I do not understand what you are describing, but if we could see an example of the proteins and peptide sequences that you are talking about it might make more sense.

It would 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 including background proteome.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

It might also be helpful if you could send us some screenshots of what you are looking at.
--Nick

Thanks for your kind response
and I apologize for my limited knowledge and English proficiency.

So, When performing the 'peptide setting -> background proteome' operation, if I set the option in 'Enforce peptide uniqueness by setting' to 'proteins', it removes all peptides overlapping with isoforms without considering isoforms.

Currently, our lab conducts protein analysis that includes isoforms. So, when we use skyline, we have to manually perform the 'unique peptide check' for all proteins, which is quite cumbersome.
Do you plan to add an additional unique peptide filter that considers 'isoforms'?
If not, I would appreciate any advice you can provide.

The file you requested couldn't be uploaded due to its large size.

thank you for reading

You can upload large files here:
https://skyline.ms/files.url

There is no limit to the size of files that you can upload there.

A different thing that might work better for you than the "enforce uniqueness by" option would be to instead use the menu item:
Refine > Associate Proteins

In the "Associate Proteins" dialog, there is the checkbox "Create protein groups".
Proteins which are not unique to a single protein will be put into a "Protein Group" and then you can look at those non-unique peptides and decide whether to delete them from the document.
-- Nick