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

Comment on “Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies”

(2011) Marshall Bern et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

Better score function for peptide identification with ETD MS/MS spectra

(2010) Xiaowen Liu et al.   BMC BIOINFORMATICS

Improved Peptide Identification for Proteomic Analysis Based on Comprehensive Characterization of Electron Transfer Dissociation Spectra

(2010) Rui-Xiang Sun 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

Protein abundances are more conserved than mRNA abundances across diverse taxa

(2010) Jon M. Laurent et al.   PROTEOMICS

Reanalysis ofTyrannosaurus rexMass Spectra

(2009) Marshall Bern et al.   JOURNAL OF PROTEOME RESEARCH

Accurate and Sensitive Peptide Identification with Mascot Percolator

(2009) Markus Brosch et al.   JOURNAL OF PROTEOME RESEARCH

Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies

(2009) Logan J. Everett 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

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