Can you send us your files?
We would like you to send us your Skyline document, some of your .raw files, and the FASTA file that you provided to the "File > Import > Peptide Search" wizard.
In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.
You can upload that .zip file, your .raw file(s) and your FASTA file here:
https://skyline.ms/files.url
Your Skyline document is probably empty because you were trying to do "File > Import > Peptide Search" into an empty document, but it will still be useful for us to see that document because it will tell us some things about your settings and the version of Skyline that you are using.
-- Nick