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

J Proteome Res. 2008 Jul;7(7):2803-11. doi: 10.1021/pr700773p. Epub 2008 Jun 13.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alzheimer Disease / metabolism
  • Brain / metabolism
  • Chromatography, Liquid
  • Databases, Factual
  • Humans
  • Phosphopeptides / analysis*
  • Phosphorylation
  • Probability
  • Protein Processing, Post-Translational
  • Tandem Mass Spectrometry
  • tau Proteins / metabolism


  • Phosphopeptides
  • tau Proteins