X!TandemPipeline 3.4.3

X!TandemPipeline is a free software (GPL v3) that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

main features

graphical user interface


gouping algorithm

Our grouping algorithm removes non informative redundant informations from your dataset and builds clusters of proteins (groups and subgroups). Redundancy of protein databases is fully filtered as follows :
  • proteins identified without specific peptides compared to others are eliminated
  • proteins identified with the same pool of peptides are assembled (subgroups)
  • proteins are grouped by functions (identified with at least one common peptide), and the specific peptides for each sub-group of proteins are higlighted


X!TandemPipeline was developped to be fast, with a low memory footprint.
For example, given a common dataset :
  • 43 complex biological samples (whole yeast protein extraction)
  • corresponding to 1728 identified proteins
  • and 292737 MS/MS spectrums
would give on a basic computer (1,4Go RAM, 3Ghz CPU) :
  • 1353 groups of proteins (same protein function, at least one common peptide)
  • 1490 subgroups of proteins (each protein sharing the same set of peptides)
  • 81 seconds total runtime to read, filter and group the 43 MS identification files
  • 28 seconds only to filter and group


Many thanks to the Global Proteome Machine organisation (the GPM) that develops the Xtandem free search engine software.
Many thanks to Kenny Helsens for the MascotDatFile free java library to parse Mascot (Matrix Science) MS/MS search results.
Many thanks to SourceSup, for effectively hosting the X!TandemPipeline project.