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.
Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L. OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results. Proteomics. 2009 Jul;9(14):3772-3774.