Thomas O. Metz Biological Sciences Division Pacific Northwest National Laboratory Biography Publications Institution JoVE Articles Thomas O. Metz has not added a biography. If you are Thomas O. Metz and would like to personalize this page please email our Author Liaison for assistance. Publications QC-ART: A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data Molecular & Cellular Proteomics : MCP. 04, 2018 | Pubmed ID: 29666158 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 International Journal of Systematic and Evolutionary Microbiology. May, 2018 | Pubmed ID: 29580321 Time-resolved Proteome Profiling of Normal Lung Development American Journal of Physiology. Lung Cellular and Molecular Physiology. Mar, 2018 | Pubmed ID: 29516783 Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut Infection and Immunity. May, 2018 | Pubmed ID: 29483291 Biallelic Mutations in ATP5F1D, Which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder American Journal of Human Genetics. Mar, 2018 | Pubmed ID: 29478781 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. Jan, 2018 | Pubmed ID: 29339515 Measurement of Fructose-Asparagine Concentrations in Human and Animal Foods Journal of Agricultural and Food Chemistry. Jan, 2018 | Pubmed ID: 29232127 Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis Cell Host & Microbe. Dec, 2017 | Pubmed ID: 29154144 Sexual Dimorphism in the Fetal Cardiac Response to Maternal Nutrient Restriction Journal of Molecular and Cellular Cardiology. Jul, 2017 | Pubmed ID: 28641979 Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in MBio. 06, 2017 | Pubmed ID: 28634240 PIXiE: an Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation Using Global Data Association Bioinformatics (Oxford, England). Sep, 2017 | Pubmed ID: 28505286 Characterizing the Lipid and Metabolite Changes Associated with Placental Function and Pregnancy Complications Using Ion Mobility Spectrometry-mass Spectrometry and Mass Spectrometry Imaging Placenta. 12, 2017 | Pubmed ID: 28392013 Effects of Delayed NSAID Administration After Experimental Eccentric Contraction Injury - A Cellular and Proteomics Study PloS One. 2017 | Pubmed ID: 28245256 LIQUID: An-open Source Software for Identifying Lipids in LC-MS/MS-based Lipidomics Data Bioinformatics (Oxford, England). Jun, 2017 | Pubmed ID: 28158427 Lipidomics Reveals Dramatic Lipid Compositional Changes in the Maturing Postnatal Lung Scientific Reports. Feb, 2017 | Pubmed ID: 28145528 Elucidation of Roles for Vitamin B in Regulation of Folate, Ubiquinone, and Methionine Metabolism Proceedings of the National Academy of Sciences of the United States of America. 02, 2017 | Pubmed ID: 28137868 MPLEx: a Method for Simultaneous Pathogen Inactivation and Extraction of Samples for Multi-omics Profiling The Analyst. Jan, 2017 | Pubmed ID: 28091625 Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go? Bioanalysis. Jan, 2017 | Pubmed ID: 27921453 SPE-IMS-MS: An Automated Platform for Sub-sixty Second Surveillance of Endogenous Metabolites and Xenobiotics in Biofluids Clinical Mass Spectrometry (Del Mar, Calif.). Dec, 2016 | Pubmed ID: 29276770 Influence of Early Life Exposure, Host Genetics and Diet on the Mouse Gut Microbiome and Metabolome Nature Microbiology. Nov, 2016 | Pubmed ID: 27892936 MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses MSystems. May-Jun, 2016 | Pubmed ID: 27822525 Sharing and Community Curation of Mass Spectrometry Data with Global Natural Products Social Molecular Networking Nature Biotechnology. Aug, 2016 | Pubmed ID: 27504778 Multi-omics Analysis Reveals Regulators of the Response to Nitrogen Limitation in Yarrowia Lipolytica BMC Genomics. Feb, 2016 | Pubmed ID: 26911370 Integrated Omics Analysis of Pathogenic Host Responses During Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism Cell Host & Microbe. Feb, 2016 | Pubmed ID: 26867183 Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry The Analyst. Mar, 2016 | Pubmed ID: 26734689 Diacyltransferase Activity and Chain Length Specificity of Mycobacterium Tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids Biochemistry. Sep, 2015 | Pubmed ID: 26271001 Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling Journal of Natural Products. Aug, 2015 | Pubmed ID: 26186142 Proteomic Analysis Reveals Down-regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus Virology. Sep, 2015 | Pubmed ID: 25965799 Diel Metabolomics Analysis of a Hot Spring Chlorophototrophic Microbial Mat Leads to New Hypotheses of Community Member Metabolisms Frontiers in Microbiology. 