Field asymmetric waveform ion mobility spectrometry (FAIMS) has emerged as an analytical tool of broad utility, especially in conjunction with mass spectrometry. Of particular promise is the use of FAIMS and 2-D ion mobility methods that combine FAIMS with conventional IMS to resolve and characterize protein and other macromolecular conformers. However, FAIMS operation requires a strong electric field, and ions are inevitably heated by energetic collisions with buffer gas molecules. This may induce ion isomerization or dissociation, which distort the separation properties of FAIMS (and subsequent stages) or reduce instrumental sensitivity. As FAIMS employs a periodic waveform, whether those processes are controlled by ion temperature at maximum or average field intensity has been debated. Here we address this issue by measuring the unfolding of compact ubiquitin ion geometries as a function of waveform amplitude (dispersion field, E(D)) and gas temperature, T. The field heating is quantified by matching the dependences of structural transitions on E(D) and T: increasing E(D) from 12 to 16 or from 16 to 20 kV/cm is equivalent to heating the (N2) gas by approximately 15-25 degrees C. The magnitude of field heating for any E(D) can be estimated using the two-temperature theory, and raising E(D) by 4 kV/cm augments heating by approximately 15-30 degrees C for maximum and approximately 4-8 degrees C for average field in the FAIMS cycle. Hence, isomerization of ions in FAIMS appears to be determined by the excitation at waveform peaks.