I am not sure I understand which part of editing the Skyline document is causing trouble.

We have the menu item:
Edit > Unique Peptides
which will show you which other proteins in your background proteome the peptides can be found in.

You can choose which peptides to add to a protein by selecting the protein in the Targets tree and choosing the menu item "Pick Children".

There's the menu item "Edit > Insert > Peptides".

Maybe it would help if you sent us your Skyline document.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files.

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

You might also want to look into the "Enforce Peptide Uniqueness By:" setting on the Peptide Settings "Digestion" tab. There you can specify that you want your document to contain only peptides which are unique to a single Protein, Gene or Species (as determined by the background proteome). It is expected that your target proteins also appear in this background proteome, for the algorithm to determine which Gene or Species they belong to.

Brian Pratt

Thank you very much but I was unable to edit the document properly ( attached).

Basically, I would like to maintain only the peptides that are exclusive to each isoform, so that I can be sure that I am monitoring isoform 1 and not 7 for example. I tried enforcing uniqueness by Proteins but all peptides get removed from the file.

How can I manage to maintain only exclusive peptides for each isoform?

Thanks. Best, Daniela

Can you send us a .sky.zip instead of the .sky file that you have attached here?
The .sky.zip will contain all the other files including the background proteome.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .sky.zip file.

You can upload that .sky.zip file here:
https://skyline.ms/files.url

I attached the document.

Thanks. Best, Daniela