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The proton is one of the three basic particles that make up the baryonic atom. It is a baryon (heavy particle), and a hadron. It is composed of two up and one down quark held together by gluons, for a total charge of +1. Its antiparticle is the antiproton, with the same mass but opposite charge.

Cosmic strings are no wider than a proton, but have gravitational fields as powerful as a black hole. (TNG: "The Loss")

Protons were found in the Denorios belt that were emitted by the Bajoran wormhole. (DS9: "Emissary", "If Wishes Were Horses")

In 2372, the crew of USS Voyager found themselves being bombarded by protons after Q reduced them and their ship to subatomic proportions in an attempt to escape from Q. Captain Janeway suggested releasing a positive ion charge to repel the protons, but the crew and ship were transported from that location before the attempt was made. (VOY: "Death Wish")

Later that year, B'Elanna Torres infused Voyager's warp core with proton bursts from the sensor array in an attempt to compensate for a drain in their antimatter supply. However, the drain was caused by a duplicate Voyager formed when the ship traveled through a divergence field, and the proton bursts caused severe damage to the other ship. (VOY: "Deadlock")

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