PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information

Yunhu Wan, Diane Cripps, Stefani Thomas, Patricia Campbell, Nicholas Ambulos, Ting Chen, Austin Yang

Research output: Contribution to journalArticle

30 Scopus citations


Phosphopeptide identification and phosphorylation site localization are crucial aspects of many biological studies. Furthermore, multiple phosphorylations of peptides make site localization even more difficult. We developed a probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions using a spectral data set from a synthetic doubly phosphorylated peptide, and the results showed that PhosphoScan analysis yielded a 63% phosphopeptide localization improvement compared with SEQUEST and a 57% improvement compared with MASCOT.

Original languageEnglish (US)
Pages (from-to)2803-2811
Number of pages9
JournalJournal of Proteome Research
Issue number7
StatePublished - Jul 1 2008
Externally publishedYes



  • MS2
  • MS3
  • Nl (neutral loss)
  • PTM (post translational modification)
  • Phosphorylation
  • Protein identification

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