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