In a mass spectrometer having ion sources capable of switching between atmospheric pressure chemical ionization and electron impact ionization, a first gas chromatography device capable of separating a sample to meet a condition suitable for atmospheric pressure chemical ionization measurement is connected to upstream of an atmospheric pressure chemical ionization ion source. Part of the sample separated by the first gas chromatography device is introduced to a second gas chromatography device by distributing a flow channel. In the second gas chromatography device, a target substance and background ingredients contained in the sample are further separated and are introduced to an electron impact ionization ion source. By separating the target substance from the background ingredients, an electron impact ionization spectrum of the target substance is obtained without an effect of the background ingredients.