PTMap - A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites

Yue Chen, Wei Chen, Melanie H. Cobb, Yingming Zhao

Research output: Contribution to journalArticle

65 Scopus citations


We present sequence alignment software, called PTMap, for the accurate identification of full-spectrum protein post-translational modifications (PTMs) and polymorphisms. The software incorporates several features to improve searching speed and accuracy, including peak selection, adjustment of inaccurate mass shifts, and precise localization of PTM sites. PTMap also automates rules, based mainly on unmatched peaks, for manual verification of identified peptides. To evaluate the quality of sequence alignment, we developed a scoring system that takes into account both matched and unmatched peaks in the mass spectrum. Incorporation of these features dramatically increased both accuracy and sensitivity of the peptide- and PTM-identifications. To our knowledge, PTMap is the first algorithm that emphasizes unmatched peaks to eliminate false positives. The superior performance and reliability of PTMap were demonstrated by confident identification of PTMs on 156 peptides from four proteins and validated by MS/MS of the synthetic peptides. Our results demonstrate that PTMap is a powerful algorithm capable of identification of all possible protein PTMs with high confidence.

Original languageEnglish (US)
Pages (from-to)761-766
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number3
StatePublished - Jan 20 2009



  • Acetylation
  • Dehydration
  • Methylation
  • Phosphorylation

ASJC Scopus subject areas

  • General

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