2015 | Pubmed ID: 25941514 Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia Lipolytica During Lipid Accumulation Identifies Targets for Increased Lipogenesis PloS One. 2015 | Pubmed ID: 25905710 Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-based Label-free Global Proteomics Journal of Proteome Research. May, 2015 | Pubmed ID: 25855118 A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection Scientific Data. 2014 | Pubmed ID: 25977790 Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Molecular & Cellular Proteomics : MCP. Dec, 2014 | Pubmed ID: 25433089 A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry Metabolomics : Official Journal of the Metabolomic Society. Oct, 2014 | Pubmed ID: 25254001 Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Molecular & Cellular Proteomics : MCP. Aug, 2014 | Pubmed ID: 25129695 The Fungus Gardens of Leaf-cutter Ants Undergo a Distinct Physiological Transition During Biomass Degradation Environmental Microbiology Reports. Aug, 2014 | Pubmed ID: 24992538 Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-stimulated Gene Responses MBio. May, 2014 | Pubmed ID: 24846384 Phototrophic Biofilm Assembly in Microbial-mat-derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-heterotroph Interactions Frontiers in Microbiology. 2014 | Pubmed ID: 24778628 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. May, 2014 | Pubmed ID: 24753604 The Succinated Proteome Mass Spectrometry Reviews. Mar-Apr, 2014 | Pubmed ID: 24115015 GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data Bioinformatics (Oxford, England). Nov, 2013 | Pubmed ID: 23975765 A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses PloS One. 2013 | Pubmed ID: 23935999 Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice BMC Systems Biology. Jul, 2013 | Pubmed ID: 23895213 A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection PloS One. 2013 | Pubmed ID: 23840608 Salmonella Modulates Metabolism During Growth Under Conditions That Induce Expression of Virulence Genes Molecular BioSystems. Jun, 2013 | Pubmed ID: 23559334 Sequential Projection Pursuit Principal Component Analysis--dealing with Missing Data Associated with New -omics Technologies BioTechniques. Mar, 2013 | Pubmed ID: 23477384 MultiAlign: a Multiple LC-MS Analysis Tool for Targeted Omics Analysis BMC Bioinformatics. Feb, 2013 | Pubmed ID: 23398735 Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells Journal of Virology. Apr, 2013 | Pubmed ID: 23365422 Serum Proteomics Reveals Systemic Dysregulation of Innate Immunity in Type 1 Diabetes The Journal of Experimental Medicine. Jan, 2013 | Pubmed ID: 23277452 A Multi-omic Systems Approach to Elucidating Yersinia Virulence Mechanisms Molecular BioSystems. Jan, 2013 | Pubmed ID: 23147219 A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments Proteomics. Feb, 2013 | Pubmed ID: 23019139 Studying Salmonellae and Yersiniae Host-pathogen Interactions Using Integrated 'omics and Modeling Current Topics in Microbiology and Immunology. 2013 | Pubmed ID: 22886542 Metabolomic Response of Human Skin Tissue to Low Dose Ionizing Radiation Molecular BioSystems. May, 2012 | Pubmed ID: 22610363 In Silico Identification Software (ISIS): a Machine Learning Approach to Tandem Mass Spectral Identification of Lipids Bioinformatics (Oxford, England). Jul, 2012 | Pubmed ID: 22592377 Discovery of Novel Glucose-regulated Proteins in Isolated Human Pancreatic Islets Using LC-MS/MS-based Proteomics Journal of Proteome Research. Jul, 2012 | Pubmed ID: 22578083 Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells PLoS Pathogens. 2012 | Pubmed ID: 22457619 Chelation: a Fundamental Mechanism of Action of AGE Inhibitors, AGE Breakers, and Other Inhibitors of Diabetes Complications Diabetes. Mar, 2012 | Pubmed ID: 22354928 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. Mar, 2012 | Pubmed ID: 22354571 Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry Journal of the American Society for Mass Spectrometry. Jul, 2011 | Pubmed ID: 21953096 Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enzyme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis Journal of Virology. Nov, 2011 | Pubmed ID: 21917952 Formation of Dehydroalanine from Mimosine and Cysteine: Artifacts in Gas Chromatography/mass Spectrometry Based Metabolomics Rapid Communications in Mass Spectrometry : RCM. Sep, 2011 | Pubmed ID: 21910289 Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data Bioinformatics (Oxford, England). Oct, 2011 | Pubmed ID: 21852304 Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella Frontiers in Microbiology. 