Compound IDs not matching with the MetaboAnalyst database

MetaboAnalyst
1

Hi there all,

I work in the R&D side of onco-pathology and recently analyzed metabolomics using GC-MS.

New to data and analytics I think MetaboAnalysit Server (MA Server) is a good choice. However, I got stuck right from the start.

Posted a few compounds on the “Pathway Analysis’ option, but saw a message

“Error Over half of the compound IDs could not be matched to our database”

I tried to see if there is any KEGG ID and HMDB ID but doesn’t show any molecules and no help

Surprisingly, all of the compounds were in PubChem. So, I used the list of Synonyms names for each metabolite in the MA server, but that also didn’t help.

Additional information:

We outsourced the GC-MS and what we received is as follows:

Component RT; Compound Name; CAS#; Formula; Component Area; Match Factor

My goal is to develop pathway network diagrams and perform further downstream analysis.

Please share your guidance/suggestions or comments, I value it very much

Thank you very much in advance for your time

2

Please carefully read and follow our post guide

3

In consideration of and in appreciation of your time, I would like to share the following additional information
I, We outsourced the GC-MS work, and received the results as follows:
Component RT; Compound Name; CAS#; Formula; Component Area; Match Factor
II,
Below is a list of small metabolites we have for one of our samples.

  1.  Benzenemethanol, .alpha.-[1-(ethylmethylamino)ethyl]-

  2.  Acetohydroxamic acid

  3.  n-Propyl acetate

  4.  Dibutyl phthalate

  5.  1,3,5,7-Tetroxane

  6.  Ethyl 2-isocyanatopropionate

  7.  Aziridine, 2,3-dimethyl-1-(1-methylethyl)-, cis-

  8.  4-Pyranone, 2,3-dihydro-

III,
Following this post, I also did intensive searches. There are some websites where the PubChem ID can be converted to KEGG ID. Even though I was able to succeed only for the first 4 metabolites to KEGG IDs (serial numbers 1 to 4, mentioned above) but couldn’t make progress for the remaining metabolites (from 5 to 8). What all I saw was IDs of PubChem Compound, ChemSpider, and PubChem CID.
Nevertheless, also cross-checked those resulting IDs (PubChem Compound, and ChemSpider) with the ID conversion websites but no progress. Furthermore, also tried with the CAS ID for the missed 4 metabolites, but unfortunately, there is no progress.
Compared to KEGG ID, HMDB ID is even lesser.

Could you please provide any suggestions or advice on how I should deal with the remaining, missing metabolites? I would value any suggestions.

My goal is to develop pathway network diagrams and perform further downstream analysis
Please share any insights, and thank you for your time.

4

I can see the main issue is that we don’t know the functions / pathways for these compounds.

You may find this post useful.

5

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