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OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results
Author(s) -
Barsnes Harald,
Huber Steffen,
Sickmann Albert,
Eidhammer Ingvar,
Martens Lennart
Publication year - 2009
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200900037
Subject(s) - computer science , parsing , open source , java , programming language , pubchem , source code , identification (biology) , software , proteome , open source software , information retrieval , computational biology , bioinformatics , biology , botany
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.