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.
Software Components
Probability Assignment and Validation
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.[4] The initial PeptideProphet used a fit of a Gaussian distribution for the correct identifications and a fit of a gamma distribution for the incorrect identification. 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.[5] In the PeptideProphet, specifying a decoy tag will use the variable component mixture model while selecting a non-parametric model will use the semi-parametric mixture model.
ProteinProphet identifies proteins based on the results of PeptideProphet.[6]
Mayu performs statistical validation of protein identification by estimating a false discovery rate (FDR) on protein level.[7]
Spectral library handling
The SpectraST tool is able to generate spectral libraries and search datasets using these libraries.[8]
^Keller, A; Nesvizhskii, A; Kolker, E; Aebersold, R. (2002). "Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search". Anal Chem. 74 (20): 5383–5392. doi:10.1021/ac025747h. PMID12403597.