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An antiproton beam was used as a mounted starship weapon on the doomsday machine planet killer The machines highly refined technology was able to fire beams of pure antiproton, a fact which Federation scientists found astounding. (TOS episode & novelization: The Doomsday Machine)
In the 25th century Voth and Fek'Ihri starships were armed with antiproton weapons. Voth infantry and exosuits were also armed with antiproton weapons. (STO episodes: "Fek'Ihri Return", "Solanae Dyson Sphere")