2011 | Pubmed ID: 21687430 Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects Journal of Proteome Research. Jul, 2011 | Pubmed ID: 21612289 Development of a Fibrinogen-specific Sandwich Enzyme-linked Immunosorbent Assay Microarray Assay for Distinguishing Between Blood Plasma and Serum Samples Analytical Biochemistry. Jul, 2011 | Pubmed ID: 21371419 Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data Journal of Proteome Research. Nov, 2010 | Pubmed ID: 20831241 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. Aug, 2010 | Pubmed ID: 20519132 Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-associated Reprogramming of Hepatocellular Metabolism and Bioenergetics PLoS Pathogens. Jan, 2010 | Pubmed ID: 20062526 Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions Methods in Molecular Biology (Clifton, N.J.). 2010 | Pubmed ID: 20013197 Deletion of GPR40 Impairs Glucose-induced Insulin Secretion in Vivo in Mice Without Affecting Intracellular Fuel Metabolism in Islets Diabetes. Nov, 2009 | Pubmed ID: 19720802 A Statistical Framework for Protein Quantitation in Bottom-up MS-based Proteomics Bioinformatics (Oxford, England). Aug, 2009 | Pubmed ID: 19535538 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. Feb, 2009 | Pubmed ID: 19093874 High Resolution Separations and Improved Ion Production and Transmission in Metabolomics Trends in Analytical Chemistry : TRAC. Mar, 2008 | Pubmed ID: 19255623 Improved Methods for the Enrichment and Analysis of Glycated Peptides Analytical Chemistry. Dec, 2008 | Pubmed ID: 18989935 Analysis of Non-enzymatically Glycated Peptides: Neutral-loss-triggered MS(3) Versus Multi-stage Activation Tandem Mass Spectrometry Rapid Communications in Mass Spectrometry : RCM. Oct, 2008 | Pubmed ID: 18763275 Application of the Accurate Mass and Time Tag Approach in Studies of the Human Blood Lipidome Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. Aug, 2008 | Pubmed ID: 18502191 Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membranes Journal of Proteome Research. May, 2008 | Pubmed ID: 18396901 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. Feb, 2008 | Pubmed ID: 18163597 Application of Proteomics in the Discovery of Candidate Protein Biomarkers in a Diabetes Autoantibody Standardization Program Sample Subset Journal of Proteome Research. Feb, 2008 | Pubmed ID: 18092746 The Future of Liquid Chromatography-mass Spectrometry (LC-MS) in Metabolic Profiling and Metabolomic Studies for Biomarker Discovery Biomarkers in Medicine. Jun, 2007 | Pubmed ID: 19177179 Capillary LC Coupled with High-mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling Analytical Chemistry. Aug, 2007 | Pubmed ID: 17636878 Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-transfer Dissociation Mass Spectrometry Journal of Proteome Research. Jun, 2007 | Pubmed ID: 17488106 Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides Rapid Communications in Mass Spectrometry : RCM. 2007 | Pubmed ID: 17279487 Targeted Protein Degradation by Salmonella Under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics Molecular & Cellular Proteomics : MCP. Apr, 2007 | Pubmed ID: 17228056 Characterization of the Human Pancreatic Islet Proteome by Two-dimensional LC/MS/MS Journal of Proteome Research. Dec, 2006 | Pubmed ID: 17137336 Making Broad Proteome Protein Measurements in 1-5 Min Using High-speed RPLC Separations and High-accuracy Mass Measurements Analytical Chemistry. Dec, 2005 | Pubmed ID: 16316187 Automated 20 Kpsi RPLC-MS and MS/MS with Chromatographic Peak Capacities of 1000-1500 and Capabilities in Proteomics and Metabolomics Analytical Chemistry. May, 2005 | Pubmed ID: 15889897 The MPLEx Protocol for Multi-omic Analyses of Soil Samples Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory JoVE 57343 Química
The MPLEx Protocol for Multi-omic Analyses of Soil Samples Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory JoVE 57343 Química