A guided tour of the Trans‐Proteomic Pipeline

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.

• NI
  National Institutes of Health

  Awards: R44HG004537, N01-HV-28179
• NH
  National Heart, Lung, and Blood Institute

  Award: N01-HV-28179