To overcome the difficulties inherent in conventional proton therapy systems, new techniques are described herein for synchronizing the application of proton radiation with the periodic movement of a target area. In an embodiment, a method is provided that combines multiple rescans of a spot scanning proton beam while monitoring the periodic motion of the target area, and aligning the applications of the proton beam with parameters of the periodic motion. For example, the direction(s) and frequency of the periodic motion may be monitored, and the timing, dose rate, and/or scanning direction and spot sequence of the beam can be adjusted to align with phases in the periodic motion.