Hi, team

I am currently analyzing DIA results using the Skyline button on DIA-NN in conjunction with Skyline24.1.
I am processing the identified proteins and peptides in Associate Proteins, and I am wondering if there is any difference in the processing when “Assigned to the protein with the most peptides” is selected in "Shared peptides are:" and when “Remove subset proteins” is additionally selected.
My understanding is that if the former process assigns the peptides to the protein with the most peptides, all subset proteins that can be explained by other proteins will be assigned to other proteins and removed, but as shown in the attached image, after selecting “Remove subset proteins”, Proteins, Peptides, and Shared Peptides were further reduced.
I would appreciate it if you could tell me which Proteins, Peptides, and Shared Peptides are removed by each command (Assigned to the protein with the most peptides, Remove subset proteins).

Sincerely,
Honda