Trans-Proteomic Pipeline

Trans-Proteomic Pipeline

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 [http://tools.proteomecenter.org/wiki/index.php?title=Software:PeptideProphet PeptideProphet] , [http://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet ProteinProphet] , ASAPRatio, XPRESS and Libra.

Please see the [http://tools.proteomecenter.org/wiki/ TPP Wiki] for the most up-to-date information, including download information.

The TPP is directly available from the [http://www.sourceforge.net/projects/sashimi Sashimi project] . TPP components are also included in other commercial and non-commercial sysems, including:
* CPAS [http://cpas.fhcrc.org/]
* Insilicos Proteomics Pipeline [http://www.insilicos.com/IPP]
* Proteus [http://www.genologics.com/products/proteus/index.php]

References

* Keller A, Nesvizhskii A, Kolker E, and Aebersold R. (2002) " [http://www.proteomecenter.org/PDFs/Keller.AnalChem.02.pdf|Empirical 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) " [http://www.proteomecenter.org/PDFs/Nesvi.stat.model.analchem.03.pdf|A statistical model for identifying proteins by tandem mass spectrometry.] " Anal Chem 75:4646-58


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