M. Monroe

发表

Integrative Analysis of the Mitochondrial Proteome in Yeast

Ronald J. Moore, Ronald W. Davis, Richard D. Smith, 2004, PLoS biology.

Advances in proteomics data analysis and display using an accurate mass and time tag approach.

Richard D. Smith, M. Monroe, W. Qian, 2006, Mass spectrometry reviews.

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

Richard D. Smith, Navdeep Jaitly, M. Monroe, 2006, Analytical chemistry.

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.

Alan R. Dabney, Ronald J. Moore, Richard D. Smith, 2008, Analytical chemistry.

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

Navdeep Jaitly, Joshua N. Adkins, Richard D. Smith, 2008, Bioinform..

An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry

Navdeep Jaitly, Ian Gorton, Joshua N. Adkins, 2009, 2009 Fifth IEEE International Conference on e-Science.

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

Richard D. Smith, K. Anderson, M. Monroe, 2005, Journal of the American Society for Mass Spectrometry.

Mixed-effects statistical model for comparative LC-MS proteomics studies.

K. Anderson, M. Monroe, D. Daly, 2008, Journal of proteome research.

Proteogenomic Characterization of Endometrial Carcinoma

Peter B. McGarvey, Ying Wang, Li Ding, 2020, Cell.

Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry.

Tao Liu, Wei-Jun Qian, Richard D. Smith, 2012, Journal of proteome research.

Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach*S

Ronald J. Moore, Stephen J. Callister, Richard D. Smith, 2006, Molecular & Cellular Proteomics.

STEPS: A grid search methodology for optimized peptide identification filtering of MS/MS database search results

J. D. Sandoval, John D. Sandoval, Richard D. Smith, 2013, Proteomics.

Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

Gordon W. Slysz, Ronald J. Moore, Samuel H. Payne, 2014, Journal of proteome research.

Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample.

Ronald J. Moore, Richard D. Smith, Navdeep Jaitly, 2009, Journal of proteome research.

Quantitative Analysis of Human Immunodeficiency Virus Type 1-Infected CD4+ Cell Proteome: Dysregulated Cell Cycle Progression and Nuclear Transport Coincide with Robust Virus Production

Richard D. Smith, M. Katze, E. Chan, 2007, Journal of Virology.

A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements.

Ronald J. Moore, Thomas L. Fillmore, Richard D. Smith, 2018, Analytical Chemistry.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

Ronald J. Moore, Samuel H. Payne, Stefani N. Thomas, 2016, Cell.

Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets

Matthew E Monroe, Feng Yang, Samuel O Purvine, 2012, Proceedings of the National Academy of Sciences.

Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.

Ronald J Moore, Matthew E Monroe, Tao Liu, 2005, Journal of proteome research.

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

Meagan C. Burnet, Samuel H. Payne, Richard D. Smith, 2011, BMC Genomics.

Targeted Protein Degradation by Salmonella under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics*S

Matthew E Monroe, Fred Heffron, Thomas O Metz, 2007, Molecular & Cellular Proteomics.

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

Matthew E Monroe, Joel G Pounds, Richard C Zangar, 2005, Proteomics.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Gordon A Anderson, John R Yates, Monica Riley, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Enhancing bottom‐up and top‐down proteomic measurements with ion mobility separations

Ronald J Moore, Matthew E Monroe, Erin Shammel Baker, 2015, Proteomics.

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

Ronald J Moore, Matthew E Monroe, Thomas O Metz, 2016, The Analyst.

Improving N-glycan coverage using HPLC-MS with electrospray ionization at subambient pressure.

Ronald J. Moore, Scott R. Kronewitter, Richard D. Smith, 2012, Analytical chemistry.

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Jeffrey R. Whiteaker, Dana R. Valley, Karna L. Robinson, 2020, Cell.

Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142

Hans C. Bernstein, Natalie C. Sadler, Richard D. Smith, 2016, Applied and Environmental Microbiology.

