An apparatus for separating ions includes providing a FAIMS analyzer region defined by a space between a first electrode surface and a second electrode surface and extending between an ion inlet end and an ion outlet end. An asymmetric waveform is applied to the first electrode surface and a compensation voltage difference is applied between the first and second electrode surfaces. An output signal is provided from a temperature sensor, the output signal relating to a temperature within the FAIMS analyzer region. In dependence upon the output signal, the temperature within the FAIMS analyzer region is controllably affected. The apparatus supports operation of FAIMS at temperatures different from the temperature of other components in a tandem multi-stage system, and supports the stable operation of FAIMS at different temperatures which increases the separation capability of FAIMS.