For the time being, there is no option for deleting protocols in the Protocol repository, since that could mean deleting them for other users as well (for the ones invited to your team). However, you can archive them and recover any archived files or projects at any time. To do this follow these steps:
Select the protocol and click Archive.
When a window appears click the red button.
If you wish to restore the archived protocol, go to the Archive, select it and click Restore.