One protocol to use would be MODBUS.
It's not rocket science but it is standardized.
If you're talking on a bus it's good to have a bit of error detection and knowing how long a message is so you can turn around the direction and respond.
Sure, you could make your own standard, but why?
I'm running a Raspberry Pi with RS-485 to a dozen nodes.
The first one already happened to be MODBUS, so I stuck with it.
There's also CANBUS, but it's a bit more tricky to deal with.