OpenMS - FeatureFinderMetabo for GC-MS data

Hello everyone!
I would like to ask how reliable is the FeatureFinderMetabo node with files originating from GC-MS experiments. From what I see quantification and identification take place with no problem.
Or is it exclusively for LC-MS data?


In general, FFM should work on GCMS as well since the structure of the data is roughly the same. However, you might need to make adjustments to the parameters regarding the expected shape of the features across retention time (in the case of GCMS temperature or something like that?).
For more detailed information or tips, it is probably better to involve people on OpenMS’ GitHub or the Mailinglist.

Thank you very much for your answer! Yes I guess you mean that with the increasing of the temperature the higher and sharper peaks are occurring, which should then affect the MapAlignerPoseClustering node. So, I should make adjustments in the MapAlignerPoseClustering in order to detect those peaks. The question is how much difference will there be in the intensity axis of samples originating from GC-MS and LC-MS. How can I come in contact with them for more details? Do you mean submit a question in the Contact tab would be an option?
Thank you very much!


Exactly. These kinds of specifics probably need to be accounted for in the settings. Also, the expected peak width (or any “retention time” cutoffs) might need to be tweaked. I am thinking of:
chrom_fwhm, epd:width_filtering, epd:min_fwhm, epd:max_fwhm

I would inspect the generated featureXMLs in the external TOPPView program of OpenMS to see if the performance was satisfying.

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