Thermal desorption has been combined with field asymmetric waveform ion mobility spectrometry and mass spectrometry for the rapid, direct analysis of isobaric potentially genotoxic impurities (PGIs) in a surrogate active pharmaceutical ingredient. FAIMS-selected PGIs were detected with limits of quantification <0.2 ppm, below the threshold of toxicological concern, with %RSD <8.4%, at the 1 ppm level.