A treatment planning system for generating a plan for treatment by radiation with charged particles beams applied by pencil beam scanning onto a target tissue comprising tumoral cells is provided. The treatment planning system performs a dose definition stage defining the doses to be deposited within the peripheral surface, a beam definition stage defining positions and dimensions of the beamlets of the PBS during the at least one high rate fraction, the beams definition stage including a dose rate definition stage comprising at least one high rate fraction, and a beamlets scanning sequence stage defining a scanning sequence of irradiation of the beamlets. The beamlets scanning sequence stage optimizes a time sequence of beamlets emission such that at the end of a fraction j, a dose is deposited onto at least a predefined fraction of each specific volume at a mean deposition rate superior or equal to a predefined value.