Update GNPSExport.cpp #5594
Update GNPSExport.cpp #5594
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I added a few more details on the proposed workflow (command examples) mainly - I think it would be great to add a link to an emptyfile.idXML at the IDMapper Requirements section "Even in untargeted metabolomics/proteomics, an empty idXML or mzid (peptide annotation format) file is needed as an input which can be found here link/to/emptyfile.idXML.
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| on the consensusXML file and corresponding mzML files to generate the files needed for FBMN on GNPS. | ||
| These two files are: | ||
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| - The MS/MS spectral data file (.MGF format) which is generated with the GNPSExport util. | ||
| - The feature quantification table (.CSV format) which is generated with the TextExport util. | ||
| - The feature quantification table (.TXT format) which is generated with the TextExport util. |
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is .txt the correct output format (TextExporter supports tsv, csv and txt)?
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When selecting OpenMS as a preprocessing tool in the FBMN workflow (GNPS), the required file format of the Feature Quant table is .txt (TextExporter supports that, yes).
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is the .txt output of textexporter compatible with the FBMN workflow? Or expects it a txt file that has the format of the .csv file?
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It should be compatible because I have used it repeatedly and it works very well. TextExporter generates a txt file that has the format of a tsv basically! So txt with tab-separated data.
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Quoting the documentation from GNPS:
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:
The feature quantification table (.TXT format) which is generated with the TextExport tool.
The MS2 spectral summary file (.MGF format) which is generated with the GNPSExport tool.
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ok great. is there a way we can test that the txt format works?
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I literally just saw this comment- sorry! So I have used those txt files generated by GNPSexport (OpenMS) in FBMN-GNPS and it works perfectly - examples:
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=441a29dc057747f094330148d40493e0
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=af126b5cd46840b79acf4b58cece09ec#
| GNPSExport -ini iniFile-GNPSExport.ini -in_cm filtered.consensusXML -in_mzml inputFile0.mzML inputFile1.mzML -out GNPSExport_output.mgf | ||
| 9. Run the @ref TOPP_TextExporter on the "filtered consensusXML file" to export an .TXT file. | ||
| TextExporter -in FileFilter.consensusXML -out FeatureQuantificationTable.txt | ||
| 10. Upload your files to GNPS and run the Feature-Based Molecular Networking workflow. Instructions are here: |
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is there a way to automatize that? e.g. we could in principle also upload the data from the tool and download results
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That's a great idea. Should I ask Ming during GNPS office hours (tomorrow 6 pm)?
src/topp/GNPSExport.cpp
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| Requirements: | ||
| - The IDMapper has to be run on the featureXML files, in order to associate MS2 scan(s) (peptide annotation) with each | ||
| features. These peptide annotations are used by the GNPSExport. | ||
| feature, using a peptide annotation file (idXML). Even in untargeted metabolomics/proteomics, an empty idXML or mzid (peptide annotation format) file is needed as an input. |
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having the empty idXML seems awkward. Could we make this optional?
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it is also confusing that it talks about protein / peptide annotations
Small corrections
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rebuild jenkins |
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@eeko-kon can you check if this is up-to-date with what you are currently doing? I would give it another quick review so we can merge that. |
A few changes to make the text clearer
I added a few more details on the proposed workflow (command examples) mainly - I think it would be great to add a link to an emptyfile.idXML at the IDMapper Requirements section
"Even in untargeted metabolomics/proteomics, an empty idXML or mzid (peptide annotation format) file is needed as an input which can be found here link/to/emptyfile.idXML.
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