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Protons were generated by a starship's sensor array, and a burst used to maintain the reaction in its warp core. Their use caused stress on the vessel's hull and could cause extensive damage if its structural integrity was not reinforced. Magnetising the hull was a method of reducing the impact. The vessel's sensor array could not be used during the procedure. (citation needed • edit)
In 2153, the Borg-assimilated transport Arctic One fired what Malcolm Reed characterized as "some kind of proton burst" at Enterprise NX-01, much to his surprise, as such a transport was normally unarmed. (ENT: "Regeneration")
In 2372, the USS Voyager attempted to use proton bursts to deal with an apparent antimatter drain. The vessel was heavily damaged by bursts generated by a duplicate of Voyager occupying the same space-time location as a result of a spatial scission. (VOY: "Deadlock")