X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers

J Proteome Res. 2008 Jan;7(1):293-9. doi: 10.1021/pr0701198. Epub 2007 Sep 29.


The widespread use of mass spectrometry for protein identification has created a demand for computationally efficient methods of matching mass spectrometry data to protein databases. A search using X!Tandem, a popular and representative program, can require hours or days to complete, particularly when missed cleavages and post-translational modifications are considered. Existing techniques for accelerating X!Tandem by employing parallelism are unsatisfactory for a variety of reasons. The paper describes a parallelization of X!Tandem, called X!!Tandem, that shows excellent speedups on commodity hardware and produces the same results as the original program. Furthermore, the parallelization technique used is unusual and potentially useful for parallelizing other complex programs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Methods
  • Protein Processing, Post-Translational
  • Proteins / analysis*
  • Software / standards*
  • Tandem Mass Spectrometry*
  • Time Factors


  • Proteins