X-ray photoelectron spectroscopy (XPS) has been employed in order to study the effects of proton irradiation on herring sperm single-stranded DNA. Systematic changes of the chemical shifts in the C, N, O, and P XPS line components as functions of the irradiation dose were observed, indicative of the bonding configurations in the DNA system. While the C 1s XPS lines showed weak blueshifts, the N 1s, O 1s, and P 2p XPS lines showed blueshifts with a marked dependence on the irradiation dose in a prominent manner. Our results show that linear energy transfer by charged particles and photons may have distinct molecular-level effects as the C 1s, N 1s, O 1s, and P 2p XPS lines showed redshifts in our previous study of effects of the γ-ray irradiation on the same system.