The use of field asymmetric waveform ion mobility spectrometry (FAIMS) has rapidly grown with the advent of commercial FAIMS systems coupled to mass spectrometry. However, many fundamental aspects of FAIMS remain obscure, hindering its technological improvement and expansion of analytical utility. Recently, we developed a comprehensive numerical simulation approach to FAIMS that can handle any device geometry and operating conditions. The formalism was originally set up in one dimension for a uniform gas flow and limited to ideal asymmetric voltage waveforms. Here we extend the model to account for a realistic gas flow velocity distribution in the analytical gap, axial ion diffusion, and waveform imperfections (e.g., noise and ripple). The nonuniformity of the gas flow velocity profile has only a minor effect, slightly improving resolution. Waveform perturbations are significant even at very low levels, in some cases ϳ0.01% of the nominal voltage. These perturbations always improve resolution and decrease sensitivity, a trade-off controllable by variation of noise or ripple amplitude. This trade-off is physically inferior to that obtained by adjusting the gap width and/or asymmetric waveform frequency. However, the disadvantage is negligible when the perturbation period is much shorter than the residence time in FAIMS, and ripple adjustment appears to offer a practical method for modifying FAIMS resolution. S eparation of ions in the gas-phase using field asymmetric waveform ion mobility spectrometry (FAIMS) extends back two decades [1][2][3][4][5][6][7]. However, FAIMS was not widely used until its coupling to electrospray ionization mass spectrometry [8,9], which has expanded its utility to environmental [10 -13] and biological [14 -18] applications, in addition to traditional detection of airborne volatiles [19 -23]. The recent advent of commercial FAIMS systems (Ionalytics Selectra [17,24] and Sionex DMS [23,25]) is increasing the acceptance of FAIMS and diversifying its applications.While FAIMS analyses have become increasingly common, the fundamentals remain relatively poorly understood [18]. Phenomenologically, ions are separated by the difference between mobilities at high and low electric fields (E) (respectively K H and K L ) that in general differ as ion mobilities in gases depend on the field. Thus, FAIMS measures the mean derivative of mobility with respect to field ͗ѨK⁄ѨE͘ (over a certain range of E), in contrast to the conventional ion mobility spectrometry [26,27] that determines absolute mobilities (K). The K(E) function can be expressed as a polynomial over even powers of E/N, where N is the buffer gas number density [28,29]:Mobilities tend to significantly deviate from zero-field values K(0) at E/N Ն ϳ30 to 40 Td, which defines the lower limit for electric fields useful in FAIMS operation. The upper limit is given by the onset of electrical breakdown in gas, which depends on the gas identity and number density, and (to a lesser extent) the width and geometry of the gap between electrodes (the...