title: jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
abstract: We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/.
authors.affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Johannes
authors.initials: J
authors.lastname: Griss
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
mesh_terms: D030562:Databases, Protein; D001330:Electronic Data Processing / Q000379:methods / Q000592:standards; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods* / Q000592:standards; D012984:Software / Q000592:standards; D014584:User-Computer Interface
chemical_list: D011506:Proteins