A smart FAIMS sensor system and method includes a 2/2-electrode filter that pumps the ions through the system and separates the ionic species, a detector for collecting the separated ions and generating a detector signal in response to the collected ions, and a controller configured to change the operating parameters of the system in response to changes in the sensor's environment detected by the sensor. The ability to dynamically change the operating parameters of the sensor enables the sensor to maintain high sensitivity to environmental threats while decreasing the incidences of false positive events.