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Comet: An open-source MS/MS sequence database search tool

Proteomics (Weinheim), 2013-01, Vol.13 (1), p.22-24

2013

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Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics

Journal of proteome research, 2020-05, Vol.19 (5), p.2026-2034

2020

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Extending Comet for Global Amino Acid Variant and Post‐Translational Modification Analysis Using the PSI Extended FASTA Format

Proteomics (Weinheim), 2020-11, Vol.20 (21-22), p.e1900362-n/a

2020

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In Vivo Conformational Dynamics of Hsp90 and Its Interactors

Cell chemical biology, 2016-06, Vol.23 (6), p.716-726

2016

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iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

Molecular & cellular proteomics, 2011-12, Vol.10 (12), p.M111.007690, Article M111.007690

2011

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guided tour of the Trans-Proteomic Pipeline

Proteomics (Weinheim), 2010-03, Vol.10 (6), p.1150-1159

2010

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A Face in the Crowd: Recognizing Peptides Through Database Search

Molecular & cellular proteomics, 2011-11, Vol.10 (11), p.R111.009522-R111.009522, Article R111.009522

2011

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Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry

Structure (London), 2015-04, Vol.23 (4), p.762-773

2015

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In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075

Nature communications, 2016-11, Vol.7 (1), p.13414-14, Article 13414

2016

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Development and validation of a spectral library searching method for peptide identification from MS/MS

Proteomics (Weinheim), 2007-03, Vol.7 (5), p.655-667

2007

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Building consensus spectral libraries for peptide identification in proteomics

Nature methods, 2008-10, Vol.5 (10), p.873-875

2008

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General framework for developing and evaluating database scoring algorithms using the TANDEM search engine

Bioinformatics, 2006-11, Vol.22 (22), p.2830-2832

2006

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A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

PloS one, 2016-12, Vol.11 (12), p.e0167547-e0167547

2016

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Proteomics Standards Initiative Extended FASTA Format

Journal of proteome research, 2019-06, Vol.18 (6), p.2686-2692

2019

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An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

Proteomics (Weinheim), 2005-08, Vol.5 (13), p.3475-3490

2005

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The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5

Nature (London), 2001-04, Vol.410 (6832), p.1099-1103

2001

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A common open representation of mass spectrometry data and its application to proteomics research

Nature biotechnology, 2004-11, Vol.22 (11), p.1459-1466

2004

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Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry

Nature methods, 2005-08, Vol.2 (8), p.591-598

2005

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The Fasted/Fed Mouse Metabolic Acetylome: N6-Acetylation Differences Suggest Acetylation Coordinates Organ-Specific Fuel Switching

Journal of proteome research, 2011-09, Vol.10 (9), p.4134-4149

2011

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Sites of ubiquitin attachment in Saccharomyces cerevisiae

Proteomics (Weinheim), 2012-01, Vol.12 (2), p.236-240

2012

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Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Journal of proteome research, 2011-06, Vol.10 (6), p.2882-2888

2011

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Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer

Journal of proteome research, 2007-10, Vol.6 (10), p.3962-3975

2007

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Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

Proceedings of the National Academy of Sciences - PNAS, 2013-02, Vol.110 (9), p.3645-3650

2013

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A Deeper Look into Comet—Implementation and Features

Journal of the American Society for Mass Spectrometry, 2015-11, Vol.26 (11), p.1865-1874

2015

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Human Plasma PeptideAtlas

Proteomics (Weinheim), 2005-08, Vol.5 (13), p.3497-3500

2005

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Comet: An open-source MS/MS sequence database search tool

Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics

Extending Comet for Global Amino Acid Variant and Post‐Translational Modification Analysis Using the PSI Extended FASTA Format

In Vivo Conformational Dynamics of Hsp90 and Its Interactors

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

guided tour of the Trans-Proteomic Pipeline

A Face in the Crowd: Recognizing Peptides Through Database Search

Probing the Protein Interaction Network of Pseudomonas aeruginosa Cells by Chemical Cross-Linking Mass Spectrometry

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075

Development and validation of a spectral library searching method for peptide identification from MS/MS

Building consensus spectral libraries for peptide identification in proteomics

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

Proteomics Standards Initiative Extended FASTA Format

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5

A common open representation of mass spectrometry data and its application to proteomics research

Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry

The Fasted/Fed Mouse Metabolic Acetylome: N6-Acetylation Differences Suggest Acetylation Coordinates Organ-Specific Fuel Switching

Sites of ubiquitin attachment in Saccharomyces cerevisiae

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

A Deeper Look into Comet—Implementation and Features

Human Plasma PeptideAtlas

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