A collection of open source applications for mass spectrometry data mining

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

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

EasyProt — An easy-to-use graphical platform for proteomics data analysis

(2012) Florent Gluck et al.   Journal of Proteomics

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

Characterization of the Human Plasma Phosphoproteome Using Linear Ion Trap Mass Spectrometry and Multiple Search Engines

(2009) Montserrat Carrascal et al.   JOURNAL OF PROTEOME RESEARCH

Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags

(2009) Loïc Dayon et al.   Journal of Proteomics

Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses

(2009) Paul A. Rudnick et al.   MOLECULAR & CELLULAR PROTEOMICS

LymPHOS: Design of a phosphosite database of primary human T cells

(2009) David Ovelleiro et al.   PROTEOMICS

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

Phosphorylation Analysis of Primary Human T Lymphocytes Using Sequential IMAC and Titanium Oxide Enrichment

(2008) Montserrat Carrascal et al.   JOURNAL OF PROTEOME RESEARCH

OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine

(2008) Ravi Tharakan et al.   PROTEOMICS