“Proton” treatment differs from standard X-ray (gamma-ray) therapy in that the precise beam is delivered by a cyclotron spinning stuff at half the speed of light. Think of the beam as delivering a packet of energy to the affected area, with minimal damage to surrounding tissue. Also, the beam does not go through the target — it delivers the energy there and then stops. There are magnets, a pole and hydrogen gas; then, magically, protons.
The whole enchilada costs about $160 million, give or take. There are 10 operational machines in the United States. More are being built, including one or two at Mayo Clinics.
As to treatment, apertures and compensators are made for each patient, and the focus is aligned by lasers. I even have tattoos on each side, so the lasers can do their work. (No, the tattoos don’t say, “Buy Berkshire Hathaway” or “I love you, Maudie Sue!”)