1. A mass spectrometry data processing method for processing mass spectrometry data that is obtained from each of a plurality of micro-regions that are set within a predetermined two-dimensional area on a specimen, said method comprising: a) a specific-site extraction step for extracting specific sites from microscopy images, which are obtained by labeling specific sites in said two-dimensional area or a portion thereof with a visualization marker; b) an analysis processing step for categorizing each of said micro-regions into a plurality of clusters based on similarity/dissimilarity of mass spectrometry data for each of the micro-regions so that micro-regions of high similarity belong to the same cluster; and c) a division count determination step for determining the total number of clusters used in said analysis processing step based on the results of a comparison between the spatial distribution of specific sites that are extracted by said specific-site extraction step and the spatial distribution of all micro-regions that belong to one of the plurality of clusters into which each of said micro-regions are classified in said analysis processing step.