In my organization we develop our own protocol, we would like to know if there's a way to sign these protocols like Skyline signs their own protocols.
This way eg. we would know if that version has passed all checks in our CI/CD flow and hasn't been altered
No, it's not possible to sign a protocol yourself. Only Skyline (or an authorized third party) can sign a protocol.
So, it's not immediately possible to know if your protocol was changed, but maybe you could consider tightening the security so that as little people as possible have access to editing protocols...