Re: Mzmed - mz of fragment or compound?
Reply #1 –
XCMS spits out "features" meaning all chromatographic peaks it can find for all masses (so think of it as XCMS doing extracted ion chromatograms for all possible masses and integrating all peaks it sees). Meaning that there might be many features in your list that come from the same compound. Some are pseudo moelcular ions, some are fragments, some are adducts, some are isotopes, some are noise, some are contaminants... You cannot even count on all compounds showing a pseudo molecular ion.
Probably the main challenge in metabolomics is exactly deciphering what is what. It is not a trivial task.
The typical first step to figuring what is what is to use the CAMERA package that try to group features according to which are likely to come from the same compound.