A proton bomb was a type of bomb, a proton weapon which only destroyed organic matter when exploded.
History and specifics[]
In 2266, when the USS Enterprise discovered an uninhabited planet which was also a duplicate of Earth, Captain James T. Kirk speculated that it may have been depopulated in a proton bomb war. However, Spock pointed out that there would still be skeletons and vehicles left behind, of which there were none. (TOS comic: "The Voodoo Planet")