Proteome Analyses of Strains Cyanothece ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp . Under Culture Conditions Resulting in Enhanced H 2 Production

Ronald J. Moore, Stephen J. Callister, Anil K. Shukla, 2015 .

Production 2 HConditions Resulting in Enhanced Cyanobacterium Cyanothece sp. under and PCC 7822 of the Diazotrophic Proteome Analyses of Strains ATCC 51142

Ronald J. Moore, Stephen J. Callister, Richard D. Smith, 2014 .

Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp. under Culture Conditions Resulting in Enhanced H2 Production

Ronald J. Moore, Stephen J. Callister, Anil K. Shukla, 2012, Applied and Environmental Microbiology.

Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry*

Gordon W. Slysz, J. D. Sandoval, Yehia M. Ibrahim, 2014, Molecular & Cellular Proteomics.

Quantitative proteomics identifies altered O‐GlcNAcylation of structural, synaptic and memory‐associated proteins in Alzheimer's disease

Anil K. Shukla, Richard D. Smith, M. Monroe, 2017, The Journal of pathology.

Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements

Yehia M. Ibrahim, Kevin L. Crowell, Samuel H. Payne, 2014, Journal of The American Society for Mass Spectrometry.

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry*

Yehia M. Ibrahim, Ronald J. Moore, Kristin E. Burnum-Johnson, 2016, Molecular & Cellular Proteomics.

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

Kristin E. Burnum-Johnson, Melanie T Odenkirk, M. Monroe, 2020, Biomolecules.

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

Lisa E. Gralinski, Kristin E. Burnum-Johnson, Kevin B. Walters, 2018, Proceedings of the National Academy of Sciences.

Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations

Kevin K. Anderson, Don Simone Daly, Matthew E. Monroe, 2004, METMBS.

Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes.

Stephen J. Callister, Richard D. Smith, T. Donohue, 2006, Journal of microbiological methods.

The fungal cultivar of leaf‐cutter ants produces specific enzymes in response to different plant substrates

Kristin E. Burnum-Johnson, Richard D. Smith, R. White, 2016, Molecular ecology.

A Method to Determine Lysine Acetylation Stoichiometries

Ronald J. Moore, Anil K. Shukla, Richard D. Smith, 2014, International journal of proteomics.

Ant Fungus Gardens Recalcitrant Plant Polymers in Leaf-Cutter Diverse Enzymes for the Degradation of Leucoagaricus gongylophorus Produces

Richard D. Smith, G. Weinstock, N. Gerardo, 2013 .

A Proteomic Study of HUPO’s Plasma Proteome Project Pilot Samples using an Accurate Mass and Time Tag Strategy

Richard D. Smith, D. Camp, M. Monroe, 2007 .

Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides.

Ronald J. Moore, Richard D. Smith, D. Camp, 2009, Analytical chemistry.

Resource Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities Graphical

Ronald J. Moore, Sara R. Savage, Richard D. Smith, 2022 .

GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization

Clay D. Hagler, Gordon W. Slysz, Ronald J. Moore, 2014, Analytical chemistry.

Enhancing Biological Analyses with Three Dimensional Field Asymmetric Ion Mobility , Low Field Drift Time Ion

Yehia M. Ibrahim, Richard D. Smith, M. Monroe, 2015 .

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

Yehia M. Ibrahim, Richard D. Smith, M. Monroe, 2015, The Analyst.

Comparative Phosphoproteomics Reveals Components of Host Cell Invasion and Post-transcriptional Regulation During Francisella Infection*

Richard D. Smith, M. Monroe, M. Gritsenko, 2013, Molecular & Cellular Proteomics.

Novel Ser/Thr protein phosphatase 5 (PP5) regulated targets during DNA damage identified by proteomics analysis.

Richard D. Smith, Navdeep Jaitly, D. Camp, 2010, Journal of proteome research.

Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation

Richard D. Smith, D. Camp, M. Monroe, 2010, PloS one.

