Currently, Skyline does nothing special to handle the case in MS1 full-scan filtering when the heavy isotope peaks of a light precursor interfere with the lighter isotope peaks of a heavy precursor. The impact, however, is highly predictable, and Skyline already has calculated the expected isotope distributions. Skyline should also be able to adjust ratios based on the proportion of the total isotope distribution captured by the chosen isotope peaks.

Part of porting Topograph features to Skyline.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.