The Trans-Proteomic Pipeline (TPP) is a widely used freely available open-source proteomics data analysis pipeline developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra.
Please see the TPP Wiki for the most up-to-date information, including download information.
The TPP is directly available from the Sashimi project. TPP components are also included in other commercial and non-commercial systems, including:
- Keller A, Nesvizhskii A, Kolker E, and Aebersold R. (2002) "Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search." Anal Chem 74:5383–5392.
- Nesvizhskii AI, Keller A, Kolker E, Aebersold R. (2003) "A statistical model for identifying proteins by tandem mass spectrometry." Anal Chem 75:4646-58
- Keller A, Eng J, Zhang N, Li XJ. Aebersold R. (2005) "A uniform proteomics MS/MS analysis platform utilizing open XML file formats." Molecular Systems Biology 2:1–8