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

Richard D. Smith, Navdeep Jaitly, M. Monroe, 2006, Analytical chemistry.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

Young-Mo Kim, Thomas O. Metz, Ryan S. Renslow, 2016, Clinical mass spectrometry.

DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets*

Gordon A. Anderson, Ashoka D. Polpitiya, Anoop M. Mayampurath, 2009, Molecular & Cellular Proteomics.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Lennart Martens, Stefano Toppo, Geoffrey C. Fox, 2013, Big Data.

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

Ronald J Moore, Matthew E Monroe, Athena A Schepmoes, 2010, Journal of proteome research.

An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies.

Gordon W. Slysz, Yehia M. Ibrahim, Kevin L. Crowell, 2017, International journal of mass spectrometry.

Muscle Segment Homeobox Genes Direct Embryonic Diapause by Limiting Inflammation in the Uterus*

Kristin E. Burnum-Johnson, A. Jegga, M. Monroe, 2015, The Journal of Biological Chemistry.

Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

Li Ding, Molly Brewer, Rui Zhao, 2020, Cell reports medicine.

Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans

Ronald J. Moore, Anil K. Shukla, M. Monroe, 2013, International journal of proteomics.

Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach*S

Ronald J Moore, Matthew E Monroe, Gordon A Anderson, 2005, Molecular & Cellular Proteomics.

– mass spectrometry voxelation integrated with high-throughput liquid Spatial mapping of protein abundances in the mouse brain by data

Richard D. Smith, Navdeep Jaitly, D. Camp, 2007 .

Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools.

Jeremy R. Ash, Melanie T Odenkirk, D. Fourches, 2020, Molecular omics.

High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model

Ronald J. Moore, Richard D. Smith, M. Monroe, 2014, PloS one.

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

Ronald J. Moore, Richard D. Smith, Navdeep Jaitly, 2007, Journal of proteome research.

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

Michael E. Miller, Ronald J. Moore, Kevin S. Smith, 2022, bioRxiv.

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

Michael E. Miller, Ronald J. Moore, Kevin S. Smith, 2022, bioRxiv.

Reversed‐phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

Ronald J. Moore, Richard D. Smith, D. Camp, 2011, Proteomics.

Nuclear Transport Coincide with Robust Virus

Richard D. Smith, M. Katze, T. Liu, 2007 .

Endogenous DOPA and Dopaquinone Modifications on Protein Tyrosine: Links to Mitochondrially-Derived Oxidative Stress via Hydroxyl Radical

Brianne Petritis, D. Camp, M. Monroe, 2010 .

Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry.

Matthew E Monroe, David G Camp, Wei-Jun Qian, 2013, Free radical biology & medicine.

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

Ronald J Moore, Matthew E Monroe, Nathan P Manes, 2008, Journal of proteome research.

Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR‐1 using LC‐MS based proteomics

Matthew E Monroe, Gordon A Anderson, James K Fredrickson, 2005, Proteomics.

Detection and identification of heme c-modified peptides by histidine affinity chromatography, high-performance liquid chromatography-mass spectrometry, and database searching.

Matthew E Monroe, Liang Shi, Eric D Merkley, 2012, Journal of proteome research.

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

Yehia M. Ibrahim, Richard D. Smith, Felicity F. Nielson, 2019, Analytical chemistry.

Dynamic Time-Warping Correction for Shifts in Ultrahigh Resolving Power Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations.

Yehia M. Ibrahim, Richard D. Smith, M. Monroe, 2021, Journal of the American Society for Mass Spectrometry.

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

Ronald J Moore, Navdeep Jaitly, Matthew E Monroe, 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

Richard D. Smith, S. Tringe, G. Weinstock, 2013, Applied and Environmental Microbiology.

Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-search Delta Score Strategy.

M. Monroe, W. Qian, P. Piehowski, 2020, Journal of proteome research.

Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-specific Redox Proteomics*

Ronald J. Moore, Richard D. Smith, M. Monroe, 2014, Molecular & Cellular Proteomics.

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

Qibin Zhang, Vladislav A Petyuk, Matthew E Monroe, 2011, Journal of proteome research.

