An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates

Large Improvements in MS/MS-Based Peptide Identification Rates using a Hybrid Analysis

(2011) William R. Cannon et al.   JOURNAL OF PROTEOME RESEARCH

QuickMod: A Tool for Open Modification Spectrum Library Searches

(2011) Erik Ahrné et al.   JOURNAL OF PROTEOME RESEARCH

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library

(2011) Chia-Yu Yen et al.   MOLECULAR & CELLULAR PROTEOMICS

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

(2010) Sujun Li et al.   ANALYTICAL CHEMISTRY

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

(2010) Ding Ye et al.   BIOINFORMATICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets

(2010) Eric W. Deutsch et al.   PROTEOMICS

A Refined Method To Calculate False Discovery Rates for Peptide Identification Using Decoy Databases

(2009) Pedro Navarro et al.   JOURNAL OF PROTEOME RESEARCH

Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics

(2009) Henry Lam et al.   JOURNAL OF PROTEOME RESEARCH

Post-acquisition ETD spectral processing for increased peptide identifications

(2009) David M. Good et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

(2009) Bernhard Y. Renard et al.   PROTEOMICS

How specific is my SRM?: The issue of precursor and product ion redundancy

(2009) Jamie Sherman et al.   PROTEOMICS

A simple workflow to increase MS2 identification rate by subsequent spectral library search

(2009) Erik Ahrné et al.   PROTEOMICS

The effect of interfering ions on search algorithm performance for electron-transfer dissociation data

(2009) David M. Good et al.   PROTEOMICS

Unrestricted identification of modified proteins using MS/MS

(2009) Erik Ahrné et al.   PROTEOMICS

Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics

(2008) Guanghui Wang et al.   ANALYTICAL CHEMISTRY

A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications

(2008) Jayson A. Falkner et al.   JOURNAL OF PROTEOME RESEARCH

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

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

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