A Protocol is any notebook Entry that has the word "protocol" in its title. Protocols are special because you can inject a copy of a protocol's content directly into another entry. You can view all the lab's protocols in the 'Protocols' link in the side menu. Lab Members with the Collaborator role don't have access to the list of Protocols.
Inserting Protocols into Entries
In the Entry type a plus character (+) at the beginning of a new line in your entry. Keep typing to filter the list and simply click one in the list to copy its content