Influence of mass spectrometry source settings on native protein ion mobility mass spectrometry measurements

Ion mobility mass spectrometry is emerging as a useful tool to probe native protein structural information. Advance ion mobility methods like collision-induced unfolding (CIU) can be used to characterize proteins’ conformational dynamics. The impact of instrument source conditions on the native protein conformations is not well characterized or standardized. High values of drying gas temperature and gas flow parameters on the Agilent IM-QTOF instrument were shown to apply collision-induced unfolding (CIU) effects on protein ions ionized from physiological solution condition. Ion conformation heat maps of model proteins ubiquitin, myoglobin, and bovine serum albumin were obtained using a novel CIU method utilizing high drying gas temperature and varying drying gas flow. Protein charge states also increased as drying gas flow was increased at high temperature indicating a thermal heating element. Overall, drying gas temperature and gas flow on IM-QTOF and the associated impacts on ionic structure need to be considered when using ion mobility mass spectrometry technology to assess protein structure.