Thomas O. Metz

Biological Sciences Division, Pacific Northwest National Laboratory

Affiliated withPacific Northwest National Laboratory

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 31	2018

Other Publications

Article	Year
Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics. Analytical chemistry\| PubMed ID: 15889897	2005
Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements. Analytical chemistry\| PubMed ID: 16316187	2005
Characterization of the human pancreatic islet proteome by two-dimensional LC/MS/MS. Journal of proteome research\| PubMed ID: 17137336	2006
Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics. Molecular & cellular proteomics : MCP\| PubMed ID: 17228056	2007
Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides. Rapid communications in mass spectrometry : RCM\| PubMed ID: 17279487	2007
Enrichment and analysis of nonenzymatically glycated peptides: boronate affinity chromatography coupled with electron-transfer dissociation mass spectrometry. Journal of proteome research\| PubMed ID: 17488106	2007
Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling. Analytical chemistry\| PubMed ID: 17636878	2007
Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset. Journal of proteome research\| PubMed ID: 18092746	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\| PubMed ID: 18163597	2008
Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes. Journal of proteome research\| PubMed ID: 18396901	2008
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\| PubMed ID: 18502191	2008
Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS(3) versus multi-stage activation tandem mass spectrometry. Rapid communications in mass spectrometry : RCM\| PubMed ID: 18763275	2008
Improved methods for the enrichment and analysis of glycated peptides. Analytical chemistry\| PubMed ID: 18989935	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\| PubMed ID: 19093874	2009
The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery. Biomarkers in medicine\| PubMed ID: 19177179	2007
High Resolution Separations and Improved Ion Production and Transmission in Metabolomics. Trends in analytical chemistry : TRAC\| PubMed ID: 19255623	2008
A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics (Oxford, England)\| PubMed ID: 19535538	2009
Deletion of GPR40 impairs glucose-induced insulin secretion in vivo in mice without affecting intracellular fuel metabolism in islets. Diabetes\| PubMed ID: 19720802	2009
Performing comparative peptidomics analyses of Salmonella from different growth conditions. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20013197	2010
Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics. PLoS pathogens\| PubMed ID: 20062526	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\| PubMed ID: 20519132	2010
Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data. Journal of proteome research\| PubMed ID: 20831241	2010
Development of a fibrinogen-specific sandwich enzyme-linked immunosorbent assay microarray assay for distinguishing between blood plasma and serum samples. Analytical biochemistry\| PubMed ID: 21371419	2011
Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects. Journal of proteome research\| PubMed ID: 21612289	2011
Technologies and approaches to elucidate and model the virulence program of salmonella. Frontiers in microbiology\| PubMed ID: 21687430	2011
Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics (Oxford, England)\| PubMed ID: 21852304	2011
Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics. Rapid communications in mass spectrometry : RCM\| PubMed ID: 21910289	2011
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\| PubMed ID: 21917952	2011
Separation and classification of lipids using differential ion mobility spectrometry. Journal of the American Society for Mass Spectrometry\| PubMed ID: 21953096	2011
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\| PubMed ID: 22354571	2012
Chelation: a fundamental mechanism of action of AGE inhibitors, AGE breakers, and other inhibitors of diabetes complications. Diabetes\| PubMed ID: 22354928	2012
Dengue virus infection perturbs lipid homeostasis in infected mosquito cells. PLoS pathogens\| PubMed ID: 22457619	2012
Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. Journal of proteome research\| PubMed ID: 22578083	2012
In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids. Bioinformatics (Oxford, England)\| PubMed ID: 22592377	2012
Metabolomic response of human skin tissue to low dose ionizing radiation. Molecular bioSystems\| PubMed ID: 22610363	2012
Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Current topics in microbiology and immunology\| PubMed ID: 22886542	2013
A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics\| PubMed ID: 23019139	2013
A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Molecular bioSystems\| PubMed ID: 23147219	2013
Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes. The Journal of experimental medicine\| PubMed ID: 23277452	2013
Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. Journal of virology\| PubMed ID: 23365422	2013
