioinformatics 28(13):1705-1713.  doi:10.1093/bioinformatics/bts194
  • Nagai R, DB Murray, TO Metz, and J Baynes. 2012. "Chelation: A Fundamental Mechanism of Action of AGE Inhibitors, AGE Breakers, and Other Inhibitors of Diabetes Complications." Diabetes 61(3):549-559.  doi:10.2337/db11-1120
  • Perera RM, C Riley, G Isaac, A Hopf- Jannasch, RJ Moore, KK Weitz, L Pasa-Tolic, TO Metz, J Adamec, and RJ Kuhn. 2012. "Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells." PLoS Pathogens 8(3):Article No. e1002584.  doi:10.1371/journal.ppat.1002584
  • Rutledge AC, G Fontes, MA Gritsenko, AD Norbeck, DJ Anderson, KM Waters, JN Adkins, RD Smith, V Poitout, and TO Metz. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11(7):3520-32.  doi:10.1021/pr3002996


  • Gonzales RM, Q Zhang, RC Zangar, RD Smith, and TO Metz. 2011. "Development of a Fibrinogen-Specific Sandwich Enzyme-Linked Immunosorbent Assay Microarray Assay for Distinguishing Between Blood Plasma and Serum Samples." Analytical Biochemistry 414(1):99-102.  doi:10.1016/j.ab.2011.02.039
  • Kim YM, TO Metz, Z Hu, SD Wiedner, JS Kim, RD Smith, WF Morgan, and Q Zhang. 2011. "Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics ." Rapid Communications in Mass Spectrometry 25:2561-2564.  doi:10.1002/rcm.5134
  • Matzke MM, KM Waters, TO Metz, JM Jacobs, A Sims, R Baric, JG Pounds, and BJM Webb-Robertson. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics 27(20):2866-2872. 
  • McDermott JE, H Yoon, ES Nakayasu, TO Metz, DR Hyduke, AS Kidwai, BO Palsson, JN Adkins, and F Heffron. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2:121.  doi:10.3389/fmicb.2011.00121
  • Rasmussen A, DL Diamond, JE McDermott, X Gao, TO Metz, MM Matzke, V Carter, S Belisle, MJ Korth, KM Waters, RD Smith, and MG Katze. 2011. "Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enyzme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis." Journal of Virology 85(22):11646-11654.  doi:10.1128/JVI.05605-11
  • Schrom BT, LJ Kangas, B Ginovska, TO Metz, and JH Miller. 2011. "Charge Prediction of Lipid Fragments in Mass Spectrometry." In 10th International Conference on Machine Learning and Applications and Workshops (ICMLA 2011), December 18-21, 2011, Honolulu, Hawaii, vol. 2, pp. 186-188.  IEEE, Piscataway, NJ.  doi:10.1109/ICMLA.2011.45
  • Shvartsburg AA, G Isaac, N Leveque, RD Smith, and TO Metz. 2011. "Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 22(7):1146-1155.  doi:10.1007/s13361-011-0114-z
  • Zhang Q, ME Monroe, AA Schepmoes, TRW Clauss, MA Gritsenko, D Meng, VA Petyuk, RD Smith, and TO Metz. 2011. "Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects." Journal of Proteome Research 10(7):3076-3088. 


  • Adkins JN, H Mottaz, TO Metz, CK Ansong, NP Manes, RD Smith, and F Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." Chapter 2 in Peptidomics: Methods and Protocols, Methods in Molecular Biology, vol. 615, ed. Mikhail Soloviev, pp. 13-27.  Humana Press, Inc., New York, NY. 
  • Diamond DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp, II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719.  doi:10.1371/journal.ppat.1000719
  • Sorensen CM, J Ding, Q Zhang, T Alquier, R Zhao, PW Mueller, RD Smith, and TO Metz. 2010. "Perturbations in the Lipid Profile of Individuals with Newly Diagnosed Type 1 Diabetes Mellitus: Lipidomics Analysis of a Diabetes Antibody Standardization Program Sample Subset." Clinical Biochemistry 43(12):948-956. 
  • Want EJ, and TO Metz. 2010. "MS Based Metabonomics." In Encyclopedia of Spectroscopy and Spectrometry , vol. 2, ed. J Lindon, GE Trantor, D. Koppenaal, pp. 1663-1674.  Elsevier Ltd., Amsterdam, Netherlands. 
  • Webb-Robertson BJM, LA McCue, KM Waters, MM Matzke, JM Jacobs, TO Metz, SM Varnum, and JG Pounds. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9(11):5748-5756. 


