A mass spectrometer 1, which is for generating a product ion from a precursor ion derived from a sample component having a hydrocarbon chain to analyze a mass, includes a reaction chamber 2 into which the precursor ion is introduced, radical generating units 51, 52, and 53 that generate a radical having an oxidizing ability or/and a radical other than a hydrogen radical having a reducing ability, a radical irradiation unit 54 that irradiates the inside of the reaction chamber 2 with the generated radical, a separation detection unit 3 that separates and detects the product ion generated from the precursor ion by a reaction with the radical according to a mass-to-charge ratio, and a structure estimation unit 14 that estimates the structure of the sample component based on the mass-to-charge ratio of the detected product ions and the information on the structure or the structure candidate.