An apparatus for analyzing mass spectrometric data is described. The apparatus has a first input section for entering first data of an ion measured by mass spectrometry, a second input section for entering second data of a dissociated ion of the ion measured by mass spectrometry, a first data storing section for storing third data of mass spectrometry of a plurality of candidates for the structure of ion, a calculation section for producing fourth data of mass spectrometry of dissociated ions to be used in analyzing the plurality of candidates and an evaluation section for evaluating the plurality of candidates by making comparisons between the first and third data and between the second and fourth data, so that the structure of ion can be identified.