Journal
JOURNAL OF PROTEOME RESEARCH
Volume 7, Issue 7, Pages 2803-2811Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr700773p
Keywords
phosphorylation; PTM (post translational modification); protein identification; MS2; MS3; NL (neutral loss)
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Funding
- NCI NIH HHS [P30 CA134274] Funding Source: Medline
- NIA NIH HHS [R01 AG025323, AG25323] Funding Source: Medline
- NIMH NIH HHS [R01 MH059786, MH59786] Funding Source: Medline
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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.
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