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Gygi-Taplin Lab

A novel probability-based approach for high-throughput protein phosphorylation analysis and site localization
Sean A. Beausoleil, Judit Villen, Scott A. Gerber, John Rush, Steven P Gygi

The Problem:
Which is the correct site of phosphorylation?

The precise site of phosphorylation can only be determined by the presence of site-determining ions

In this example, the presence of the y-3, 4, and 5 ions, and the b-8, 9, and 10 in the MS/MS will determine if the phosphorylation site is on T8 or S10

Search algorithms like Sequest or Mascot often successfully identify the proper peptide sequence, but fail to provide information about the presence or absence of site-determining ions. As a result, users must manually inspect each spectrum to confirm proper site localization. Here, we present a probability-based score, named the Ascore, which measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We also provide users with the ability to analyze their own data through this website (currently under construction) or to download there own version of the ascore here.

Supplemental Data:
  The Excel spreadsheet contained in the supplemental data download contain links to tandem Mass Spectrometry spectra.

  A tool to calculate the Ascore for a phosphpeptide. Currently under construction

Ascore Download
  Downloadable version of the Ascore to run on your own computers