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
Please carefully read and follow our post guide
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.
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Benzenemethanol, .alpha.-[1-(ethylmethylamino)ethyl]-
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Acetohydroxamic acid
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n-Propyl acetate
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Dibutyl phthalate
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1,3,5,7-Tetroxane
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Ethyl 2-isocyanatopropionate
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Aziridine, 2,3-dimethyl-1-(1-methylethyl)-, cis-
-
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.
I can see the main issue is that we don’t know the functions / pathways for these compounds.
You may find this post useful.