The review is devoted to the development of new technologies for diagnostics and radiotherapy in oncology using the "Prometheus" proton therapy complex based on the LPI proton synchrotron. The approaches of proton radiography and tomography and scanning "pencil" beam proton therapy taking into account the intrafractional tumour motion are presented. The outcomes of research in the field of evolvement of new binary technologies for sensitization of proton therapy applying targeted nanoparticles are tested on the Russian-made proton therapy complex in the A. Tsyb Medical Radiological Research Centre — Branch of the National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, which provides the transfer of elaborated technologies into medical practice. Optimization of modes is achieved with the help of mathematical modelling of nuclear reactions and sensitization reactions in proton therapy. The project of modernization of the proton therapy complex "Prometheus" for irradiation of tumours of different localization is presented.