Software

Ascore

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

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
http://ascore.med.harvard.edu

Motif-X

Motif-x (short for motif extractor) is a software tool designed to extract over-represented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

Schwartz, D. & Gygi, S.P. (2005). An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nature Biotechnology 23(11), 1391-1398.
http://motif-x.med.harvard.edu/