Patent ID: 6992285

Claim:
A method of analyzing a substance, the method comprising: (1) creating a continuous stream of ions in said substance and supplying the stream of ions to a mass selection device; (2) performing a mass analysis of the stream of ions in the mass selection device to select precursor ions of a selected mass to charge ratio of interest; (3) transmitting from said mass selection device a continuous stream of the precursor ions of the selected mass to charge ratio of interest; (4) supplying the continuous stream of the precursor ions from the mass selection device and a collision gas to a multipole and providing an RF signal to the multipole, the multipole is operated at a higher pressure than the mass selection device and functions as a collision cell; (5) fragmenting said precursor ions in the RF multipole by collisions with the gas molecules, in order to form primary fragment ions; (6) supplying additional alternating current to the multipole at a frequency selected to cause resonance excitation of a desired primary fragment ion mass-to-charge ratio, whereby ions with said desired primary fragment ion mass-to-charge ratio are excited and undergo collisions with the gas molecules causing production of secondary fragment ions; (7) modulating the alternating current signal applied in step (6) whereby periods in which said alternating current signal is applied alternate with periods in which the alternating signal is not applied; and (8) detecting the ion signal after fragmentation with a mass spectrometer and collecting one set of data for one spectrum, representative of the ion spectrum when the alternating current signal is applied and another set of data for another spectrum, representative of the ion spectrum when the alternating current signal is not applied, wherein said other spectrum can be subtracted from said one spectrum, to generate a subtracted spectrum showing the secondary fragment ions without the presence of the primary fragment ions except for any said primary fragment ions which are generated by step (6).