Combining Fourier Transform Ion Mobility with Charge Detection Mass Spectrometry for the Analysis of Multimeric Protein Complexes

Charge detection mass spectrometry (CDMS) allows direct mass measurement of heterogeneous samples by simultaneously determining the charge state and the mass-to-charge ratio (m/z) of individual ions, unlike conventional MS methods that use large ensembles of ions. CDMS typically requires long acquisition times and the collection of thousands of spectra, each containing tens to hundreds of ions, to generate sufficient ion statistics, making it difficult to interface with the time scales of online separation techniques such as ion mobility. Here, we demonstrate the application of Fourier transform multiplexing and drift tube ion mobility joined with Orbitrap-based CDMS for the analysis of multimeric protein complexes. Stepped frequency modulation was utilized to enable unambiguous frequency assignment during mobility sweeps and allow spectral averaging, which improves the accuracy and signal-to-noise of ion mobility spectra and CDMS measurements. Fourier transformation of the signal reveals the arrival times and collision cross sections of ions while simultaneously collecting charge information for thousands of individual ions. Combining Fourier transform multiplexing ion mobility and CDMS provides insight into each ion’s size and mass while showcasing a potential solution to the duty cycle mismatch of online separation techniques in the single ion regime.