An imaging mass spectrometer, an image of a sample is generated, and a region in the image is selected in accordance with predetermined criteria. Then, a mass analysis of the region is performed while scanning the sample in the selected region with a laser beam spot. By computing the total or average of the results in the region, a high precision analytical value in the region can be obtained. In a biological sample, by preliminarily performing a staining process on the biological sample using a certain dye, only the objective tissues can be analyzed. Also, a fluorescence microscope can be used.