In the present work we investigate the denaturation of a functional protein, horseradish peroxidase (HRP), under various experimental conditions using time-of-flight secondary ion mass spectrometry. HRP was immobilized on TiO(2), and the samples were stored under different conditions. The activity of the enzyme was assessed colorimetrically and compared to ToF-SIMS spectra. We show that denaturation of the protein can be monitored using the ToF-SIMS signal of the disulfide bonds, which is related to the tertiary structure of the protein. As disulfide bonds appear in a vast range of proteins, the present findings may be of wide significance; i.e., a tool is provided that can allow the investigation of the presence of an active protein structure by a comparably simple surface analytical method.