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Topic: Peak deconvolution and identification (Read 4616 times) previous topic - next topic

Peak deconvolution and identification

We are new in using XCMS and we have some questions.
-Is there a package in R that can be used for peak deconvolution?

-Once you have a XCMS peak table or a table made with CAMERA, how do you indentify the different metabolites?
Is their an automated tool, where you can upload your table, which then identifies the different compounds and puts a name on it?

Re: Peak deconvolution and identification

Reply #1 –
Hi @LiseD , that is a good question. If such a package would exist, than lots of metabolomics researchers would be out of work. There is plenty of literature that can help you on the way on how to identify/annotate the different metabolites in your sample. If you run standards with your experiments, it would be a good start to see if they co-elute with any of the LC-MS peaks in your sample. Then, you could use literature data to find masses (and perhaps an indication of the retention times) of expected metabolites and see if you can find any potential matches. Be careful, however, as a match based on mass (or most likely elemental formula), is no definite identification. For an overview of (quite) recent metabolomics tools, see: http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract For more information on metabolite ID using mass spectrometry data, see papers like http://link.springer.com/article/10.1007/s11306-013-0519-8 (and refs therein) and http://pubs.acs.org/doi/abs/10.1021/ac503325c
Hope this helps! Sorry there is no short and easy answer to this question :-)