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jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, VizcaĆ­no JA - Proteomics (2012)

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.

View Article: PubMed Central - PubMed

Affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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Screenshot of the jmzReader GUI after opening a mzXML file. The selected spectrum is displayed using the mzGraphBrowser library (http://code.google.com/p/pride-toolsuite/wiki/PRIDEmzGraphBrowser). This library allows the user to manually annotate a spectrum and export the loaded file into MGF format. The jmzReader GUI is built using the jmzReader interface and, thus, supports all file formats supported by the jmzReader library.
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fig02: Screenshot of the jmzReader GUI after opening a mzXML file. The selected spectrum is displayed using the mzGraphBrowser library (http://code.google.com/p/pride-toolsuite/wiki/PRIDEmzGraphBrowser). This library allows the user to manually annotate a spectrum and export the loaded file into MGF format. The jmzReader GUI is built using the jmzReader interface and, thus, supports all file formats supported by the jmzReader library.

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.


jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, VizcaĆ­no JA - Proteomics (2012)

Screenshot of the jmzReader GUI after opening a mzXML file. The selected spectrum is displayed using the mzGraphBrowser library (http://code.google.com/p/pride-toolsuite/wiki/PRIDEmzGraphBrowser). This library allows the user to manually annotate a spectrum and export the loaded file into MGF format. The jmzReader GUI is built using the jmzReader interface and, thus, supports all file formats supported by the jmzReader library.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472022&req=5

fig02: Screenshot of the jmzReader GUI after opening a mzXML file. The selected spectrum is displayed using the mzGraphBrowser library (http://code.google.com/p/pride-toolsuite/wiki/PRIDEmzGraphBrowser). This library allows the user to manually annotate a spectrum and export the loaded file into MGF format. The jmzReader GUI is built using the jmzReader interface and, thus, supports all file formats supported by the jmzReader library.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Show MeSH