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!

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