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

Ronald J. Moore, Stefani N. Thomas, Richard D. Smith, 2018, Nature Protocols.

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

Vladislav A Petyuk, Matthew E Monroe, Athena A Schepmoes, 2010, Journal of proteome research.

Proteogenomic and metabolomic characterization of human glioblastoma.

Joshua F. McMichael, Sneha P. Couvillion, Matthew A. Wyczalkowski, 2021, Cancer cell.

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Guo Ci Teo, Allison P. Heath, Marilyn M. Li, 2020, Cell.

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

Ronald J. Moore, Stefani N. Thomas, Richard D. Smith, 2018, Nature Protocols.

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses.

Yehia M. Ibrahim, Ronald J. Moore, Kristin E. Burnum-Johnson, 2017, Annual review of analytical chemistry.

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

Ronald J. Moore, M. Monroe, K. Hixson, 2021, Frontiers in Plant Science.

Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data

Matthew E Monroe, Kelly G Stratton, Charles Ansong, 2019, Bioinform..

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Guo Ci Teo, Meghan C. Burke, Jeffrey R. Whiteaker, 2020, Cell.

Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome

Ronald J. Moore, Richard D. Smith, D. Camp, 2005, Proteomics.

Uterine deletion of Trp53 compromises antioxidant responses in the mouse decidua.

Yehia M. Ibrahim, Richard D. Smith, M. Monroe, 2012, Endocrinology.

Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome

Richard D. Smith, D. Camp, M. Monroe, 2004, Journal of Virology.

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Subha Madhavan, Peter B. McGarvey, Li Ding, 2019, Cell.

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

Ronald J. Moore, Richard D. Smith, D. Camp, 2008, Journal of proteome research.

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

Matthew E Monroe, Feng Yang, Xiuxia Du, 2008, Journal of proteome research.

Accounting for population variation in targeted proteomics.

Grant M Fujimoto, Samuel H Payne, Matthew E Monroe, 2014, Journal of proteome research.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Lennart Martens, Doron Lancet, Dmitrij Frishman, 2014, Omics : a journal of integrative biology.

Multidimensional proteome analysis of human mammary epithelial cells.

Ronald J Moore, Matthew E Monroe, David G Camp, 2004, Journal of proteome research.

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

Ying Xu, Ronald J Moore, Matthew E Monroe, 2006, Analytical chemistry.

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

Richard D. Smith, H. Wiley, D. Camp, 2009, Journal of proteome research.

Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry

Ronald J Moore, Matthew E Monroe, Marina A Gritsenko, 2005, Proteomics.

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

M. Monroe, B. Webb-Robertson, T. Metz, 2021, Scientific data.

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

Kevin B. Walters, Cameron P. Casey, Anil K. Shukla, 2017, Cell host & microbe.

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

Joshua N. Adkins, Lee Ann McCue, Kenneth J. Auberry, 2008, PloS one.

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

Qibin Zhang, Brian D. Aevermann, Brett E. Pickett, 2014, Scientific Data.

Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling.

Ronald J. Moore, Richard D. Smith, M. Monroe, 2010, Journal of proteome research.

High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex*

Richard D. Smith, D. Camp, M. Monroe, 2008, Journal of Biological Chemistry.

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

Joshua N. Adkins, Richard D. Smith, Don Simone Daly, 2008, Comput. Biol. Chem..

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

Ronald J Moore, Matthew E Monroe, Athena A Schepmoes, 2010, Journal of proteome research.

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Joshua N. Adkins, Scott N. Peterson, Charles Ansong, 2012, PloS one.

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

Ronald J Moore, Matthew E Monroe, Marina A Gritsenko, 2008, Journal of proteome research.

Ultra-sensitive, high throughput and quantitative proteomics measurements

Richard D. Smith, M. Monroe, G. Anderson, 2005 .

Spectral Archives: Extending Spectral Libraries to Analyze both Identified and Unidentified Spectra

Pavel A. Pevzner, Ari M. Frank, Gordon A. Anderson, 2011, Nature Methods.

