DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

J Proteome Res. 2002 Jan-Feb;1(1):21-6. doi: 10.1021/pr015504q.


The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST algorithm. Inferring a mixture's source proteins requires that the identified peptides be reassociated. This process becomes more challenging as the number of peptides increases. DTASelect, a new software package, assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed and precision of proteomic data analysis.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Mass Spectrometry
  • Molecular Sequence Data
  • Peptides / analysis*
  • Proteins / analysis*
  • Proteomics*
  • Software*


  • Peptides
  • Proteins