A preparative mass spectrometer to deposit intact large native protein complexes

TL;DR

This paper introduces a new module for a commercial mass spectrometer that enables gentle deposition of large native protein complexes, preserving their structure and activity for structural biology applications.

Contribution

It presents a commercially compatible ion-beam deposition module integrated with a standard mass spectrometer, expanding accessibility and functionality for structural studies of proteins.

Findings

Demonstrated retention of native protein structure after deposition.

Achieved controlled deposition with adjustable landing energy and spot size.

Confirmed biological activity of deposited protein complexes.

Abstract

Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase where they can be accurately manipulated and purified, followed by controlled deposition onto various substrates. In combination with imaging techniques, direct structural information of well-defined molecules can be obtained, which is essential to test and interpret results from indirect mass spectrometry techniques. To date, ion-beam deposition experiments are limited to a small number of custom instruments worldwide, and there are no commercial alternatives. Here we present a module that adds ion-beam deposition capabilities to a popular commercial MS platform (Thermo Scientific$^{\mathrm{TM}}$ Q Exactive$^{\mathrm{TM}}$ UHMR). This combination significantly reduces the overhead associated with custom instruments, while benefiting from established high performance and reliability. We present current performance characteristics including beam intensity, landing-energy control, and deposition spot size for a broad range of molecules. In combination with atomic force microscopy (AFM) and transmission electron microscopy (TEM), we distinguish near-native from unfolded proteins and show retention of native shape of protein assemblies after dehydration and deposition. Further, we use an enzymatic assay to quantify activity of an non-covalent protein complex after deposition an a dry surface. Together, these results indicate a great potential of ES-IBD for applications in structural biology, but also outline the challenges that need to be solved for it to reach its full potential.