Why my total abudance on the chormatograms change if I chnege the retention extraction window??

holly1984
holly1984
in Instrumentation and Mass Spectrometry
Good afternoon everyone,

I am having issues with a couple of isomers. They share the same ion transition but they have different retention time. When I process the results I exctract the same transition and I offset only the time windowm to better center the two peaks. However then I have a different total abundance reported in the chromatograms (value reported in the red boxes) which makes it seems like I am taking them from two different samples. Is it normal or I am making some mistakes? Should not this value stay constant if my refernce peak, i.e. 100% peak, did not change?

Thanks

Holly


Answers

  • MarcNoble
    MarcNoble
    Hi Holly - It looks like that might just be a function of smoothing during the integration step.  Maybe make some changes to the processing method and see if they have an effect on the TIC measurement to verify.  Good luck!
  • holly1984
    holly1984
    Thanks a lot,
    I will try.
  • holly1984
    holly1984
    if I have the same smoothing parameters tho for both isomers, should it not be the same?

    Thanks

    Again

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