GNPS FBMN export

[VinzentRisch]

Hello
I wanted to ask what currently the bast way is to export preprocessing results for GNPS FBMN.
I tried different strategies and all failed so far.

1. Export with xcms-gnps-tools

• I tried this workflow and the function formatSpectraForGNPS fails because I was running this workflow with the newest version of xcms and the object I was working with is a Spectra object and not an MSnExp object.
• Is there a way to convert the Spectra object to an MSnExp object, or is it possible to extract the scans from the XCMSExperiment into an MSnExp directly.
• Are there any plans to update the functions in xcms-gnps-tools to work with the newest xcms or would it be best to just downgrade xcms to make the export possible?

2. Export mzTab-M

• In the GNPS documentation it says that the export from xcms was also possible through a mzTab-M file.
• I tried this with the writeMzTab function but this led to an error saying that the SML data was not populated.
• I also tried it with the MsIO mzTabParam function. This also failed with an error saying the SME data was not populated.

[jorainer]

Oh, true - we have the workflow developed for the old xcms result objects. I think the best solution is if I update the original workflow using the new objects - which should also simplify the process and is also a bit more efficient/faster.

[jorainer]

I've updated the workflow to support xcms version >= 4 : currently the workflow is available in my fork: https://github.com/jorainer/XCMS3_FeatureBasedMN - I made also a PR to the official repo but I don't know how long it will take to get merged.

Also, I'm closing the issue with this - feel free to re-open if needed.

[VinzentRisch]

Thank you so much for the quick solution!