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

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

Author information

1
Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA. ywan@som.umaryland.edu

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.

PMID:
18549264
PMCID:
PMC4711369
DOI:
10.1021/pr700773p
[Indexed for MEDLINE]
Free PMC Article

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