PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications

J Proteome Res. 2011 Jul 1;10(7):2930-6. doi: 10.1021/pr200153k. Epub 2011 May 24.


Tandem mass spectrometry (MS/MS) has been routinely used to identify peptides from a protein sequence database. To identify post-translationally modified peptides, most existing software requires the specification of a few possible modifications. However, such knowledge of possible modifications is not always available. In this paper, we describe a new algorithm for identifying modified peptides without requiring the user to specify the possible modifications; instead, all modifications from the Unimod database are considered. Meanwhile, several new techniques are employed to avoid the exponential growth of the search space, as well as to control the false discoveries due to this unrestricted search approach. Finally, a software tool, PeaksPTM, has been developed and already achieved a stronger performance than competitive tools for unrestricted identification of post-translational modifications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Databases, Protein
  • Humans
  • Myocardium / chemistry*
  • Peptide Fragments / analysis*
  • Peptide Fragments / chemistry
  • Protein Processing, Post-Translational*
  • Proteins / analysis*
  • Proteins / chemistry
  • Proteomics / methods*
  • Research Design
  • Software
  • Tandem Mass Spectrometry / methods*
  • Yeasts


  • Peptide Fragments
  • Proteins