Basically, the components of a protobomb is the same as any normal bomb, the only difference is that the plasma is heated well beyond the 500 degree limit of the plasma heaters in toxins.
To make any bomb, you get an igniter, a signaling device*, and a small tank of (heated) plasma, and a screwdriver and welder to construct it. You use the screwdriver on the igniter and signaling device, put them together, use the screwdriver on the resulting component, put that on the tank of plasma, and use the welder (after turning it on, of course) on the bomb. There are guides that explain it better, but those are the basics.
* A Remote Signaling Radio, a Timer, or A Proximity Device. Timers are the most common, and if you're actually considering a protobomb, there's no reason to use anything else.
Heating the plasma, specifically to levels capable of ruining the game for everyone, is accomplished from taking plasma from an engine. That's done by hooking an empty large plasma tank to an inlet, draining some plasma from the engine, and then hooking up an empty small plasma tank to the large tank and filling it with the superhot plasma. Now, main-engine plasma can get hot enough to destroy much of the station itself, but the protobomb, one capable of knocking out the server, is largely possible only with the prototype engine and the sheer amount of heat that's generated when several tanks of burning plasma occupy only three squares. It takes a lot of setup to get it running, and if you aren't allowed to get the prototype engine up you're screwed (or at least hindered), but if you've got access to engineering, you've got all the tools to make one.