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CAMERA / Variable isotope labeling
I have a large dataset of standard compound mixtures that have been isotope labeled to varying degrees such that the basepeak in many cases is not the monoisotopic peak. I'd like to characterize the isotope envelope of the average MS spectrum for each compound across all my samples. Is there way that I can use XCMS alone or together with CAMERA to export this information in batch for each compound as a .csv file?
My initial attempts using default settings to create the xcmsSet object together with the findIsotopes function is not doing a good job finding isotopes in the test file I'm using. I noticed there is a C12/C13 ratio slot with 3 possible settings (not sure what they mean) that may prevent analysis of my data.
Your thoughts are much appreciated!