Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis

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

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Peptide Identification from Mixture Tandem Mass Spectra

(2010) Jian Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets

(2010) Kang Ning et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Correlation between y-Type Ions Observed in Ion Trap and Triple Quadrupole Mass Spectrometers

(2009) Carly A. Sherwood et al.   JOURNAL OF PROTEOME RESEARCH

MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly

(2009) Carly A. Sherwood 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

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

(2009) Erik Ahrné et al.   PROTEOMICS

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

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

A Simulated MS/MS Library for Spectrum-to-spectrum Searching in Large Scale Identification of Proteins

(2008) Chia-Yu Yen et al.   MOLECULAR & CELLULAR PROTEOMICS

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH