PhosphoScan: a probability-based method for phosphorylation site prediction using MS2/MS3 pair information.
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.
Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA. ywan@som.umaryland.edu
Yunhu
Y
Wan
Diane
D
Cripps
Stefani
S
Thomas
Patricia
P
Campbell
Nicholas
N
Ambulos
Ting
T
Chen
Austin
A
Yang
D000544:Alzheimer Disease / Q000378:metabolism; D001921:Brain / Q000378:metabolism; D002853:Chromatography, Liquid; D016208:Databases, Factual; D006801:Humans; D010748:Phosphopeptides / Q000032:analysis*; D010766:Phosphorylation; D011336:Probability; D011499:Protein Processing, Post-Translational; D053719:Tandem Mass Spectrometry; D016875:tau Proteins / Q000378:metabolism
D010748:Phosphopeptides; D016875:tau Proteins