List of works - Matthew E Monroe

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

scientific article

A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy

scientific article

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

scientific article published on 21 April 2021

A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

scientific article published on 15 July 2011

An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells

scientific article

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 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

Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition

scientific article published on 12 October 2007

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments

scientific article

Comparative bacterial proteomics: analysis of the core genome concept

scientific article

Comparative omics-driven genome annotation refinement: application across Yersiniae

scientific article

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions

scientific article published on 19 January 2008

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

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

Endogenous 3,4-dihydroxyphenylalanine and dopaquinone modifications on protein tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical

scientific article

Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations.

scientific article

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

scientific article

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions

scientific article published on 30 December 2020

Improved LC-MS/MS spectral counting statistics by recovering low-scoring spectra matched to confidently identified peptide sequences

scientific article

Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information.

scientific article published in July 2006

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data

scientific article

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

scientific article published on 19 April 2008

MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features

scientific article published on 26 February 2008

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

scientific article published on 16 January 2018

Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration

scientific article

Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress

scientific article published on 17 August 2021

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

Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation.

scientific article published in May 2006

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

scientific article

Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics

scientific article

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation

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

Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production

scientific article published on 9 May 2007

Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography.

scientific article published on 12 September 2008

Region-specific protein abundance changes in the brain of MPTP-induced Parkinson's disease mouse model

scientific article

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline

scientific article

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

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

scientific article published on 16 January 2007

The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage

scientific article published on 16 April 2008

The utility of accurate mass and LC elution time information in the analysis of complex proteomes

scientific article published on August 2005

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

scientific article published on 6 January 2016

List of works by Matthew E Monroe

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

A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy

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

A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells

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

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

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

Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments

Comparative bacterial proteomics: analysis of the core genome concept

Comparative omics-driven genome annotation refinement: application across Yersiniae

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions

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

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

Endogenous 3,4-dihydroxyphenylalanine and dopaquinone modifications on protein tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical

Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (μFAIMS/IMS-MS) separations.

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions

Improved LC-MS/MS spectral counting statistics by recovering low-scoring spectra matched to confidently identified peptide sequences

Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information.

Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features

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

Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration

Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress

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

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

Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation.

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics

Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation

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

Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production

Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography.

Region-specific protein abundance changes in the brain of MPTP-induced Parkinson's disease mouse model

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline

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

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

The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage

The utility of accurate mass and LC elution time information in the analysis of complex proteomes

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