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) (https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/) and Ion Identity Molecular Networking (IIMN) (https://ccms-ucsd.github.io/GNPSDocumentation/fbmn-iin/) workflows.
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 TOPP tool can be used on the consensusXML file and the mzML files to generate the files needed for FBMN and IIMN. Those files are:
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 MetaboliteAdductDecharger on the featureXML files (optional, for Ion Identity Molecular Networking).
- Run the MapAlignerPoseClustering tool on the featureXML files.
MapAlignerPoseClustering -in FFM_inputFile0.featureXML FFM_inputFile1.featureXML -out MapAlignerPoseClustering_inputFile0.featureXML MapAlignerPoseClustering_inputFile1.featureXML -trafo_out MapAlignerPoseClustering_inputFile0.trafoXML MapAlignerPoseClustering_inputFile1.trafoXML
- Run the MapRTTransformer tool on the mzML files to transform retention times based on the feature map alignment by MapAlignerPoseClustering.
MapRTTransformer -in inputFile0.mzML -out MapRTTransformer_inputFile0.mzML -trafo_in MapAlignerPoseClustering_inputFile0.trafoXML
MapRTTransformer -in inputFile1.mzML -out MapRTTransformer_inputFile1.mzML -trafo_in MapAlignerPoseClustering_inputFile1.trafoXML
- Run the IDMapper tool on the featureXML and mzML files.
IDMapper -id emptyfile.idXML -in MapAlignerPoseClustering_inputFile0.featureXML -spectra:in MapRTTransformer_inputFile0.mzML -out IDMapper_inputFile0.featureXML
IDMapper -id emptyfile.idXML -in MapAlignerPoseClustering_inputFile1.featureXML -spectra:in MapRTTransformer_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 -in_cm filtered.consensusXML -in_mzml MapRTTransformer_inputFile0.mzML MapRTTransformer_inputFile1.mzML -out GNPSExport_output.mgf -out_quantification FeatureQuantificationTable.txt -out_pairs SupplementaryPairsTable.csv -out_meta_values MetaValues.tsv
- 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: