Thanks for sending that Skyline document.
In your document, the light and heavy precursors have a different number of transitions, and the transitions have not been given any Product Names. When the transitions do not have names, Skyline matches up the light and heavy transitions based on their position under their parent precursor. This can lead to (for some) unexpected results, especially if a different pattern of transitions in the heavy and light precursor have been marked as non-quantitative.
If you would like Skyline to calculate ratios by summing up the light and heavy quantitative peak areas, without trying to match up the light and heavy transitions with each other, you can check the "Simple precursor ratios" checkbox at "Settings > Molecule Settings > Quantification".
-- Nick |