Functional Analysis returning Compound.Matches fitting the regex "^CE\\d{4}$"

MetaboAnalyst
,
1

Hello,

I am a MetaboAnalystR user, and I am interested in using the MS1-based annotations obtained from the Functional Analysis module to map input features to putative annotations in my custom workflow. I am querying against the “Homo sapiens (human) [MFN]” pathway library. In the output “mummichog_matched_compound_all.csv”, I would like to use database APIs to obtain compound names in my custom workflow by matching them against their respective database. Of course, the majority of the Compound.Matches are of a pattern fitting the regex "^C\\d{5}$", corresponding to KEGG Compound IDs. The names are then easy to retrieve from the KEGG REST API. However, Compound.Matches sometimes are of a pattern fitting the regex "CE\\d{4}$". I have not been able to find the source of these compound IDs, and therefore cannot translate them into compound common names.

Any help with how this is handled internally in MetaboAnalyst would be deeply appreciated!

2

I was able to find that the CE compounds come from BiGG. For example, CE0347 is the ID for 12-hydroxyeicosatetraenoate in the BiGG metabolite namespace. http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt

3

One quick follow-up to this: some compounds with CE naming are not found in BiGG…one example is a compound that was annotated in my data as “CE5121”, which does not exist anywhere in the BiGG Universal Metabolite Namespace. Any thoughts on this?