Bioinformatics for Comparative Proteomics

Volume 694 of the series Methods in Molecular Biology pp 169-189


Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline

  • Andrew KellerAffiliated withRosetta Biosoftware Email author 
  • , David ShteynbergAffiliated withInstitute for Systems Biology

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The LC-MS/MS shotgun proteomics workflow is widely used to identify and quantify sample peptides and proteins. The technique, however, presents a number of challenges for large-scale use, including the diverse raw data file formats output by mass spectrometers, the large false positive rate among peptide assignments to MS/MS spectra, and the loss of connectivity between identified peptides and the sample proteins that gave rise to them. Here we describe the Trans-Proteomic Pipeline, a freely available open source software suite that provides uniform analysis of LC-MS/MS data from raw data to quantified sample proteins. In a straightforward manner, users can extract MS/MS information from raw data of many instrument formats, submit them to search engines for peptide identification, validate the results to remove false hits, combine together results of multiple search engines, infer sample proteins that gave rise to the identified peptides, and perform quantitation at the peptide and protein levels.

Key words

Shotgun proteomics Freeware Machine learning Protein inference