If you look at existing protocols, they do seem to mostly use MAJOR.MINOR.
e.g. HTML/1.1, SSH 2.0, USB 3.1
Some only use MAJOR, presumably as they don't generally support backwards compatible changes or as the change in version number is so infrequent that it doesn't seem worth using two fields.
So it sounds like PATCH doesn't make much sense for a protocol and you should be good using MAJOR.MINOR.