High-field asymmetric waveform ion mobility spectrometry (FAIMS) focuses and separates gas-phase analyte ions from chemical background, offering substantial improvements in the detection of targeted species in biological matrices. Ion separations have been typically performed at atmospheric pressure and ambient temperature, although routine small molecule quantitation by LC-MS (and thus LC-FAIMS-MS) is generally performed at liquid flow rates (e.g., in excess of 200 L/min) in which atmospheric pressure ionization sources (e.g., APCI and ESI) need to be run at elevated temperatures to enhance ion desolvation. Heat from the ionization source and/or the mass spectrometer capillary interface is shown to have a significant impact on the performance of a conventional FAIMS electrode set. This study introduces a new FAIMS system that uses gas heating/cooling to quickly reach temperature equilibrium independent of the external temperature conditions. A series of equations and balance plots, which look at the effect of temperature and other variables, on the normalized field strength (E/N), are introduced and used to explain experimental observations. Examples where the ion behavior deviates from the predicted behavior are presented and explanations based on clusters or changes in ion-neutral interactions are given. Consequences of the use of temperature control, and in particular advantages of using different temperature settings on the inner and outer electrodes, for the purpose of manipulating ion separation are described. ecause of its high sensitivity and selectivity, liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) has become the method of choice for quantitation of bioorganic compounds in biological matrices such as urine or blood plasma [1][2][3]. To preserve LC conditions and flow rates typically used with LC-UV (e.g., 1 mL/min), mass spectrometer manufacturers needed to adapt electrospray ionization (ESI) sources, which were initially operated at much lower liquid flow rates [4,5], to achieve sufficient ion desolvation. Consequently, sources that use the addition of heat to accelerate ion desolvation were created [6,7] and further developed into the commercial sources that are used today (e.g., Heated Electrospray; H-ESI™ and TurboIonSpray; TIS™). Despite the widespread utility offered by LC-MS/MS, because of the complexity of biological matrices, in many instances (e.g., high background [8], co-eluting interferences [9]) additional selectivity in an analysis is still required.High-field asymmetric waveform ion mobility spectrometry (FAIMS) is a gas-phase ion-separation technique that is based on compound-dependent differences in an ion's mobility at high field (K h ) relative to low field (K) [10,11]. With FAIMS, deviations in ion mobility resulting from the high electric fields are reflected experimentally by the compensation voltage (CV) of transmission for a particular analyte. Consequently, by fixing the CV value, a subset of ions is allowed to pass through the FAIMS, whereas other i...