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

Yunhu Wan; Diane Cripps; Stefani Thomas; Patricia Campbell; Nicholas Ambulos; Ting Chen; Austin Yang

doi:10.1021/pr700773p

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

Yunhu Wan, Diane Cripps, Stefani Thomas, Patricia Campbell, Nicholas Ambulos, Ting Chen, Austin Yang

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

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.

Original language	English (US)
Pages (from-to)	2803-2811
Number of pages	9
Journal	Journal of Proteome Research
Volume	7
Issue number	7
DOIs	https://doi.org/10.1021/pr700773p
State	Published - Jul 2008
Externally published	Yes

Keywords

MS2
MS3
Nl (neutral loss)
PTM (post translational modification)
Phosphorylation
Protein identification

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10.1021/pr700773p

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title = "PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information",

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.",

keywords = "MS2, MS3, Nl (neutral loss), PTM (post translational modification), Phosphorylation, Protein identification",

author = "Yunhu Wan and Diane Cripps and Stefani Thomas and Patricia Campbell and Nicholas Ambulos and Ting Chen and Austin Yang",

year = "2008",

month = jul,

doi = "10.1021/pr700773p",

language = "English (US)",

volume = "7",

pages = "2803--2811",

journal = "Journal of Proteome Research",

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TY - JOUR

T1 - PhosphoScan

T2 - A probability-based method for phosphorylation site prediction using MS2/MS3 pair information

AU - Wan, Yunhu

AU - Cripps, Diane

AU - Thomas, Stefani

AU - Campbell, Patricia

AU - Ambulos, Nicholas

AU - Chen, Ting

AU - Yang, Austin

PY - 2008/7

Y1 - 2008/7

N2 - 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.

AB - 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.

KW - MS2

KW - MS3

KW - Nl (neutral loss)

KW - PTM (post translational modification)

KW - Phosphorylation

KW - Protein identification

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U2 - 10.1021/pr700773p

DO - 10.1021/pr700773p

M3 - Article

C2 - 18549264

AN - SCOPUS:49849092381

SN - 1535-3893

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EP - 2811

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 7

ER -

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

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