How can i run GSEA on a ranked list of annotated compounds?

MetaboAnalyst
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1

Hi,
I have a table of metabolites with fold-change values, t-stat and pval.
I would like to run GSEA on the entire list of ranked metabolites (in order of tstat).
I see this is possible in the “Functional enrichment” module, however it requires the m/z value.
Can this be done on a list of annotated compounds without the m/z values?
Thanks!

2

In general, GSEA-based approach expects a complete (or very comprehensive) metabolome coverage - which is sort of OK for global or untargeted metabolomics. For untargeted metabolomics, ORA-based approach is more powerful than GSEA. See our comprehensive evaluation here.

For targeted metabolomics with ~100 metabolites, similar evaluation is needed before we can provide this option.

3

Thanks for your reply!
I would like to run the GSEA on untargeted metabolomics data already annotated (complete list)
I cannot use the ORA approach, as only 1 metabolites is significantly altered (by FDR).

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