Abstract
Correct phosphorylation site assignment for high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. In this report, we present a graphical user interface (GUI) implemented in JAVA for phosphorylation site assignment. The GUI implements the PhosSA algorithm and is tested on a variety of operating systems and computing platforms. The GUI is divided into two parts: The first part takes input from multiple search engines (ie Sequest and Mascot) and converts it into PhosSA compatible format. The second part of the GUI runs the site assignment algorithm using varying thresholds for HCD and CID fragmentation methodologies. The software is accessible for free at: http://helixweb. nih. gov/ESBL/PhosSA/for all non-commercial purposes.