Trans-Proteomic Pipeline

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The Trans-Proteomic Pipeline (TPP) is a widely-used open source proteomics data analysis pipeline developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group. TPP includes PeptideProphet, ProteinProphet, ASAPRatio, XPRESS and Libra.

TPP is directly available from the Sashimi project [1]. TPP components are also included in other commercial and non-commercial sysems, including:

• CPAS [2]
• Insilicos Proteomics Pipeline [3]
• Proteus [4]

[edit] References

• Keller A, Nesvizhskii A, Kolker E, and Aebersold R. (2002) "statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search." Anal Chem74:5383-5392.
• Nesvizhskii AI, Keller A, Kolker E, Aebersold R. (2003) "statistical model for identifying proteins by tandem mass spectrometry." Anal Chem 75:4646-58