List of works by Tom Metz

<i>Chespa</i>: Streamlining Expansive Chemical Space Evaluation of Molecular Sets

scientific article published on 07 December 2020

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

scientific article

A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry ⬇️

scientific article

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.

scientific article

A compendium of multi-omics data illuminating host responses to lethal human virus infections

scientific article published in 2024

A comprehensive collection of systems biology data characterizing the host response to viral infection.

scientific article

A global lipid map defines a network essential for Zika virus replication

scientific article published on 21 July 2020

A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants

scientific article published in 2022

A multi-omic systems approach to elucidating Yersinia virulence mechanisms.

scientific article

A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses

scientific article

A perspective on the Maillard reaction and the analysis of protein glycation by mass spectrometry: probing the pathogenesis of chronic disease

scientific article published on February 2009

A post-Amadori inhibitor pyridoxamine also inhibits chemical modification of proteins by scavenging carbonyl intermediates of carbohydrate and lipid degradation

scientific article published on 29 November 2001

A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases

scientific article published on 21 April 2021

A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling

scientific article

A statistical framework for protein quantitation in bottom-up MS-based proteomics.

scientific article published on 17 June 2009

An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells

scientific article published on 22 May 2020

Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS(3) versus multi-stage activation tandem mass spectrometry

scientific article published on October 2008

Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides

scientific article

Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset.

scientific article published on 20 December 2007

Application of the accurate mass and time tag approach in studies of the human blood lipidome.

scientific article published on 07 May 2008

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

scientific article published on 09 November 2020

Automated 20 kpsi RPLC-MS and MS/MS with Chromatographic Peak Capacities of 1000−1500 and Capabilities in Proteomics and Metabolomics

scientific article published in 2005

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

scientific article published on 16 August 2014

Bayesian proteoform modeling improves protein quantification of global proteomic measurements.

scientific article

Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling

scientific article published in 2007

Characterization of the human pancreatic islet proteome by two-dimensional LC/MS/MS

scientific article

Characterizing the lipid and metabolite changes associated with placental function and pregnancy complications using ion mobility spectrometry-mass spectrometry and mass spectrometry imaging.

scientific article published on 29 March 2017

Chelation: a fundamental mechanism of action of AGE inhibitors, AGE breakers, and other inhibitors of diabetes complications

scientific article published on March 2012

Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data

scientific article

Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

scientific article

Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects

scientific article

DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data

scientific article published in 2022

Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae ⬇️

scientific article

Deletion of GPR40 impairs glucose-induced insulin secretion in vivo in mice without affecting intracellular fuel metabolism in islets

scientific article published on 31 August 2009

Dengue virus infection perturbs lipid homeostasis in infected mosquito cells

scientific article

Development of a fibrinogen-specific sandwich enzyme-linked immunosorbent assay microarray assay for distinguishing between blood plasma and serum samples

scientific article

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

scientific article

Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics

scientific article

Effect of antioxidants and ACE inhibition on chemical modification of proteins and progression of nephropathy in the streptozotocin diabetic rat.

scientific article

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

scientific article published on 29 December 2007

Enrichment and analysis of nonenzymatically glycated peptides: boronate affinity chromatography coupled with electron-transfer dissociation mass spectrometry

scientific article published on 09 May 2007

Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples

scientific article published on 20 August 2019

Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics

scientific article

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

scientific article

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics

scientific article published on March 2008

ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries

scientific article published on 06 March 2019

Improved methods for the enrichment and analysis of glycated peptides

scientific article published on December 2008

Improved quality control processing of peptide-centric LC-MS proteomics data

scientific article

In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids.

scientific article

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing

scientific article published on 26 June 2019

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.

scientific article

Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples

scientific article published on 29 April 2019

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

scientific article published on 16 January 2018

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

scientific article published on 10 May 2016

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

scientific article published on 16 January 2017

Making Broad Proteome Protein Measurements in 1−5 min Using High-Speed RPLC Separations and High-Accuracy Mass Measurements

scientific article published in 2005

Mass Spectrometry Adduct Calculator

scientific article published in 2021

Mass spectrometric analysis of glucose-modified ribonuclease

scientific article

Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury

scientific article published on 06 August 2013

MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments

scientific article published in 2021

Metabolomic response of human skin tissue to low dose ionizing radiation

scientific article published on 18 May 2012

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

scientific article

Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis

scientific article published on 15 November 2017

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis

scientific article

New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

scientific article published on 06 February 2019

Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses.

scientific article

Performing comparative peptidomics analyses of Salmonella from different growth conditions

scientific article published on January 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

scientific article

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

scientific article (publication date: 2014)

Prediction of the development of islet autoantibodies through integration of environmental, genetic, and metabolic markers

scientific article published on 22 July 2020

Proteomic analysis of arginine adducts on glyoxal-modified ribonuclease.

scientific article

Proteomic analysis of the site specificity of glycation and carboxymethylation of ribonuclease

scientific article published in September 2003

Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus.

scientific article published on 15 May 2015

Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes

scientific article published on 09 April 2008

Pyridoxamine traps intermediates in lipid peroxidation reactions in vivo: evidence on the role of lipids in chemical modification of protein and development of diabetic complications

scientific article published on 15 August 2003

Pyridoxamine, an inhibitor of advanced glycation and lipoxidation reactions: a novel therapy for treatment of diabetic complications

scientific article

QC-ART: A tool for real-time quality control assessment of mass spectrometry-based proteomics data.

scientific article published on 17 April 2018

Quantum Chemistry Calculations for Metabolomics

scientific article published in 2021

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards.

scientific article published on 19 December 2018

Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells

scientific article published on 30 January 2013

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

scientific article published on 22 April 2015

Role of lipids in chemical modification of proteins and development of complications in diabetes

scientific article published on December 2003

SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes

scientific article published on 06 September 2019

Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes ⬇️

scientific article published on 5 April 2013

Separation and classification of lipids using differential ion mobility spectrometry

scientific article

Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies

scientific article

Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes

scientific article published on 31 December 2012

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

scientific article (publication date: 9 August 2016)

Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling

scientific article

Similarity Downselection: Finding the n Most Dissimilar Molecular Conformers for Reference-Free Metabolomics

scientific article published in 2023

Simulated Night-Shift Schedule Disrupts the Plasma Lipidome and Reveals Early Markers of Cardiovascular Disease Risk

scientific article published on 21 May 2022

Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland

scientific article published in 2022

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

scientific article

Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network

scientific article published on 05 December 2019

Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling

scientific article published on January 2013

Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis

scientific article

Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.

scientific article published on 16 January 2007

Technologies and approaches to elucidate and model the virulence program of salmonella

scientific article

Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics

scientific article (publication date: 2010)

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery

scientific article published on 13 March 2020

The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation

scientific article

The future of liquid chromatography-mass spectrometry (LC-MS) in metabolic profiling and metabolomic studies for biomarker discovery

scientific article published on June 2007

The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes

scientific article published on 24 June 2019

The succinated proteome

scientific article

Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry.

scientific article published on 6 January 2016

Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites

scientific article published on 12 November 2019

yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development

scientific article published on 16 June 2020

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