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OpenMS
2.5.0
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Export MS/MS data in .MGF format for GNPS (http://gnps.ucsd.edu).
GNPS (Global Natural Products Social Molecular Networking, http://gnps.ucsd.edu) is an open-access knowledge base for community-wide organisation and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. The GNPS web-platform makes possible to perform spectral library search against public MS/MS spectral libraries, as well as to perform various data analysis such as MS/MS molecular networking, network annotation propagation (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006089), and the Dereplicator-based annotation (https://www.nature.com/articles/nchembio.2219). The GNPS manuscript is available here: https://www.nature.com/articles/nbt.3597
This tool was developed for the OpenMS-GNPS workflow. It can be accessed on GNPS (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-experimental.jsp). The steps used by that workflow are as following: 1. Input mzML files 2. Run the FeatureFinderMetabo tool 3. Run the IDMapper tool 4. Run the MapAlignerPoseClustering tool 5. Run the FeautureLinkerUnlabeledKD tool 6. Run the FileConverter tool (output FeatureXML format) 7. Run the MetaboliteAdductDecharger 8. Run the GNPSExport to export an .MGF 9. Upload the .MGF file on http://gnps.ucsd.edu and follow the instructions here: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/
The command line parameters of this tool are:
INI file documentation of this tool: