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Photonic torpedoes were armed with antimatter warheads. The fact that the Earth Starfleet vessel Enterprise NX-01 was using weapons with antimatter warheads in 2153 came as a surprise to the Klingons. (ENT: "The Expanse")
In 2268, the crew of the USS Enterprise utilized a telemetry probe armed with an antimatter warhead to destroy the space amoeba. The warhead was a simple magnetic bottle containing the charge, programmed with a timing detonator fuse. (TOS: "The Immunity Syndrome")