A method and apparatus for estimating the structure of an unidentified substance produced from an original substance having a known structural formula through partial structural change caused by metabolism or the like. A mass difference between a product ion, originating from the unidentified substance and having a partial structure including a structural change site, and a product ion, originating from the original substance and having a partial structure prior to the structural change, is equal to the mass difference between the original substance and the unidentified substance. Therefore, when pairs of product ions each having such a mass difference are selected to be compared with partial structures obtained from the known structural formula of the original substance, a minimum common partial structure having the structural change site is obtained.