The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center.
The TPP includes PeptideProphet,[2] ProteinProphet,[3] ASAPRatio, XPRESS and Libra.
PeptideProphet performs statistical validation of peptide-spectra-matches (PSM) using the results of search engines by estimating a false discovery rate (FDR) on PSM level.
A later modification of the program allowed the usage of a target-decoy approach, using either a variable component mixture model or a semi-parametric mixture model.
ProteinProphet identifies proteins based on the results of PeptideProphet.