Try this query, this is what runs when pulling up the full protocol list on the protocol groups page, except I removed the 1000 limit. This command can be run from a regular cmd prompt and it will pipe the results to protocols.txt in the directory where you ran the command.
mysql -D reporter -t -e "SELECT ID, IfNull(pd.Name, p.Name) as 'Name', Encapsulation, IfNull(pd.Description, p.Description) as 'Description' FROM protocol_definitions p left outer join protocol_domains pd on pd.protocolId = p.id and pd.domainId = 1 INNER JOIN protocol_groups pg on p.ID=pg.ProtocolID and groupID=1 ORDER BY Name, Encapsulation;" > protocols.txt