National Heart, Lung, and Blood Institute

Epithelial Systems Biology Laboratory (ESBL)


PhosSA: Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data

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). Contact us for questions or reporting bugs.

A User Manual for Graphical User Interface (GUI) for PhosSA Algorithm: Download PDF

Download PhosSA (msf to out convertor)

Download PhosSA (Mascot pepXml to out convertor)

Download PhosSA (Sequest pepXml to out convertor)

Download Test data

If you use the software please cite: Fahad Saeed, Trairak Pisitkun, Jason Hoffert, Guanghui Wang, Marjan Gucek and Mark Knepper, "An Efficient Dynamic Programming Algorithm for Phosphorylation Site Assignment of Large-Scale Mass Spectrometry Data", Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on , vol., no., pp.618,625, 4-7 Oct. 2012 doi: 10.1109/BIBMW.2012.6470210 IEEE PubMed