In a method of measuring by a tandem mass spectrometer a sample labeled with an isotope, measuring throughput is improved. In a technique in which tandem mass spectrometer is used to analyze a sample labeled with an isotope, spectra obtained by a first-stage measurement (MS.sup.1) are analyzed during a measuring session in a realtime fashion to determine ions to be used in second-stage and subsequent dissociation.cndot. spectral measurement (MS2).