One thing that you should do in Skyline is go to:
Tools > Tool Store
and install the external tool called "MSstatsShiny".

This external tool in Skyline does not actually do anything, but when you install it, it does add some annotations and a report.
The annotations that it adds are named "BioReplicate", and "Condition".
It also adds a report called "MSstatsShiny".

I have never used MSstatsShiny, but what I am guessing you should do is go to "Settings > Document Settings > Annotations" and check the checkbox next to "BioReplicate" and "Condition" and then look at the Replicates report in the Document Grid and fill in values for those two columns to indicate which replicates are in which cohort (e.g. "healthy" and "diseased") and which are your technical replicates. If you do not have technical replicates then you should just set the BioReplicate value for each Skyline Replicate to a different integer.

Then you can use "File > Export > Report" and export the "MSstatsShiny" report to a CSV file. You should choose "Invariant" in the "Language" dropdown at the bottom of the Export Report dialog.

After that, I am not sure what you should do with the CSV file but hopefully you will be able to figure it out from there.
-- Nick