pathway analysis for metabolites

Question

[mrashad]

I need to ask about something I noticed in processed file for group of metabolites: I have a file like this https://ibb.co/hRS6jf1

this file contain many records of header [compound_ID , metabolite , KEGG , HMDB , chemical class , pathway] As it was shown some records have no KEGG ID and HMDB ID my questions:

1. Is there away to determine their KEGG or HMDB ID ?
2. There are a pathway related to metabolites called FAtty Acid, Dihydroxy or it is just related to its chemical class and I should find their associated pathways again using some packages like metaboanalystR?
3. If I should find their pathways again, on which criteria I should select the R package ?, Does it depend on recent packages or the more citated packages?
4. Is there away to identify the metabolite for example with this code C20:0,2OH FA ?

Look forward to hearing from you soon. Thanks in advance. Regards,

[Kevin Blighe]

1- Is there away to determine their KEGG or HMDB ID ?

We know next-to-nothing about ~90% of metabolites that can be detected in human blood; so, the possibility exists that there is no known pathway. Check with the service provider who conducted the experiment.

2- There are a pathway related to metabolites called FAtty Acid, Dihydroxy or it is just related to its chemical class and I should find their associated pathways again using some packages like metaboanalystR?

Check with the service provider who conducted the experiment.

3- If I should find their pathways again, on which criteria I should select the R package ?, Does it depend on recent packages or the more citated packages?

MetaboAnalyst is the leading R package and web-platform.

4- Is there away to identify the metabolite for example with this code C20:0,2OH FA ?

That is the chemical formula. Again, next-to-nothing may be known about it. Check with the service provider who conducted the experiment.

[mrashad]

Thanks a lot for your fruitful answer

[mrashad]

By the way, I send to service provider who conducted the experiment and they answered mostly like you answered. Thanks again.

Answer 1

[Egon Willighagen]

For an overview of R packages, check out this open access book: https://rformassspectrometry.github.io/metaRbolomics-book/

For ID mapping, check out BridgeDbR.

[Kevin Blighe]

Good book

[mrashad]

Thanks a lot for this suggestion.