The insulin-producing INS-1E rat cell line is widely used as a model for studying β-cells. It is a well-characterized cell line, mainly used in diabetes research. We established a 2-DE reference map for INS-1E cells. Using MALDI-TOF/TOF-MS/MS, we identified 546 spots. These included various proteins with an important role in β-cell physiology and with known roles as crucial proteins for diabetes development. We believe that the availability of this reference map will enhance our knowledge of β-cell physiology.