Hi, I have used XCMS to preprocess my GCMS data and for the first column it is mass value. Is the value the molecular weight of molecular ion? For GCMC, the ionization energy is 70ev, so i don't think we can see molecular ion. Then if it is not the mass of molecular ion, what is it?
Thanks very much!
That should be the de-convolved unique mass. You can check it by doing an extracted-ion-chromatogram use one of those m/z and check the RT in your samples.
In GC-MS if you have performed EI (electron impact ionization), then of-course what you see in a deconvoluted spectra is the M+ (molecular ion) which is ~ to the nominal mass (molecular weight) of the substance/ compound. However, if you have performed CI (gas based reactive- chemical ionization) then you would see [M+ Adducts] such as M+H, M+CH3 and so on. EI would match to your databases exactly (as all GC-MS operate at 70 ev unless changed purposefully), while CI would help you in unknown discovery etc. XC-MS's online version also works equally good.
If you are not seeing molecular mass, which you may not see for many of the compound types then you are seeing one of the fragment ions, which could be due to loss of fragments such as water if the hydroxy group is present or loss of methyl group etc. Depends on type of compounds you have.
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