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Strange peak quantification behavior

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Strange peak quantification behavior gabe  2017-10-12 16:13
 
I'm encountering a strange behavior lately that I hope someone could comment on. The automatically picked peak will show a surprisingly low AUC and when I look at the chromatograph the dashed lines (showing the area for quantitation) are in the right place. But the little black arrow showing which peak is picked is pointing at one of the less-abundant transition ions. If I manually re-select the RT-range, the black arrow jumps to the top transition and the AUC goes up to normal. Why is this happening?

Here's an example

Thanks
 
 
Brendan MacLean responded:  2017-10-12 16:49
Hi Gabe,
Please make sure Settings > Integrate All is checked. What you are seeing will happen when it is not checked and for some reason, Skyline decides the major peak you are seeing is not actually coeluting with the smaller ones.

Having "Integrate All" unchecked is really for when you are doing refinement and not quantification. It is intended to help you pick transitions that you might want to remove. This really needs to be improved, because a lot has changed in Skyline since I implemented it 8 or so years ago, but for the moment I just try to teach people to remember to check Integrate All for quantification.

Thanks for the nice example.

--Brendan