The review is devoted to the development of promising new technologies for diagnostics and radiotherapy in oncology using the Prometheus proton therapy complex based on the Lebedev Physical Institute proton synchrotron. The technologies of proton radiography and tomography, proton therapy with a scanning 'pencil' beam taking into account the intrafractional movement of a tumor, are presented. The results of research in the field of developing new binary technologies for sensitization of proton therapy using targeted nanoparticles are undergoing evaluation at the Russian proton therapy complex at the A’Tsyb Medical Radiological Research Center — a branch of the National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, which ensures the implementation of developed technologies in medical practice. Optimization of the modes is achieved with the support of mathematical modeling of nuclear reactions and sensitization reactions in proton therapy. A project for upgrading the Prometheus proton therapy complex for irradiating tumors of various localizations is presented.