A variety of widely used mass spectrometers apply multipole ion guides to transport ions from one location to another and fragment them within the instrument. This fragmentation allows scientists to analyze the structure of materials. However, particularly in multiplexed collision-induced dissociation experiments, this transport approach either under-fragments or over-fragments the ions, yielding results that do not allow for structural characterization. PNNL's newly developed multipole ion guide solves that problem by supplying a stream of charged ions to the ion guide and applying a radio frequency (RF) field to confine ions through the guide.  When a particular excitation RF field is applied to one or more of the rods associated with the guide, ions at a particular secular frequency are disassociated while other ions are left intact, yielding more representative results.  The invention is particularly useful as a means of disassociating ions separated based upon mobility in an ion mobility spectrometer.