You cannot have all of your replicates be the same condition. The Group Comparison is comparing values between two different groups.
You are not required to call your two conditions "Healthy" and "Diseased". You can change the annotation definition by going to:
Settings > Document Settings > Annotations > Edit List > Edit
and either type in some different values in the Value List or change the Annotation Type to "Text".
Then, make it so that the Condition of each replicate is the name of its drug treatment.
If you are getting errors about duplicate rows, one thing that you can do is go to:
Refine > Remove Repeated Peptides
This will make it so that your document contains only one copy of each peptide. This ends up removing more than is strictly necessary to get MSstats working, since MSstats can handle duplicate peptides so long as they belong to separate proteins.
If you would like, you could send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here: