GNPS FBMN and Compound Discoverer

[Brie Garcia]

Hi GNPS community, 

Has anyone had success using Compound Discoverer .mgf files and feature tables for GNPS FBMN. I've been able to use the .mgf file for Molecular Networking but when trying to us the FBMN I continue to get an error which I'm curious if this is due to incompatibilities with Compound Discoverer. 

Thanks, 

Brianna M. Garcia

University of Georgia

[Mingxun Wang]

Hi Brian,

We've never tried ourselves as we don't have a license for compound discoverer. However, if you do want to work together and have some concrete data out of there, we can definitely get support into FBMN. 

Best,

Ming

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Mingxun Wang

UCSD CSE Graduate Student

miw...@cs.ucsd.edu

[Mingxun Wang]

Apologies, Brie, not Brian. 

Best,

Ming

[Louis-Félix Nothias]

Yes exactly. If you could share some representative input files (MGF and feature table) in the coming days, we should be able to add support for Compound Discoverer with the next release cycle. 

[Nicole DiDonato]

Hi all, just wondering if there has been any progress on support for Compound Discoverer in GNPS? If not I can send some representative files. Thank you!

[Mingxun Wang]

Hi Nicole,

Apologies for the slowness, I think you might have given us some examples, but I can't for the life of me find them. We're moving a lot of stuff to GNPS2 so FBMN is getting some TLC so might be a good time to try to get this injected in there. 

Best,

Ming

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[Nicole DiDonato]

Sounds great, thanks for the update! Compound Discover exports mgf files in the attached format. Unfortunately Thermo does not support export of a scan number or row ID for the feature list, just m/z and RT. Can you work with this?

[Mingxun Wang]

Thanks Nicole,

I think this can work for FBMN, but the one thing we're missing out on is any quantification across samples. So if that isn't a huge concern, then we can likely forgo it for now. 

Best,

Ming

[Nicole DiDonato]

Thank you, Ming! It would be great if this format can work for FBMN. Quantification across samples is not a huge concern since we do that external to GNPS anyway. More important is the additional matches and networks gained from FBMN, if that can be done at a minimum, with this format. Perhaps in the future we can find a work-around by modifying the mgf and feature list to allow for quantification in GNPS. Is it just the row id or scan number that would be needed for this or something else?