What do you mean "not recognized"?
Typically you would build a library from these peptide search results using "File > Import > Peptide Search" or the "Build" button on the Library tab at Settings > Peptide Settings.

Are you seeing some sort of error message?

It would be helpful if you could send us your files.

Files which are less than 50MB can be attached to these support requests.

You can always upload larger files here:
https://skyline.ms/files.url
-- Nick