The present invention relates to a method for identifying a chemical structure of a wide variety of low molecular weight compounds using mass-to-charge ratio and collision cross section of fragment ions of an analyte compound. The analyte compound is ionized and fragmented, and the fragment ions are measured by a mass spectrometer with an ion mobility spectrometry measurement device. According to the present method, it does not depend on any compound class-specific characteristics or structural features, therefore enabling determinations of any classes of low molecular weight compounds, which does not limit to a specific compound class. The present invention comprises three methods which share a common data structure and s data processing method.