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Tom Metz

Tom Metz

Integrative Omics
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352
509/371-6581

Biography

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. My post-doc was performed under the mentorship of Dick Smith at Pacific Northwest National Laboratory (PNNL) with a major focus on metabolomics and minor focus on proteomics.

My research at PNNL has focused on the development of both global and targeted metabolomics and lipidomics capabilities based on liquid and gas chromatography 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 mellitus.

Research Interests

  • Metabolomics
  • Lipidomics
  • Proteomics
  • Systems Biology
  • Maillard chemistry
  • Diabetes and diabetic complications

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

PNNL Publications

2014

  • 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 1(12):, doi:10.1007/s11306-014-0642-1

2013

  • 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

2012

  • 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. 
  • 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
  • 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

2011

  • 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
  • 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. 
  • 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
  • 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. 

2010

  • 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. 
  • 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
  • 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. 

2009

  • 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. 
  • 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. 

2008

  • 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, 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

2007

  • 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
  • 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. 

2006

  • 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

2005

  • 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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