Proton weapons, which could be used in the form of proton beams or proton bursts, were proton-based directed energy particle weapon or beams used in weaponry. Proton beams were very tightly focused so that it was as if the target was hit by thousands of needles. They could penetrate any shield even if the modulations were changed.
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")
Ramuran vessels utilized proton weapons, whbich proved to be particularly effective against USS Voyager, in a 2374 encounter. However, Ensign Harry Kim and a tracer called Kellin became the first to develop a defense against the weapons, by tying USS Voyager's baryon sensors into the deflector controls. This allowed the deflector to scatter the incoming beams, making it harder for them to penetrate the shields. (VOY: "Unforgettable")