![]() |
OpenMS
2.7.0
|
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 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 Feature Based Molecular Networking (FBMN) workflow on GNPS (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash2.jsp)
Please cite our preprint: Nothias, LF., Petras, D., Schmid, R. et al. Feature-based molecular networking in the GNPS analysis environment. Nat Methods 17, 905–908 (2020). https://doi.org/10.1038/s41592-020-0933-6
See the FBMN workflow documentation here (https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking/)
In brief, after running an OpenMS "metabolomics" pipeline, the GNPSExport TOPP tool can be used on the consensusXML file and corresponding mzML files to generate the files needed for FBMN on GNPS. These two files are:
For each consensusElement in the consensusXML file, the GNPSExport produces one representative consensus MS/MS spectrum (named peptide annotation in OpenMS jargon) outputted in the MS/MS spectral file (.MGF file). Several modes for the generation of the consensus MS/MS spectrum are available and described below. Note that these parameters are defined in the GNPSExport INI parameters file.
Representative command:
The GNPSExport TOPP tool can be run on a consensusXML file and the corresponding mzML files to generate a MS/MS spectral file (MGF format) and corresponding feature quantification table (.TXT format) that contains the LC-MS peak area intensity.
Requirements:
Parameters:
Note that mass accuracy and the retention time window for the pairing between MS/MS scans and a LC-MS feature or consensusElement is defined at the IDMapper tool step.
A representative OpenMS-GNPS workflow would sequentially use these OpenMS TOPP tools:
The GitHub for that ProteoSAFe workflow and an 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 on GNPS: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-openms/
GNPS (Global Natural Products Social Molecular Networking, https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash2.jsp) 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 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 Network Annotation Propagation (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006089) and the DEREPLICATOR (https://www.nature.com/articles/nchembio.2219) The GNPS paper is available here (https://www.nature.com/articles/nbt.3597)
The command line parameters of this tool are:
INI file documentation of this tool: