MS2-Deisotoper: a tool for deisotoping high-resolution MS/MS spectra in normal and heavy isotope-labelled samples

Aidan P. Tay, Angelita Liang, Joshua J. Hamey, Gene Hart-Smith, Marc R. Wilkins*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


High-resolution MS/MS spectra of peptides can be deisotoped to identify monoisotopic masses of peptide fragments. The use of such masses should improve protein identification rates. However, deisotoping is not universally used and its benefits have not been fully explored. Here, MS2-Deisotoper, a tool for use prior to database search, is used to identify monoisotopic peaks in centroided MS/MS spectra. MS2-Deisotoper works by comparing the mass and relative intensity of each peptide fragment peak to every other peak of greater mass, and by applying a set of rules concerning mass and intensity differences. After comprehensive parameter optimization, it is shown that MS2-Deisotoper can improve the number of peptide spectrum matches (PSMs) identified by up to 8.2% and proteins by up to 2.8%. It is effective with SILAC and non-SILAC MS/MS data. The identification of unique peptide sequences is also improved, increasing the number of human proteoforms by 3.7%. Detailed investigation of results shows that deisotoping increases Mascot ion scores, improves FDR estimation for PSMs, and leads to greater protein sequence coverage. At a peptide level, it is found that the efficacy of deisotoping is affected by peptide mass and charge. MS2-Deisotoper can be used via a user interface or as a command-line tool.

Original languageEnglish
Article number1800444
Pages (from-to)1-13
Number of pages13
Issue number17
Publication statusPublished - Sept 2019
Externally publishedYes


  • deisotoping
  • monoisotopic mass
  • protein identification
  • proteomic software
  • tandem mass spectrometry


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