A guided tour of the Trans-Proteomic Pipeline

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Computational Biology
  • Databases, Protein*
  • Information Storage and Retrieval
  • Isotope Labeling
  • Proteomics / methods*
  • Sequence Analysis, Protein
  • Software*
  • Tandem Mass Spectrometry