Which product ion is used as Qualifier and Quantifier

Which product ion is used as Qualifier and Quantifier johannes jaegers  2023-02-24

I use Skyline for metabolic flux analysis. I am tracing the conversion of isotopic labeled substrates into different metabolites. For this purpose I define the count of labeled ions in the precursor ion and let Skyline calculate the Ratio between the unlabeled and the different labeled metabolites in my samples.

Lately I want to trace the fate of nitrogen and on what position they will appear in amino acids (sidechain or headgroup). In this special case the precursor ions have the same mass but differ in only one product ion.

How can I define this ion to be the one being used as the quantifier for the calculation of the ratio?

Nick Shulman responded:  2023-02-25
The Qualitative Ion Ratio is the ratio of the sum of the non-quantitative peak areas to the quantitative peak areas.
You can change whether a particular transition is quantitative or not by right-clicking on the transition in the Targets tree.

Here is a .pdf file which I made showing how the Qualitative Ion Ratio feature works. This file was made before the feature was actually implemented in Skyline so it is possible there are some differences between what the feature looks like in the .pdf file versus what actually ended up getting implemented but as far as I know it is accurate.
-- Nick