Thanks for your question. Can you please send me a link to your library folder on PanoramaWeb so that I can better understand what you need? You can send it to me separately at firstname.lastname@example.org if you prefer.
It sounds like you have several Skyline documents with the same protein (i.e. same sequence) but with a different label/name in each document. And when you are looking at the protein details in PanoramaWeb, for example, you want to be able to see coverage from peptides in all proteins in the library folder that have the same sequence. Does this sound right? Or are you looking at different protein isoforms? I assume this is a peptide-level (not protein-level) library folder on PanoramaWeb since protein uniqueness in a protein-library folder is determined by the protein sequence if the Skyline document has that information. And you should only be able to have one "version" of a protein (unique sequence) in the library.