Another question: When using Refine Advanced Document Remove repeated peptides - does Skyline remove the extra copies of each peptide from the protein entries with the lowest number of peptides? This would be highly desirable to remove proteins with the lowest number of peptides from an assay library. For instance, if a protein is only represented by a single peptide that is also matching to another protein that is represented by multiple other peptides then it would make no sense to leave the protein represented by a single peptide and remove the peptide from the other protein that also contains additional peptides.
Thanks for any feedback on this question!
Dietmar