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.
Barsnes
Harald
H
Department of Informatics, University of Bergen, N-5020 Norway. Harald.Barsnes@ii.uib.no
Huber
Steffen
S
Sickmann
Albert
A
Eidhammer
Ingvar
I
Martens
Lennart
L
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface