A sample analysis system, comprising: an ion source; a differential mobility cell for passing through a first group of ions; a mass analyzer for analyzing the first group of ions and comprising a Q1 quadrupole analyzer, a Q2 collision cell, a Q3 quadrupole analyzer and a detector; an ion optics assembly for transporting the first group of ions from the differential mobility cell to the mass analyzer, the ion optics assembly comprising an ion removal mechanism for removing residual ions from the ion optics assembly, wherein the residual ions are ions from the first group of ions that remain within the ion optic assembly; and a controller coupled to the ion optics assembly, the ion removal mechanism and the differential mobility cell, the controller having a timer that defines at least a first time period representative of a time for passing the first group of ions through the differential mobility cell and ion optics assembly, a second time period representative of a time for operating the ion removal mechanism to remove the residual ions from the ion optics assembly prior to passing through a second group of ions through the differential mobility cell, the second group of ions being different from the first group of ions, and a third time period representative of a time for passing the second group of ions through the differential mobility cell and the ion optics assembly; wherein the controller is configured to operate the ion removal mechanism during the second time period to either: i) decrease an RF potential within the ion optics assembly to defocus ions and remove the ions from the ion optics assembly; or ii) apply a DC potential to electrodes in the ion optics assembly to cause the electrodes to generate an electric field to radially expel ions out of the ion optics assembly. an ion source; a differential mobility cell for passing through a first group of ions; a mass analyzer for analyzing the first group of ions and comprising a Q1 quadrupole analyzer, a Q2 collision cell, a Q3 quadrupole analyzer and a detector; an ion optics assembly for transporting the first group of ions from the differential mobility cell to the mass analyzer, the ion optics assembly comprising an ion removal mechanism for removing residual ions from the ion optics assembly, wherein the residual ions are ions from the first group of ions that remain within the ion optic assembly; and a controller coupled to the ion optics assembly, the ion removal mechanism and the differential mobility cell, the controller having a timer that defines at least a first time period representative of a time for passing the first group of ions through the differential mobility cell and ion optics assembly, a second time period representative of a time for operating the ion removal mechanism to remove the residual ions from the ion optics assembly prior to passing through a second group of ions through the differential mobility cell, the second group of ions being different from the first group of ions, and a third time period representative of a time for passing the second group of ions through the differential mobility cell and the ion optics assembly; wherein the controller is configured to operate the ion removal mechanism during the second time period to either: i) decrease an RF potential within the ion optics assembly to defocus ions and remove the ions from the ion optics assembly; or ii) apply a DC potential to electrodes in the ion optics assembly to cause the electrodes to generate an electric field to radially expel ions out of the ion optics assembly. i) decrease an RF potential within the ion optics assembly to defocus ions and remove the ions from the ion optics assembly; or ii) apply a DC potential to electrodes in the ion optics assembly to cause the electrodes to generate an electric field to radially expel ions out of the ion optics assembly.