Ok, great ask!
So Protonic energy is a unique form of energy that was initially created by the science experiment that blew up when young proton was visiting a science exhibition and bathed him with said energy.
It's unique to him, (it is in fact kind of a total scientific mystery, the scientist who made the machine died in the explosion) and he has, over years of training, gained masterful control over it, allowing him to use it as a high intensity beam, or a more physical energy manifestation like a force beam or a glowing fist, or even a barrier, very handy.
One important aspect of his power is his ability to absorb energy and convert it into protonic energy. However, he has to be sort of, tuned to it and/or expecting the energy to come into contact with it, so blindsiding him with a bolt of electricity that he isn't expecting can still hurt him.
The energy also fuels his super strength and such. He's always fairly strong, extra so when properly geared up with his protonic gear, but It's when he's properly powered up that he can do the real super stuff.
So, on to limits. One of the major limits is he has an 'internal battery', let's say, of energy. He can absorb more as the battle goes on, but the more power and super-strength he uses, the more it runs down.
Additionally, the longer whatever situation is going on, the higher the cost of energy uses gets. The more his body wears down, the more it costs to keep going at the same level, basically.
He CAN push past this limitation, using force of will to muster more protonic energy from his depleted body, but if he goes past his natural threshold it has a pretty heavy psychical cost on him afterwards. Even going over the limit a small amount can leave him totally exhausted for a day, and going further than that can have even more debilitating effects. Back when he was a sidekick, he once took it on himself to keep a suspension bridge from collapsing, and the resulting power-cost left him laid up for a solid two weeks.
As he's grown and honed his powers, the threshold has gradually increased, but he can never get too complacent, especially when greater threats loom on the horizon.