Sheath-Liquid CE-MS Interface: A Robust Infusion Platform for Native IMS-MS Analysis of Protein Assemblies and Their Conformers.

Dynamic protein complexes are central to cellular function, but capturing their native architectures remains challenging. While native ion mobility spectrometry-mass spectrometry (IMS-MS) can characterize these assemblies, its broader adoption is limited by the need for robust and automated sample introduction platforms. Here, we integrate a sheath-liquid capillary electrophoresis interface with traveling-wave IMS-MS (CE-TWIMS-MS) to interrogate intact protein assemblies across a wide range of infusion flow rates. Using streptavidin as a benchmark, we show that native-like structures are preserved across infusion flows, in excellent agreement with previously reported TWIMS-MS measurements. The CE-TWIMS-MS platform provides precise fluidic control, enabling a tunable balance between sensitivity and spectral resolution. Low infusion flows enhance detection of low charge state populations, whereas intermediate flows maximize overall ion signal intensity. Flow-dependent effects influence ion transmission efficiency and peak definition rather than gas-phase conformations. Collectively, these results demonstrate that CE-TWIMS-MS provides a robust platform for native analysis, enabling reproducible and flow-tunable characterization of intact protein assemblies.