Mining phosphopeptide signals in liquid chromatography-mass spectrometry data for protein phosphorylation analysis

Hsin Yi Wu, Vincent Shin Mu Tseng, Pao-Chi Liao

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Protein phosphorylation is a key post-translational modification that governs biological processes. Despite the fact that a number of analytical strategies have been exploited for the characterization of protein phosphorylation, the identification of protein phosphorylation sites is still challenging. We proposed here an alternative approach to mine phosphopeptide signals generated from a mixture of proteins when liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis is involved. The approach combined dephosphorylation reaction, accurate mass measurements from a quadrupole/ time-of-flight mass spectrometer, and a computing algorithm to differentiate possible phosphopeptide signals obtained from the LC-MS analyses by taking advantage of the mass shift generated by alkaline phosphatase treatment. The retention times and m/z values of these selected LC-MS signals were used to facilitate subsequent LC-MS/MS experiments for phosphorylation site determination. Unlike commonly used neutral loss scan experiments for phosphopeptide detection, this strategy may not bias against tyrosine-phosphorylated peptides. We have demonstrated the applicability of this strategy to sequence more, in comparison with conventional data-dependent LC-MS/MS experiments, phosphopeptides in a mixture of α- and β-caseins. The analytical scheme was applied to characterize the nasopharyngeal carcinoma (NPC) cellular phosphoproteome and yielded 221 distinct phosphorylation sites. Our data presented in this paper demonstrated the merits of computation in mining phosphopeptide signals from a complex mass spectrometric data set.

Original languageEnglish
Pages (from-to)1812-1821
Number of pages10
JournalJournal of Proteome Research
Volume6
Issue number5
DOIs
Publication statusPublished - 2007 May 1

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Phosphopeptides
Phosphorylation
Liquid chromatography
Liquid Chromatography
Mass spectrometry
Mass Spectrometry
Proteins
Biological Phenomena
Experiments
Mass spectrometers
Post Translational Protein Processing
Tandem Mass Spectrometry
Caseins
Alkaline Phosphatase
Tyrosine
Peptides

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

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title = "Mining phosphopeptide signals in liquid chromatography-mass spectrometry data for protein phosphorylation analysis",
abstract = "Protein phosphorylation is a key post-translational modification that governs biological processes. Despite the fact that a number of analytical strategies have been exploited for the characterization of protein phosphorylation, the identification of protein phosphorylation sites is still challenging. We proposed here an alternative approach to mine phosphopeptide signals generated from a mixture of proteins when liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis is involved. The approach combined dephosphorylation reaction, accurate mass measurements from a quadrupole/ time-of-flight mass spectrometer, and a computing algorithm to differentiate possible phosphopeptide signals obtained from the LC-MS analyses by taking advantage of the mass shift generated by alkaline phosphatase treatment. The retention times and m/z values of these selected LC-MS signals were used to facilitate subsequent LC-MS/MS experiments for phosphorylation site determination. Unlike commonly used neutral loss scan experiments for phosphopeptide detection, this strategy may not bias against tyrosine-phosphorylated peptides. We have demonstrated the applicability of this strategy to sequence more, in comparison with conventional data-dependent LC-MS/MS experiments, phosphopeptides in a mixture of α- and β-caseins. The analytical scheme was applied to characterize the nasopharyngeal carcinoma (NPC) cellular phosphoproteome and yielded 221 distinct phosphorylation sites. Our data presented in this paper demonstrated the merits of computation in mining phosphopeptide signals from a complex mass spectrometric data set.",
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Mining phosphopeptide signals in liquid chromatography-mass spectrometry data for protein phosphorylation analysis. / Wu, Hsin Yi; Tseng, Vincent Shin Mu; Liao, Pao-Chi.

In: Journal of Proteome Research, Vol. 6, No. 5, 01.05.2007, p. 1812-1821.

Research output: Contribution to journalArticle

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