Radiotherapy is an effective type of anticancer treatment due to its localized impact and fewer side effects. Nowadays, proton therapy has become a more common choice than photon-based radiotherapy due to its advantages, including independence from tumor oxygen supply and the deposition of energy at the end of the penetration path (the Bragg curve). However, the benefits of radiotherapy are limited by the radioresistance of the irradiated cells. Several approaches have been proposed to overcome this limitation, including the use of radiosensitizers - molecules that selectively increase the damaging effects of irradiation on cancer cells. This kind of combined therapy (chemoradiotherapy) improves the anticancer treatment efficiency, increasing the patient's survival rate. However, biochemical changes induced in cancer cells by chemoradiotherapy are still unexplored at the submicroscale. In this study, Raman microspectroscopy was employed to monitor such changes in radioresistant prostate cancer cells exposed to proton therapy and a combined treatment of protons and selected radiosensitizers (C75, silibinin). Since the irradiation-induced effects are very weak, the analysis was supported by statistical methods (Partial Least Squares Regression, Random Forest classification). Our results reveal an overall cell response to proton therapy similar to that of X-ray treatment. However, a detailed analysis indicated a different protein-to-nucleic acids ratio between these types of radiotherapy. Finally, the chemometric analysis suggests clear differences in cell response to chemo-, radio-, and chemoradiotherapy, which has been confirmed by high output from Random Forest classification.