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

Abstract

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
Volume7
Issue number7
DOIs
StatePublished - Jul 1 2008

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Fingerprint Dive into the research topics of 'PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information'. Together they form a unique fingerprint.

  • Cite this