Morphology Assessment Enabled by Room-Temperature Soft-Landing in Native MS

Native mass spectrometry (nMS) preserves non-covalent interactions, thereby maintaining native-like protein complex assemblies in the gas phase. Herein, the combination of nMS and room temperature ion soft-landing is assessed as a preparation technique for individual protein particle electron microscopy imaging. In this work, we first assessed Coon's room-temperature ion soft-landing setup by landing two selected protein complexes, trp RNA-binding attenuation protein (TRAP), and a modified SARS-CoV-2 protein (VFLIP). The low-resolution negative-stain TEM of landed particles shows reasonable agreement with the published structures of these two protein complexes. Then, we both replicated Coon's ion soft-landing setup at OSU and redesigned the soft-landing setup to retain the HCD cell. This configuration largely minimizes the disruption of the standard instrument operation with or without an electron capture surface induced dissociation (ExD-SID) cell, allowing HCD MS/MS and/or allowing ExD and/or SID-produced fragments to be collisionally-cooled in the HCD cell prior to mass analysis in the Orbitrap. Collectively, our results have confirmed and expanded the application of room-temperature ion soft-landing. With this multidimensional information, including masses for biomolecular assemblies and rough shape screening, we foresee this method facilitating sample preparation and evaluation in the early stages of structural biology research. Importantly, the redesigned soft-landing setup was present on a UHMR with ExD-SID (in place of the multipole between the selection quad and C-trap) for 9 months, during which other group members carried out their routine nMS experiments, fully utilizing the HCD cell and obtaining results comparable to instruments with no soft-landing device installed. This setup will allow future work involving soft-landing of charge-reduced precursors and ExD, HCD, and SID fragment ions of protein complexes.