A mass spectrometry using helium as cooling gas is performed to obtain a first mass spectrum (S1), and another mass spectrometry using argon, which is heavier than helium, as cooling gas is performed to obtain a second mass spectrum for the same sample (S2). Due to the difference between the two gases in terms of the effect of promoting dissociation of modifications, an ion peak originating from a target compound from which all the modifications have been dissociated will appear with a higher intensity on the second mass spectrum. The peak patterns of the two mass spectra are compared to locate the all-dissociated ion peak while excluding unnecessary peaks (S3). Based on that peak, the assignment of each peak is determined (S4). Such a method is effective for enhancing the accuracy of the determination of the assignment of the peaks on the mass spectra and for improving the accuracy of identification or structural analysis in the case of a mass spectrometry of a compound to which an easily dissociable modification, such as a Sialylated glycosylated peptide, is bonded.