Despite the widespread use of UV254 irradiation and solar disinfection for water treatment, little is known about the photochemical pathways that lead to virus inactivation by these treatments. The goal of this study was to identify reactions that occur in virus capsid proteins upon treatment by UV254 irradiation and 1O2, an important oxidant involved in sunlight-mediated disinfection. Bacteriophage MS2 was inactivated via UV254 irradiation and exposure to 1O2 in buffered water, and their capsid proteins were then analyzed with MALDI-TOF-TOF and ESI-TOF before and after digestion with protease enzymes. The results demonstrate that chemical modifications occur in the MS2 major capsid protein with both treatments. One oxidation event was detected following 1O2 treatment in an amino acid residue located on the capsid outer surface. UV254 treatment caused three chemical reactions in the capsid proteins, two of which were oxidation reactions with residues on the capsid outer surface. A site-specific cleavage also occurred with UV254 irradiation at a protein chain location on the inside face of the capsid shell. We attribute this UV254 induced protein scission, which is nearly unprecedented in the literature, to a close association between the affected residues and viral RNA, an efficient UV254 absorber. These results suggest that viral protein oxidation by UV254 and 1O2 may play a role in virus inactivation and that viral inactivation may be tracked with mass spectrometric measurements.