Being a Tac officer, I was looking at what skills would improve the already-awesome dps of the proton rifle, and discovered something interesting. According to the skill tree, the antiproton bolt (default attack) is modified by Assault Training, Special Forces and Firearms. The proton beam (secondary attack) is linked to Close Combat, Soldier and Firearms.
If the gun is a rifle (as its name indicates), it should be tied to Assault Training and Soldier. If it's an assault weapon (as it's model suggests), it should be AT and SF. Why it's linked to Close Combat, I have no idea; that's supposed to be pistols and melee.
I'm pretty sure this is the only weapon that uses different skills for the two ranged attacks. Is this intended?