Have you tried using the Group Comparison feature in Skyline? You can get to it with the menu item:
View > Other Grids > Group Comparisons > Add
Settings > Document Settings > Group Comparisons
The Grouped Studies tutorial also talks about this feature ("Simple group comparisons in Skyline), starting at page 63 in the tutorial:
The group comparison feature in Skyline is almost as good as MSstats, and works well on small molecule data.