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PhosphoScore: an open-source phosphorylation site assignment tool for MSn data.

Brian E Ruttenberg1, Trairak Pisitkun, Mark A Knepper

  • 1Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, USA.

Journal of Proteome Research
|June 12, 2008
PubMed
Summary
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PhosphoScore accurately assigns phosphorylation sites from mass spectrometry data. This open-source tool enhances phosphoproteomic analysis by validating numerous phosphorylation sites efficiently.

Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Proteomics

Background:

  • Accurate phosphorylation site assignment is crucial for phosphoproteomics.
  • Large-scale LC-MS/MS generates extensive phosphopeptide datasets requiring validation.

Purpose of the Study:

  • To develop an open-source program, PhosphoScore, for reliable phosphopeptide data assignment.
  • To validate phosphorylation sites across multiple mass spectrometry (MS) levels (MS(n)).

Main Methods:

  • Developed PhosphoScore, an algorithm considering spectral peak match quality and normalized intensity.
  • Utilized synthetic data and compared results with Ascore and visual inspection for validation.

Main Results:

  • PhosphoScore achieved >95% correct MS(2) assignments on synthetic data.

Related Experiment Videos

  • Demonstrated >98% agreement with the Ascore algorithm for MS(2) assignments.
  • Showed >92% agreement with manual visual inspection for MS(3) and MS(4) spectra.

    • Conclusions:

    • PhosphoScore provides a robust and accurate method for phosphopeptide assignment.
    • The tool is compatible with various MS levels, improving phosphoproteomic data analysis.
    • PhosphoScore offers a validated solution for the high-throughput validation of phosphorylation sites.