A sample analysis system incorporates an ion removal mechanism for removing residual ions from the sample analysis system. The ion removal mechanism can be included in an ion optics assembly, which connects an ion mobility filter to a mass analyzer. A sample to be analyzed by the sample analysis system may be entered into an ion mobility filter. The ion mobility filter filters the ions of the sample and passes the filtered group of ions to the ion optics assembly. The ion optics assembly transports the filtered group of ions to a mass analyzer where some or all of the ions in the group are detected. The ion removal mechanism then removes all or substantially all residual ions from the ion optics that were left over from the first filtered group before a second filtered group is passed through.