An inexpensive mass spectrometer system is provided. This mass spectrometer is capable obtaining structural information of a substance at an improved efficiency, and the time required for the analysis and identification of the substance has been reduced. Identification precision has also been improved. More specifically, this invention provides a tandem mass spectrometer system in which the sample is ionized at the desired polarity, fragment ions obtained by dissociating the ion is analyzed in first or second mass spectrometer section, polarity of the second mass spectrometer is determined based on the result of the analysis, and the mass spectroscopy is carried out. A method for the mass spectroscopy is also provided.