Pathway/Enrichment analysis is NOT dependent on whether the compounds exist in current HMDB. It depends on whether the compounds are included in our pathway libraries. The compound annotation in MetaboAnalyst is for pathway analysis, not for general purpose HMDB compound annotation. All compounds defined in our pathway libraries will be annotated. If they are not recognized (even they have valid HMDB IDs), there will be no effect on the results. The information is stated in the compound mapping result table (see below)
(Updated in 2025) We intend to add a permutation based approach taking into account of all compounds detected. The results will be less biased but also will have less power (i.e. p-values will be less signficant in general) - due to the signal dilution as well as the non-parameteric nature of this approach.
