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The proton is a subatomic particle, a type of hadron and baryon. Together with neutrons and electrons, protons make up atoms.

The hydrogen atom consisted of an electron circling a proton. (TNG: "Night Terrors")

Cosmic strings were no wider than a proton, but had 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")

A set of binary pulsars encountered by Voyager in 2374 emitted random proton bursts, which Ensign Harry Kim believed might pose a hazard to the ship's shields. (VOY: "Scientific Method")

These "proton bursts" were referenced in the same context as those mentioned as being weapons.

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