COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

Virtual Expert Mass Spectrometrist: iTRAQ tool for database-dependent search, quantitation and result storage

(2010) Eva Rodríguez-Suárez et al.   PROTEOMICS

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

(2010) Eric W. Deutsch et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Comparison of Novel Decoy Database Designs for Optimizing Protein Identification Searches Using ABRF sPRG2006 Standard MS/MS Data Sets

(2009) Luca Bianco et al.   JOURNAL OF PROTEOME RESEARCH

The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data

(2009) Jari Häkkinen et al.   JOURNAL OF PROTEOME RESEARCH

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh 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

Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags

(2008) Loïc Dayon et al.   ANALYTICAL CHEMISTRY

An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data

(2008) Lukas N. Mueller et al.   JOURNAL OF PROTEOME RESEARCH

Peptide and Protein Quantification Using iTRAQ with Electron Transfer Dissociation

(2008) D PHANSTIEL et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

Decision tree–driven tandem mass spectrometry for shotgun proteomics

(2008) Danielle L Swaney et al.   NATURE METHODS

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools

(2007) John Klimek et al.   JOURNAL OF PROTEOME RESEARCH

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

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

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

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