The answer depends on how exactly the protons collide. In many circumstances the results of the collision can be explained in terms of electromagnetic forces and classical scattering theory. As long as the protons remain far enough apart during the collision, then the protons can be treated like two positively charged classical point particles. Even in a "head-on" collision, if the collision is low-energy, the protons may very well remain far enough apart to be treated classically since (classically) the closest they can get to one another is approximately $d\sim \frac{ke^2}{E}$, where e is the unit electric charge, E is the initial kinetic energy of the colliding particles, and k is the electric force constant (i.e., the magnitude of the force between two charged particles a distance $R$ apart is $\frac{kQ_1Q_2}{R^2}$).
On the other hand, if the collision is energetic enough that the protons can approach each other more closely that about $10^{-15}$ meters, then the so-called "strong force" comes into play, and a lot of interesting things can start to happen. This regime is the subject of advanced quantum mechanics and particle physics. You can find a fairly accessible (relatively speaking) description of this topic in Griffith's book "Introduction to Elementary Particle".
Cheers.