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC bioinformatics\| PubMed ID: 23398735	2013
Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies. BioTechniques\| PubMed ID: 23477384	2013
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Molecular bioSystems\| PubMed ID: 23559334	2013
A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. PloS one\| PubMed ID: 23840608	2013
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC systems biology\| PubMed ID: 23895213	2013
A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. PloS one\| PubMed ID: 23935999	2013
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics (Oxford, England)\| PubMed ID: 23975765	2013
The succinated proteome. Mass spectrometry reviews\| PubMed ID: 24115015	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\| PubMed ID: 24753604	2014
Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions. Frontiers in microbiology\| PubMed ID: 24778628	2014
Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. mBio\| PubMed ID: 24846384	2014
The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation. Environmental microbiology reports\| PubMed ID: 24992538	2014
Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements. Molecular & cellular proteomics : MCP\| PubMed ID: 25129695	2014
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\| PubMed ID: 25254001	2014
Bayesian proteoform modeling improves protein quantification of global proteomic measurements. Molecular & cellular proteomics : MCP\| PubMed ID: 25433089	2014
Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. Journal of proteome research\| PubMed ID: 25855118	2015
Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis. PloS one\| PubMed ID: 25905710	2015
Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Frontiers in microbiology\| PubMed ID: 25941514	2015
Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus. Virology\| PubMed ID: 25965799	2015
A comprehensive collection of systems biology data characterizing the host response to viral infection. Scientific data\| PubMed ID: 25977790	2014
Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling. Journal of natural products\| PubMed ID: 26186142	2015
Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids. Biochemistry\| PubMed ID: 26271001	2015
Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. The Analyst\| PubMed ID: 26734689	2016
Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism. Cell host & microbe\| PubMed ID: 26867183	2016
Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. BMC genomics\| PubMed ID: 26911370	2016
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature biotechnology\| PubMed ID: 27504778	2016
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. mSystems\| PubMed ID: 27822525	2016
Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nature microbiology\| PubMed ID: 27892936	2016
Integrating ion mobility spectrometry into mass spectrometry-based exposome measurements: what can it add and how far can it go? Bioanalysis\| PubMed ID: 27921453	2017
MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. The Analyst\| PubMed ID: 28091625	2017
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\| PubMed ID: 28137868	2017
Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung. Scientific reports\| PubMed ID: 28145528	2017
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics (Oxford, England)\| PubMed ID: 28158427	2017
Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study. PloS one\| PubMed ID: 28245256	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\| PubMed ID: 28392013	2017
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. Bioinformatics (Oxford, England)\| PubMed ID: 28505286	2017
Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in . mBio\| PubMed ID: 28634240	2017
Sexual dimorphism in the fetal cardiac response to maternal nutrient restriction. Journal of molecular and cellular cardiology\| PubMed ID: 28641979	2017
Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell host & microbe\| PubMed ID: 29154144	2017
Measurement of Fructose-Asparagine Concentrations in Human and Animal Foods. Journal of agricultural and food chemistry\| PubMed ID: 29232127	2018
SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. Clinical mass spectrometry (Del Mar, Calif.)\| PubMed ID: 29276770	2016
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\| PubMed ID: 29339515	2018
Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. American journal of human genetics\| PubMed ID: 29478781	2018
Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut. Infection and immunity\| PubMed ID: 29483291	2018
Time-resolved Proteome Profiling of Normal Lung Development. American journal of physiology. Lung cellular and molecular physiology\| PubMed ID: 29516783	2018
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 Rhizo... International journal of systematic and evolutionary microbiology\| PubMed ID: 29580321	2018
QC-ART: A tool for real-time quality control assessment of mass spectrometry-based proteomics data. Molecular & cellular proteomics : MCP\| PubMed ID: 29666158	2018