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

J Proteome Res. 2008 Jul;7(7):3054-9. doi: 10.1021/pr800169k. Epub 2008 Jun 11.


Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Animals
  • Aquaporin 2 / metabolism
  • Chromatography, Liquid
  • Databases, Factual
  • HeLa Cells
  • Humans
  • Kidney Tubules, Collecting / chemistry
  • Markov Chains
  • Monte Carlo Method
  • Phosphopeptides / analysis*
  • Phosphorylation
  • Proteomics
  • Rats
  • Software
  • Spectrometry, Mass, Electrospray Ionization
  • Tandem Mass Spectrometry


  • Aquaporin 2
  • Phosphopeptides