You must use a protocol to establish meaningful communication across a channel. It is important that both parties to the communication use the same protocol.

This is particularly important for the D channel. Your signalling requests and responses must be understandable by the network. Even if your ISDN device and ISDN line are both functioning correctly, you might not be able to make successful calls if you're using a D channel protocol that isn't the same as the network's.

ISDN requires that you use a protocol defined by the ITU-T called Q.931 for signalling in the D channel.  However, there are several signalling protocols based on Q.931 in use round the world.  For instance, NI-1 and 5ESS are used in North America while much of the rest of the world is now using EuroISDN (also called ETSI or DSS1).

You have a much greater choice of protocols for the B channel since the B channel is a neutral conduit for data of any type. You can use it to transmit any protocol you wish (eg. SNA or PPP). However, if the network doesn't understand the protocol it cannot give you any assistance if your call has to be delivered to a different type of network (eg. PSTN) where data conversion is required.