JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

UniNovo: a universal tool for de novo peptide sequencing

(2013) Kyowon Jeong et al.   BIOINFORMATICS

A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra

(2013) Craig D. Wenger et al.   JOURNAL OF PROTEOME RESEARCH

LuciPHOr: Algorithm for Phosphorylation Site Localization with False Localization Rate Estimation Using Modified Target-Decoy Approach

(2013) Damian Fermin et al.   MOLECULAR & CELLULAR PROTEOMICS

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

False discovery rates in spectral identification

(2012) Kyowon Jeong et al.   BMC BIOINFORMATICS

Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment

(2012) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Computational and Statistical Analysis of Protein Mass Spectrometry Data

(2012) William Stafford Noble et al.   PLoS Computational Biology

Rapid and Reproducible Single-Stage Phosphopeptide Enrichment of Complex Peptide Mixtures: Application to General and Phosphotyrosine-Specific Phosphoproteomics Experiments

(2011) Arminja N. Kettenbach et al.   ANALYTICAL CHEMISTRY

The Problem with Peptide Presumption and Low Mascot Scoring

(2011) Bret Cooper   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Editorial: From Data to Results

(2011) Ruedi Aebersold   MOLECULAR & CELLULAR PROTEOMICS

A Face in the Crowd: Recognizing Peptides Through Database Search

(2011) Jimmy K. Eng et al.   MOLECULAR & CELLULAR PROTEOMICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

(2010) Chongle Pan et al.   BMC BIOINFORMATICS

Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies

(2010) Stephane Houel et al.   JOURNAL OF PROTEOME RESEARCH

pNovo:De novoPeptide Sequencing and Identification Using HCD Spectra

(2010) Hao Chi et al.   JOURNAL OF PROTEOME RESEARCH

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematical Optimization of Reverse-Phase Chromatography for Shotgun Proteomics

(2009) Ping Xu et al.   JOURNAL OF PROTEOME RESEARCH

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

(2009) Alexander W Bell et al.   NATURE METHODS

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

(2008) Christopher Y. Park et al.   JOURNAL OF PROTEOME RESEARCH

DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

(2008) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH