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.

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.

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

Substances

  • Phosphopeptides
  • tau Proteins