PhosSA is a program for phosphorylation site assignment of LC-MS/MS data. It uses a linear-time and linear space dynamic programming strategy for phosphorylation site assignment. The algorithm optimizes the objective function defined as the summation of intensity peaks that are associated with theoretical peptide fragmentation ions. A classifier introduced in the algorithm exploits the specific characteristics of mass spectrometry data to distinguish between the correctly and incorrectly assigned site(s).
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Proteome Sci. 2013 Nov 7;11(Suppl 1):S14. doi: 10.1186/1477-5956-11-S1-S14. Epub 2013 Nov 7.
PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.
Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA.