The high precision of PT comes as a double-edged sword since PT is normally less robust than X-ray radiotherapy. Several uncertainties, such as changes in anatomy, positioning, organ delineation and systematic uncertainties can have a significant impact on where the final dose is delivered. The reliability of PT has increased in recent years with robust treatment planning, however, it still remains sensitive to larger uncertainties that have to be minimized to exploit the full benefit of PT.

The clinical workflow in PT has been adopted from conventional X-ray radiotherapy, where the treatment plan is based on the initial computed tomography (CT) scan of a patient. Since, the treatment usually lasts several weeks, it is likely that the initial treatment plan becomes less valid due to the changes of the patient anatomy as the treatment progresses.