Antiproton's (often referred to as "AP's") are the exact opposite of regular protons.
As a form of antimatter, Antiprotons react violently with all forms of regular matter in an annihilation reaction, releasing energy. Hydrogen (in essence, individual protons) and AP's interact in a matter-antimatter reaction in controlled reactors, which then creates the power that runs the ship. Almost every ship of every race uses AP's to fuel and power their systems, because it is extremely efficient. The Andromeda Ascendant has massive Antiproton Storage Tanks, which are very well armored because of the potential risk of explosion. The Andromeda also uses Antiproton Cannons to help defend herself from incoming missiles.