Block design with common reference samples enables robust large-scale label-free quantitative proteome profiling.

Paul D Piehowski, Ronald J Moore, Vladislav A Petyuk, 2020, Journal of proteome research.

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

Richard D. Smith, D. Camp, M. Monroe, 2008, Journal of proteome research.

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies.

Young-Mo Kim, Karl K. Weitz, Yehia M. Ibrahim, 2017, Rapid communications in mass spectrometry : RCM.

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

Matthew E Monroe, Marina A Gritsenko, Kathie-Anne Walters, 2012, Hepatology.

Correcting systematic bias and instrument measurement drift with mzRefinery

Matthew Chambers, David L. Tabb, Matthew E. Monroe, 2015, Bioinform..

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

Alan R. Dabney, Richard D. Smith, Richard D. Smith, 2011, Analytical chemistry.

AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis.

Matthew E Monroe, Gordon A Anderson, Nikola Tolic, 2005, Methods of biochemical analysis.

VIPER: an advanced software package to support high-throughput LC-MS peptide identification

Navdeep Jaitly, Joshua N. Adkins, Richard D. Smith, 2007, Bioinform..

Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry.

Vladislav A Petyuk, Navdeep Jaitly, Matthew E Monroe, 2007, Genome research.

Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome.

Matthew E Monroe, Tao Liu, Lars J Kangas, 2005, Journal of proteome research.

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

Ronald J. Moore, M. Monroe, W. Qian, 2021, Redox biology.

Identification of shed proteins from chinese hamster ovary cells: Application of statistical confidence using human and mouse protein databases

Mamoun Ahram, M. Monroe, M. Ahram, 2005, Proteomics.

Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants

Ronald J. Moore, Kristin E. Burnum-Johnson, Richard D. Smith, 2015, PloS one.

An efficient data format for mass spectrometry-based proteomics

Matthew E Monroe, Gordon A Anderson, Anuj R Shah, 2010, Journal of the American Society for Mass Spectrometry.

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets

Brian L. LaMarche, Richard D. Smith, Gordon A. Anderson, 2013, Bioinform..

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Jian Ma, Thomas O. Metz, Ryan S. Renslow, 2017, Bioinform..

High Dynamic Range Characterization of the Trauma Patient Plasma Proteome*S

Ronald G. Tompkins, Tao Liu, Marina A. Gritsenko, 2006, Molecular & Cellular Proteomics.

Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data*

Paul D Piehowski, Ronald J Moore, Richard D Smith, 2018, Molecular & Cellular Proteomics.

Proteomic approaches to bacterial differentiation.

Stephen J. Callister, Richard D. Smith, M. Monroe, 2006, Journal of microbiological methods.

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles

Richard D. Smith, David W. Koppenaal, Marina A. Gritsenko, 2011, BMC Systems Biology.

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

Richard D. Smith, M. Monroe, V. Petyuk, 2008, Rapid communications in mass spectrometry : RCM.

PRISM: A data management system for high‐throughput proteomics

Nikola Tolić, Richard D Smith, Gary R Kiebel, 2006, Proteomics.

Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues.

Richard D. Smith, D. Camp, M. Monroe, 2008, Journal of proteome research.

Machine learning based prediction for peptide drift times in ion mobility spectrometry

Mudita Singhal, Khushbu Agarwal, Richard D. Smith, 2010, Bioinform..

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

Matthew E Monroe, Feng Yang, Ruihua Fang, 2006, Journal of proteome research.

Multi-omic Data Integration Links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response*

Richard D. Smith, M. Monroe, K. Hixson, 2013, Molecular & Cellular Proteomics.

Signatures for Mass Spectrometry Data Quality

Brian L. LaMarche, Landon H. Sego, Mark F. Tardiff, 2014, Journal of proteome research.

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

Navdeep Jaitly, Brian L. LaMarche, Richard D. Smith, 2013, BMC Bioinformatics.

