Question: Metabolite identification package
0
gravatar for johnhamre3
16 months ago by
johnhamre30
johnhamre30 wrote:

I am using xcms to analyze mass spec data.  However, I have been unable to find a package that can identify metabolites.  I tried MAIT but that doesn't seem to be working as well as I had hoped.  If anyone could steer me to a better package that would be appreciated.  Also, if you know of any tips to help it run that would also be appreciated.  I have raw data that can be converted to CDF, mzdata, etc.  Thanks!

ADD COMMENTlink modified 16 months ago by Johannes Rainer1.5k • written 16 months ago by johnhamre30
Answer: Metabolite identification package
0
gravatar for Johannes Rainer
16 months ago by
Johannes Rainer1.5k
Italy
Johannes Rainer1.5k wrote:

I guess you have already identified the chromatographic peaks/features with xcms, what you could do then is to use the CAMERA package to find adducts and isotopes in your data. Ultimately you will however have to look up the m/z of your peaks in a database (like hmdb (https://hmdb.ca)) to find possible candidate metabolites.

Some time ago I did start a package that would build metabolite annotation packages to aid in this identification step - but didn't have the time to finish that yet. You could get the package from https://github.com/EuracBiomedicalResearch/CompoundDb

cheers, jo

ADD COMMENTlink written 16 months ago by Johannes Rainer1.5k
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