OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results

Protein identification by MS is an important technique in both gel-based and gel-free proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) (http:// pubchem.ncbi.nlm.nih.gov/omssa) is an open-source search engine that can be used to identify MS/MS spectra acquired in these experiments. We here present a lightweight, open-source Java software library, OMSSA Parser (http://code.google.com/p/omssa-parser), which parses OMSSA omx result files into easy accessible and fully functional object models. In addition, we also provide examples illustrating the usage of our library.