Correction: Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Joshua N. Adkins, Scott N. Peterson, Charles Ansong, 2012, PLoS ONE.

Endogenous 3,4-Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine

Richard D. Smith, Brianne Petritis, Baowei Chen, 2010, Molecular & Cellular Proteomics.

In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics.

Matthew E Monroe, David G Camp, Wei-Jun Qian, 2013, Journal of proteome research.

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.

Evan A. Martin, M. Monroe, V. Petyuk, 2023, Journal of proteome research.

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

Kevin L. Crowell, John D. Sandoval, Stephen J. Callister, 2013, BMC Bioinformatics.

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

Ronald J. Moore, Richard D. Smith, D. Camp, 2010, Analytical chemistry.

Estimating probabilities of peptide database identifications to LC-FTICR-MS observations

Matthew E Monroe, Kevin K Anderson, Don S Daly, 2006, Proteome Science.

Identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation.

Ronald J. Moore, Richard D. Smith, M. Monroe, 2011, Analytical chemistry.

Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis.

Matthew E Monroe, Gordon A Anderson, Ruihua Fang, 2004, Omics : a journal of integrative biology.

Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry.

Paul D Piehowski, Vladislav A Petyuk, Samuel H Payne, 2013, International journal of mass spectrometry.

Proteome analyses of diazotrophic cyanobacteria Cyanothece ATCC 51142 and 1 PCC 7822 under culture conditions of enhanced H 2-production 2

Stephen J. Callister, Anil K. Shukla, Richard D. Smith, 2012 .

Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1.

Richard D. Smith, M. Monroe, M. Lipton, 2006, Journal of microbiological methods.

Erratum: Identification of proteins in human cytomegalovirus (HCMV) particles: The HCMV proteome (Journal of Virology (2004) 78:20 (10960-10966))

Richard D. Smith, D. Camp, M. Monroe, 2004 .

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

Ronald J. Moore, Richard D. Smith, M. Monroe, 2008, Analytical chemistry.

Proteogenomic insights suggest druggable pathways in endometrial carcinoma.

Matthew A. Wyczalkowski, Ratna R. Thangudu, Ronald J. Moore, 2023, Cancer cell.

Reversible cation response with a protein-modified nanopipette.

Alan R. Dabney, Gordon W. Slysz, Richard D. Smith, 2011, Analytical chemistry.

Temporal dynamics of the multi-omic response to endurance exercise training across tissues

Michael E. Miller, Ronald J. Moore, Ian R. Lanza, 2023, bioRxiv.

Rapid sample processing for LC-MS-based quantitative proteomics using high intensity focused ultrasound.

Ronald J. Moore, Richard D. Smith, D. Camp, 2008, Journal of proteome research.

Human cerebrospinal fluid contains diverse lipoprotein subspecies enriched in proteins implicated in central nervous system health

W. S. Davidson, Nathaniel J. Merrill, J. Quinn, 2023, Science advances.

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies.

Yehia M. Ibrahim, Ronald J. Moore, Kristin E. Burnum-Johnson, 2017, Rapid communications in mass spectrometry : RCM.

Machine learning based prediction for peptide drift times in ion mobility spectrometry

Yehia M. Ibrahim, Richard D. Smith, M. Monroe, 2010, Bioinform..

Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information.

Richard D Smith, Gary R Kiebel, Ken J Auberry, 2010, Journal of proteomics & bioinformatics.

Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling.

Ronald J. Moore, Richard D. Smith, M. Monroe, 2010, Journal of proteome research.

Deciphering ApoE Genotype-Driven Proteomic and Lipidomic Alterations in Alzheimer's Disease Across Distinct Brain Regions.

Kristin E. Burnum-Johnson, M. Monroe, C. Nicora, 2024, Journal of proteome research.

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

R. Mural, S. Somiari, M. Monroe, 2024, Breast cancer research : BCR.

Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

Gordon W. Slysz, Grant M. Fujimoto, M. Ellis, 2014, Journal of proteome research.