An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio ( m/ z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase

Shipping routes through core habitat of endangered sperm whales along the Hellenic Trench, Greece: Can we reduce collision risks?

The Mediterranean sperm whale population is listed as 'Endangered". The Hellenic Trench is the core habitat of the eastern Mediterranean sperm whale sub-population that numbers two to three hundred individuals. Major shipping routes running on or very close to the 1000 m depth contour along the Hellenic Trench are causing an unsustainable number of ship-strikes with sperm whales reviewed in this paper. Sperm whale sighting and density data were combined with specific information on the vessel traffic in the area (e.g., types of vessels, traffic patterns, speed and traffic density), in order to estimate the risk of a whale/ship interaction. Routing options to significantly reduce ship strike risk by a small offshore shift in shipping routes were identified. The overall collision risk for sperm whales in the study area would be reduced by around 70%, while a maximum of 11 nautical miles would be added to major routes and only around 5 nautical miles for the majority of ships. No negative impacts were associated with re-routing by shipping away from sperm whale habitat and there would be additional shipping safety and environmental benefits. A significant contribution to the overall conservation status of the marine Natura2000 sites in the area and very important population units of threatened species such as Cuvier's beaked whales, monk seals and loggerhead turtles would be achieved, by the reduction of shipping noise and reduced risk of any oil spills reaching the coasts, which are also important touristic destinations in Greece

Experimental and numerical investigations of under-expanded gas flows for optimal operation of a novel multipole differential ion mobility filter in the first vacuum-stage of a mass spectrometer

Summarization: The integration process of a higher-order multipole differential mobility spectrometer in the first vacuum stage of a mass spectrometer is described and separation of ions under the influence of a pair of antiphase asymmetric rectangular RF waveforms is demonstrated experimentally. The superposition of quadrupole RF and DC components to the main dipole field is investigated and directional focusing of ions controlled via adjustments in the electrical potentials applied to the pole-electrodes is accomplished. The requirement for laminar flow to minimize perturbations on the oscillatory motion of the ions inside the separation field of the differential mobility spectrometer is obtained by incorporating a carefully dimensioned duct to confine the free jet expansion and suppress turbulence typically observed in the far-field region of the expanding flow. The transitions of the flow and relaminarization effects established within the duct are visualized by particle tracking velocimetry. Monodisperse and polydisperse nanoparticles produced by spark discharge are employed as tracers to visualize the gas dynamic effects at low pressure. Particle tracking velocimetry is extended to free jets and experimental data are contrasted to numerical solutions of the flow to understand time relaxation effects of particles and evaluate the applicability of numerical methods at low pressure.Presented on: International Journal of Mass Spectrometr

An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies

We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase.</p

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

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 &lt; 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

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

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