In an ion source that generates ions by matrix-assisted laser desorption (MALDI), ion acceleration diaphragms having apertures though which ions are accelerated and which have become contaminated by matrix material, are cleaned by temporarily heating the diaphragms. During the cleaning process, the sample support plate is moved aside but remains in the ion source housing, and the heating is preferably limited to regions surrounding the apertures in the diaphragms. In one embodiment, the diaphragms are heated by irradiation generated by infrared laser diodes.