I’ve been doing enrichment analysis tested against a reference metabolome. Before, I’ve had no issues uploading my own metabolome (so it’s not a format issue), but I’ve been trying to upload a bigger metabolome lately and I keep getting the error message : “Over half of your uploaded IDs cannot be matched to our database! Please make sure they are valid HMDB names!”.
However, I’ve checked using the Compound ID conversion tool and all my HMDB names are properly matched to their corresponding compounds. I’ve tried exporting the data from the conversion tool and using that list and I’m still getting that error message. I’ve also tried MetabolomicsWorkbench conversion tool.
I looked it up on the forum and read “Pathway analysis is NOT dependent on whether the compounds exist in current HMDB. It depends on whether the compounds are included in our pathway libraries.” So what I also tried is to filter my list and remove those that are not found in the KEGG metabolomic pathways library and pick KEGG for the enrichment analysis… Same error.
Is there any way I could fix my metabolome list ? Are more than half of “my” metabolites truly not matched in the database ?? They’re all very common (amino acids, TCA, glycolysis etc.).
Thank you !