PeptideProphet, ProteinProphet, and iProphet
Core components of the open source data analysis pipeline (Trans-Proteomic Pipeline, TPP) for primary processing of mass spectrometry-based proteomic data. PeptideProphet performs statistical validation of peptide identifications from tandem mass (MS/MS) spectra. It can analyze the results of all most commonly used MS/MS database search tools, including SEQUEST, MASCOT, and X! Tandem. iProphet further improves upon PeptideProphet modeling and allows integration of multiple search tools. ProteinProphet continues the analysis at the protein level. It accurately addresses the protein inference problem of shared peptides (peptides present in multiple protein database entries), estimates the number of correct protein identifications in a dataset, as well as the false discovery rates (FDR). TPP also includes tools for viewing raw LC/MS data, peptide quantification, spectral quality scoring, and other useful tools. The pipeline is maintained by the Seattle Proteomics Center at the Institute for Systems Biology http://www.systemsbiology.org/.
PeptideProphet: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Anal Chem. 2002 Oct 15;74(20):5383-92.
ProteinProphet: A statistical model for identifying proteins by tandem mass spectrometry. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. Anal Chem. 2003 Sep 1;75(17):4646-58.
iProphet: In preparation.
Review: Analysis and validation of proteomic data generated by tandem mass spectrometry. Nesvizhskii AI, Vitek O, Aebersold R. Nat Methods. 2007 Oct;4(10):787-97.
Google Discussion Group: http://groups.google.com/group/spctools-discuss