  • Alquier T, ML Peyot, MG Latour, M Kebede, CM Sorensen, S Gesta, CR Kahn, RD Smith, TL Jetton, TO Metz, M Prentki, and VJ Poitout. 2009. "Deletion of GPR40 Impairs Glucose-Induced Insulin Secretion In Vivo in Mice Without Affecting Intracellular Fuel Metabolism in Islets ." Diabetes 58(11):2607-2615. 
  • Karpievitch Y, JR Stanley, T Taverner, J Huang, JN Adkins, C Ansong, F Heffron, TO Metz, W Qian, H Yoon, RD Smith, and AR Dabney. 2009. "A statistical framework for protein quantitation in bottom-up MS-based proteomics ." Bioinformatics 25(16):2028-2034.  doi:10.1093/bioinformatics/btp362
  • Karpievitch Y, JR Stanley, T Taverner, J Huang, JN Adkins, C Ansong, F Heffron, TO Metz, W Qian, H Yoon, RD Smith, and AR Dabney. 2009. "A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics." Bioinformatics 25(16):2028-2034. 
  • Metz TO. 2009. "The Analysis of AGEs and ALEs by Mass Spectrometry: What does the Future Hold?" International Maillard Reaction Society Highlights 4(5):2-9. 


  • Ding J, CM Sorensen, N Jaitly, H Jiang, DJ Orton, ME Monroe, RJ Moore, RD Smith, and TO Metz. 2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." Journal of Chromatography B 871(2):243-252.  doi:10.1016/j.jchromb.2008.04.040
  • Metz TO, JS Page, ES Baker, K Tang, J Ding, Y Shen, and RD Smith. 2008. "High Resolution Separations and Improved Ion Production and Transmission in Metabolomics." Trends in Analytical Chemistry. TrAC 27(3):205-214.  doi:10.1016/j.trac.2007.11.003
  • Metz TO, W Qian, JM Jacobs, MA Gritsenko, RJ Moore, AD Polpitiya, ME Monroe, DG Camp, II, PW mueller, and RD Smith. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset ." Journal of Proteome Research 7(2):698-707.  doi:10.1021/pr700606w
  • Petyuk VA, N Jaitly, RJ Moore, J Ding, TO Metz, K Tang, ME Monroe, AV Tolmachev, JN Adkins, ME Belov, AR Dabney, W Qian, DG Camp, II, and RD Smith. 2008. "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 ." Analytical Chemistry 80(3):693-706.  doi:10.1021/ac701863d
  • Zhang Q, AA Schepmoes, JW Brock, S Wu, RJ Moore, SO Purvine, J Baynes, RD Smith, and TO Metz. 2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides ." Analytical Chemistry 80(24):9822-9829.  doi:10.1021/ac801704j
  • Zhang Q, JM Ames, RD Smith, J Baynes, and TO Metz. 2008. "A Perspective on the Maillard Reaction and the Analysis of Protein Glycation by Mass Spectrometry: Probing the Pathogenesis of Chronic Disease." Journal of Proteome Research 8(2):754-769. 
  • Zhang Q, N Tang, AA Schepmoes, LS Phillips, RD Smith, and TO Metz. 2008. "Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membrane." Journal of Proteome Research 7(5):2025-2032.  doi:10.1021/pr700763r
  • Zhang Q, VA Petyuk, AA Schepmoes, DJ Orton, ME Monroe, F Yang, RD Smith, and TO Metz. 2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(19):3027-3034.  doi:10.1002/rcm.3703


  • Ding J, CM Sorensen, Q Zhang, H Jiang, N Jaitly, EA Livesay, Y Shen, RD Smith, and TO Metz. 2007. "Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling." Analytical Chemistry 79(16):6081-6093.  doi:10.1021/ac070064t
  • Manes NP, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, and F Heffron. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6(4):717-727.  doi:10.1074/mcp.M600282-MCP200
  • Metz TO, Q Zhang, JS Page, Y Shen, SJ Callister, JM Jacobs, and RD Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1(1):159-185. 
  • Zhang Q, A Frolov, N Tang, R Hoffman, T van der Goor, TO Metz, and RD Smith. 2007. "Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides." Rapid Communications in Mass Spectrometry 21(5):661-666.  doi:10.1002/rcm.2884
  • Zhang Q, N Tang, JW Brock, HM Mottaz, JM Ames, J Baynes, RD Smith, and TO Metz. 2007. "Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry." Journal of Proteome Research 6(6):2323-2330.  doi:doi:10.1021/pr070112q


  • Metz TO, JM Jacobs, MA Gritsenko, G Fontes, W Qian, DG Camp, II, VJ Poitout, and RD Smith. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5(12):3345-3354.  doi: 10.1021/pr060322n


  • Shen Y, EF Strittmatter, R Zhang, TO Metz, RJ Moore, F Li, HR Udseth, RD Smith, KK Unger, D Kumar, and D Lubda. 2005. "Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurments." Analytical Chemistry 77(23):7763-7773.  doi: 10.1021/ac051257o
  • Shen Y, R Zhang, RJ Moore, J Kim, TO Metz, KK Hixson, R Zhao, EA Livesay, HR Udseth, and RD Smith. 2005. "Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics ." Analytical Chemistry 77(10):3090-3100. 

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