Adapting a trapped ion mobility spectrometry-Q-TOF mass spectrometer for native mass spectrometry

Native mass spectrometry (nMS) is increasingly popular for studying intact protein quaternary structure. When coupled with ion mobility, which separates ions based on their size, charge, and shape, it provides additional structural information on the protein complex of interest. In this study, we present a novel prototype TIMS (trapped ion mobility spectrometry)-Quadrupole-SID (surface-induced dissociation)-Time of Flight, TIMS-Q-SID-TOF, instrument for nMS. The modifications include changing the TIMS cartridge from concave to convex geometry electrodes and operating TIMS at 425 kHz to improve the trapping efficiency for high mass-to-charge (m/z) ion mobility analysis, such as 3 and 4 MDa hepatitis B virus capsids. The quadrupole radiofrequency driver was lowered to 385 kHz, which extends the isolation range from 3,000 to 17,000 m/z and allows isolation of a single charge state of GroEL at 16,200 m/z with an isolation window of 25 m/z. Finally, a 6-mm thick, 2-lens SID device replaced the collision cell entrance lens. SID dissociated 801 kDa GroEL into all combinations of subcomplexes, and the peaks were well-resolved allowing for confident assignment of product ions. This is the first time a novel prototype timsTOF Pro for nMS has been introduced with high resolving power ion mobility separation coupled to high m/z quadrupole selection and SID for protein complex fragmentation with product ion collection and detection across a broad m/z range of 1,500 to 40,000.