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Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375.

A guided tour of the Trans-Proteomic Pipeline.

Author information

1
Institute for Systems Biology, Seattle, WA, USA. edeutsch@systemsbiology.org

Abstract

The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.

PMID:
20101611
PMCID:
PMC3017125
DOI:
10.1002/pmic.200900375
[Indexed for MEDLINE]
Free PMC Article

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