Cannot upload a -reference metabolome based on your analytical platform-

Hi all! First thing, big fan of Metaboanalyst! It has helped my research for many projects :slight_smile:

I am trying to do some enrichment analysis using as a starting point metabolomics data generated by Metabolon from mouse plasma samples. So I have a list of metabolites (I have both HMDB and KEGG ids) after statistical analysis.

I have tried Enrichment and Pathway analysis and I get only a result when using universal libraries as a reference.
However, I would like to get a result using as a reference metabolome the list of metabolites identified in this dataset (regardless of significance).
I created a single-column file with all the metabolites identified, like this:

And then got an error like this when uploading

Tried to upload both a list of KEGG id metabolites, and also with HMDB id metabolites. Same problem

What am I doing wrong? is it just because too many metabolites cannot be mapped? Any suggestions on how can I overcome this obstacle?

Thanks for your amazing work again!

Thanks for the note. As indicated by the error message, there are a lot of compounds detected (i.e. your reference IDs), but their functional annotations (i.e. pathways in our libraries) are sparse. This is similar to limited gene ontology coverage in early days, will require a lot manual effort to address this issue.

We will soon add a new algorithm to take account of the reference metabolome in detecting enriched pathways. The approach should be more robust than the current one

Hi Jeff, thank you very much for your swift reply and for clarifying, I will stick with the universal reference for the moment then.


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