Waveform activated rearrangement of n-butylbenzene molecular ions during tandem mass spectrometry in the quadrupole ion trap

The "molecular thermometer," n-butylbenzene, when analyzed by tandem mass spectrometry, produced an unusual product ion mass spectrum. Instead of the expected tandem mass spectrum containing fragments at m/z 91 and m/z 92, an unexpected base peak at m/z 119 was observed. Tandem parameters such as q_z, collision-induced dissociation (CID) voltage, trap temperature, and space charge were examined. When n-butylbenzene was analyzed by other ion trap mass spectrometers in our laboratory and other laboratories, analogous results were obtained. This phenomenon was investigated and found to be associated with the Varian protocol used in ion isolation during the tandem mass spectrometry experiment on commercial instruments. Studies were performed in an attempt to cool the precursor ion prior to activation with no change in the mass spectrum. Comparison of n-butylbenzene with other butylbenzene isomers gave evidence that rearrangement was taking place during the isolation of the precursor in the tandem experiment. Thorough investigation of the commercial protocol was undertaken that linked the cause of the rearrangement to the broadband waveform used in the precursor ion isolation step of the tandem mass spectrometry experiment.