A surface plasmon measurement instrument measures a change in a property (e.g., refractive index) of a material layer. The method includes providing a prism with a rear surface having a metal layer disposed thereon; providing the material layer on the metal layer on the rear surface of the prism; directing a source beam through the prism toward the rear surface in a vicinity of the material layer; performing at least two sampled measurements to detect light reflected from the rear surface and to produce two corresponding data sets; transforming the data sets to a transform domain; processing the transformed data sets to estimate a sample shift between the two data sets; and determining a change in a property of the material layer using the estimated sample shift.