Thomas O. Metz

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