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A guided tour of the Trans-Proteomic Pipeline.

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.

SUBMITTER: Deutsch EW

PROVIDER: S-EPMC3017125 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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A guided tour of the Trans-Proteomic Pipeline.

Deutsch Eric W EW Mendoza Luis L Shteynberg David D Farrah Terry T Lam Henry H Tasman Natalie N Sun Zhi Z Nilsson Erik E Pratt Brian B Prazen Bryan B Eng Jimmy K JK Martin Daniel B DB Nesvizhskii Alexey I AI Aebersold Ruedi R

Proteomics 20100301 6

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 ...[more]

PMID: 20101611

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