Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy

J Proteome Res. 2008 Apr;7(4):1640-9. doi: 10.1021/pr700675j. Epub 2008 Mar 4.


Manual checking is commonly employed to validate the phosphopeptide identifications from database searching of tandem mass spectra. It is very time-consuming and labor intensive as the number of phosphopeptide identifications increases greatly. In this study, a simple automatic validation approach was developed for phosphopeptide identification by combining consecutive stage mass spectrometry data and the target-decoy database searching strategy. Only phosphopeptides identified from both MS2 and its corresponding MS3 were accepted for further filtering, which greatly improved the reliability in phosphopeptide identification. Before database searching, the spectra were validated for charge state and neutral loss peak intensity, and then the invalid MS2/MS3 spectra were removed, which greatly reduced the database searching time. It was found that the sensitivity was significantly improved in MS2/MS3 strategy as the number of identified phosphopeptides was 2.5 times that obtained by the conventional filter-based MS2 approach. Because of the use of the target-decoy database, the false-discovery rate (FDR) of the identified phosphopeptides could be easily determined, and it was demonstrated that the determined FDR can precisely reflect the actual FDR without any manual validation stage.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Caseins / chemistry
  • Chromatography, High Pressure Liquid
  • Databases, Protein
  • Electronic Data Processing / methods*
  • HeLa Cells
  • Humans
  • Internet
  • Phosphopeptides / analysis*
  • Phosphorylation
  • Reproducibility of Results
  • Software
  • Software Design
  • Tandem Mass Spectrometry / methods*
  • Trypsin / chemistry
  • Zirconium / chemistry


  • Caseins
  • Phosphopeptides
  • Zirconium
  • Trypsin
  • zirconium oxide