We report a method to establish experimental conditions for surface-enhanced Raman scattering (SERS) spectroscopy in order to avoid thermal damage on heat-sensitive materials by monitoring thermal desorption of thiolate molecules from a metal surface. Thiolate molecules adsorbed on gold desorb at 60-100 degrees C, which corresponds to the denaturation or degradation temperature of heat-sensitive materials (e.g. DNA, proteins, polymers, and lipid membranes). By observing the change in Raman signal from the thiolates on SERS substrate, it is possible to estimate the maximum power of excitation laser required for the samples to reach their critical temperatures for thermal degradation.