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Topic: Variable isotope labeling (Read 6925 times) previous topic - next topic

Variable isotope labeling

Hi,

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!

Re: Variable isotope labeling

Reply #1 –
Quote from: "Resveratrol99"
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? 
I'm not 100 percent positive, if I understand your problem, but I think it's possible with some R scripting. You have a list of (know) compounds and hence also their m/z value
and you want to retrieve the isotope intensities from all aligned samples. Is that so far correct?

Quote from: "Resveratrol99"
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.
The isotope detection assumes, as a general screening, unmodified/unlabled compounds, so this moderate performance is not surprising.
The next update for CAMERA includes a possibility to adjusted the allowed m/z differences and the intensity window, so molecules with heteroatoms like Cl should be recognized.
But as I mentioned above, a small script should solve your problem.