Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC

Abstract

MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm−1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.

Commissioning the digital mass-filter/ion-trap module for the MS SPIDOC prototype

“…For testing of high-mass non-covalent protein complexes (i.e. Hb and GroEL) at the European XFEL facility, the module is mounted together with an upstream Ion-Transfer-Interface (ITI) module [35] of the MS SPIDOC prototype [6,7] preceded by a static nanoESI source [36]. The 10 μM is buffer exchanged into 100 mM ammonium acetate (pH 8.0, Sigma-Aldrich, 99.999% trace metals basis) by two cycles of Micro BioSpin P-6 gel filtration (Bio-Rad).…”

“…The knowledge of the molecular structure of proteins is fundamental for the understanding of biological processes and for the development of new medical treatments [1][2][3]. The Mass Spectrometry for Single Particle Imaging of Dipole Oriented protein Complexes (MS SPIDOC) project aims to study mass-and conformation-separated protein complexes via single-particle X-ray diffraction [4][5][6][7]. To this end, a sample-delivering prototype has been developed, which aims to provide native protein complexes with a mass 𝑚 up to the megadalton (MDa) mass range for single-particle-imaging (SPI) experiments at, e.g., the European X-Ray Free-Electron Laser (XFEL) facility [8][9][10].…”