jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Bottom Line: 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.
Affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.Show MeSH
Mentions: The jmzReader library also comes with a simple but powerful, interactive viewer (Fig. 2) to demonstrate the use of the common interface. It can be used to load and view spectra from all supported file formats, simultaneously illustrating the usefulness of the low-memory footprint achieved by the whole library as well as the advantage of the common interface. This viewer can also export any of the loaded MS data files to the commonly used Mascot MGF format.
Affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.