It has been pointed out that the Skyline modification mechanism could be improved for glycans:

"For glycans, there is a straightforward way to get the chemical formulas, though it would take a bit more work. While there is a huge diversity in glycans (thousands of different ones), they are made up of relatively few building blocks (e.g., Hex, short for Hexose, or HexNAc, short for N-Acetylhexosamine). Having Skyline be able to understand a half dozen building blocks would allow it to get exact chemical formulas to a rich variety of glycans (e.g., HexNAc(4)Hex(5)NeuAc(1)) "

https://skyline.gs.washington.edu/labkey/announcements/home/support/thread.view?entityId=755c7aa2-5fd9-1032-950a-da202582e074&_anchor=17875#row:17875

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