Could you send me your FASTA file?
It looks like that error could be caused by a protein name being blank. I am not sure whether the protein name I'm talking about is coming from your FASTA file, or from somewhere else.
If your FASTA file is less than 50MB you can attach it to this support request. Larger files can always be uploaded here:
https://skyline.ms/files.url
It might also be helpful if 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.
The particular line of code that the error is happening on is new code that was added to Skyline a few months ago (part of the "Group at gene level" new feature, although this code gets executed regardless of whether you check that option).
-- Nick