OpenMS  2.8.0
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GNPSExport

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 organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. The GNPS web-platform makes it 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, and the Dereplicator-based annotation. The GNPS manuscript is available here: https://www.nature.com/articles/nbt.3597 This tool was developed for the Feature Based Molecular Networking (FBMN) workflow (https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/)

### Please cite: Nothias, L.-F., Petras, D., Schmid, R. et al. [Feature-based molecular networking in the GNPS analysis environment](https://www.nature.com/articles/s41592-020-0933-6). Nat. Methods 17, 905–908 (2020).

In brief, after running an OpenMS metabolomics pipeline, the **GNPSExport**, together with the **TextExporter** TOPP tool, can be used on the consensusXML file and the mzML files to generate the files needed for FBMN. Those files are:

  • A **MS/MS spectral data file** (.MGF format) which is generated with the GNPSExport util.
  • A **feature quantification table** (.TXT format) which is generated with the TextExport util.

A representative OpenMS-GNPS workflow would use the following OpenMS TOPP tools sequentially:

  • Input mzML files
  • Run the FeatureFinderMetabo tool on the mzML files.
  • Run the MapAlignerPoseClustering tool on the featureXML files. `MapAlignerPoseClustering -in FFM_inputFile0.featureXML FFM_inputFile1.featureXML -out MapAlignerPoseClustering_inputFile0.featureXML MapAlignerPoseClustering_inputFile1.featureXML`
  • Run the IDMapper tool on the featureXML and mzML files. `IDMapper -id emptyfile.idXML -in MapAlignerPoseClustering_inputFile0.featureXML -spectra:in MapAlignerPoseClustering_inputFile0.mzML -out IDMapper_inputFile0.featureXML` `IDMapper -id emptyfile.idXML -in MapAlignerPoseClustering_inputFile1.featureXML -spectra:in MapAlignerPoseClustering_inputFile1.mzML -out IDMapper_inputFile1.featureXML`
  • Run the *MetaboliteAdductDecharger* tool on the featureXML files.
  • Run the FeatureLinkerUnlabeledKD tool or FeatureLinkerUnlabeledQT, on the featureXML files and output a consensusXML file. `FeatureLinkerUnlabeledKD -in IDMapper_inputFile0.featureXML IDMapper_inputFile1.featureXML -out FeatureLinkerUnlabeledKD.consensusXML`
  • Run the FileFilter on the consensusXML file to keep only consensusElements with at least MS/MS scan (peptide identification). `FileFilter -id:remove_unannotated_features -in FeatureLinkerUnlabeledKD.consensusXML -out FileFilter.consensusXML`
  • Run the GNPSExport on the "filtered consensusXML file" to export an .MGF file. For each consensusElement in the consensusXML file, the GNPSExport command produces one representative consensus MS/MS spectrum (named peptide annotation in OpenMS jargon) which is appended in the MS/MS spectral file (.MGF file). (Note that the parameters for the spectral file generation are defined in the GNPSExport INI parameters file, available here: https://ccms-ucsd.github.io/GNPSDocumentation/openms_gnpsexport/GNPSExport.ini `GNPSExport -ini iniFile-GNPSExport.ini -in_cm filtered.consensusXML -in_mzml inputFile0.mzML inputFile1.mzML -out GNPSExport_output.mgf`
  • Run the TextExporter on the "filtered consensusXML file" to export a .TXT file. `TextExporter -in FileFilter.consensusXML -out FeatureQuantificationTable.txt`
  • Upload your files to GNPS and run the Feature-Based Molecular Networking workflow. Instructions can be found here: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/

The GitHub page for the ProteoSAFe workflow and the OpenMS python wrappers is available here: https://github.com/Bioinformatic-squad-DorresteinLab/openms-gnps-workflow An online version of the OpenMS-GNPS pipeline for FBMN running on CCMS server (http://proteomics.ucsd.edu/) is available here: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms/ The command line parameters of this tool are:

INI file documentation of this tool: