The present invention aims at providing a method and apparatus for analyzing a mass spectrum on which multivalent ion peaks originating from a target compound appear, and calculating the mass of the target compound. First, each peak on the mass spectrum is analyzed to detect isotopic clusters, and the valence and the representative point (m/z value) of each isotopic cluster are obtained (S1 through S3). Since the range of the m/z value of the component which is added to or desorbed from the compound is limited, by using this factor, the isotopic clusters originating from the same compound are deduced. By combining the deduced isotopic clusters, the candidates for the m/z value of the added/desorbed component are deduced (S5). Among the plurality of selected candidates, clearly abnormal candidates are eliminated by using a plurality of conditions such as the degree of distribution of the m/z values and the similarity of the relative intensities of the representative points of the isotopic clusters (S6 through S9). The candidate having the smallest distribution of m/z values or the candidate having the highest similarity of the relative intensities of the representative points is finally selected. After the m/z value of the added/desorbed component is determined, the mass of the compound is calculated (S10 through S16).