Multipole ion guide ion trap mass spectrometry with ms/ms.sup.n analysis

Abstract

A Time-Of-Flight (TOF) mass analyzer is configured with a multipole ion guide in the ion path between the ion source and pulsing region of the mass analyzer, and enables trapping or transmission of ions from an atmospheric pressure ion source. The mass-to-charge (m/z) range(s) of ions transmitted through or trapped in the ion guide can be selected. Ions with stable trajectories can undergo Collisional Induced Dissociation (CID). During ion fragmentation, the ion guide potentials can be set to transmit or trap fragment ions produced by CID. The parent and fragment ion population can be delivered from the ion guide to the pulsing region of the TOF mass analyzer for mass analysis. After the first fragmentation step, the ion guide potentials can again be set to select a narrow m/z range to clear the ion guide in trapping mode of all but a selected set of fragment ions. M/z selection and ion fragmentation can be repeated a number of times with mass analysis occurring at the end of all the MS/MS.sup.n steps or at various times during the MS/MS.sup.n stepwise process. Additionally, the normally stepwise MS/MS.sup.n analysis function can be merged into a single step, increasing the effective duty cycle. In all embodiments, the ion guide can reside in one vacuum pumping stage or can extend continuously into more than one vacuum pumping stage.