Superior Differential Ion Mobility Spectrometry of Pendular Macromolecules Using Low-Frequency Rectangular Waveforms

Ion mobility spectrometry (IMS) can delineate gas-phase ions and probe their geometries. Coupling with electrospray ionization and MS has brought IMS to structural biology, revealing the macromolecular folding and subunit connectivity. However, the orientational averaging of ion-molecule collision cross sections (Ω) in the linear and field asymmetric waveform IMS (FAIMS) diminishes the resolution and structural specificity. In the novel low-field differential (LOD) IMS, a field too weak for ion heating (and thus FAIMS) aligns strong macrodipoles, capturing their magnitudes and directional Ω across the dipole (Ω_⊥). However, the bisinusoidal waveforms (from FAIMS) have compromised the resolution, measurement accuracy, and correlation to the ion properties. Large ions amenable to LODIMS have low mobility and diffuse slowly, allowing the waveform frequencies down to ∼10 kHz. The low field and frequency permit generating the ideal rectangular waveforms with a flexible frequency and duty cycle by direct switching (impractical for FAIMS) in a miniature low-power format. This new IMS stage is evaluated for the exemplary large protein albumin (66 kDa) previously studied using the bisinusoidal waveform. The flat voltages and greater form factor initiate the differential IMS effect at lower fields, expand the separation space, and enable the quantification of Ω_⊥ values by varying the duty cycle.