title: OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results.
abstract: 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.
authors.affiliation: Department of Informatics, University of Bergen, N-5020 Norway. Harald.Barsnes@ii.uib.no
authors.forename: Harald
authors.initials: H
authors.lastname: Barsnes
authors.forename: Steffen
authors.initials: S
authors.lastname: Huber
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry; D012984:Software; D053719:Tandem Mass Spectrometry; D014584:User-Computer Interface