The insulin-producing beta cell in the islet of Langerhans is central in glucose homeostasis. Its dysfunction is part of the pathogenesis of both Type 1 and 2 diabetes mellitus. In both forms of the disease, there is a cytotoxic component either induced by cytokines, as in Type 1 diabetes, or by elevated levels of glucose and fatty acids, as in Type 2 diabetes. To find the mechanisms responsible for the cytotoxic effects of these compounds proteomic approaches with 2D gel electrophoresis and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry have been undertaken. In this article, we describe these methods, and other methodological aspects of protein profiling of pancreatic islets, and summarize the results obtained with these methods.