Comprehensive de novo glycan sequencing remains an elusive goal due to the structural diversity and complexity of glycans. Present strategies employing collision-induced dissociation (CID) and higher energy collisional dissociation (HCD)-based multi-stage tandem mass spectrometry (MSn) or MS/MS combined with sequential exoglycosidase digestions are inherently low-throughput and difficult to automate. Compared to CID and HCD, electron transfer dissociation (ETD) and electron capture dissociation (ECD) each generate more cross-ring cleavages informative about linkage positions, but electronic excitation dissociation (EED) exceeds the information content of all other methods and is also applicable to analysis of singly charged precursors. Although EED can provide extensive glycan structural information in a single stage of MS/MS, its performance has largely been limited to FTICR MS, and thus it has not been widely adopted by the glycoscience research community. Here, the effective performance of EED MS/MS was demonstrated on a hybrid Orbitrap-Omnitrap QE-HF instrument, with high sensitivity, fragmentation efficiency, and analysis speed. In addition, a novel EED MS2-guided MS3 approach was developed for detailed glycan structural analysis. Automated topology reconstruction from MS2 and MS3 spectra could be achieved with a modified GlycoDeNovo software. We showed that the topology and linkage configurations of the Man(9)GlcNAc(2) glycan can be accurately determined from first principles based on one EED MS2 and two CID-EED MS3 analyses, without reliance on biological knowledge, a structure database or a spectral library. The presented approach holds great promise for autonomous, comprehensive and de novo glycan sequencing.

We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions that can be used to perform resonant-based collision-induced dissociation, several forms of electron-associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation in a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the investigation of polypeptides.

We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions, that can be used to perform resonant based collision induced dissociation, several forms of electron associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation on a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the interrogation of polypeptides.### Competing Interest StatementThe authors have declared no competing interest.

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.

Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.

Long‐lasting underwater superhydrophobicity involves stable‐in‐time air layer trapped and retained between a submersed surface and the overlying liquid. Due to its underwater nature, it is rather difficult to accurately observe this air layer in submerged systems, let alone to measure it. Here, white light reflectance spectroscopy is used for real‐time monitoring (acquisition speed 50–200 ms) of underwater superhydrophobicity as well as for the calculation of the entrapped air layer thickness on “everlasting” underwater polymeric superhydrophobic surfaces fabricated by plasma micro‐nanotexturing. The proposed method enables real‐time monitoring and accurate calculation of air layers with thicknesses ranging from a few nanometers to several tens of micrometers involving small underwater bubbles. In addition, different scale topographies of superhydrophobic plasma micro‐nanotextured surfaces are tested and found to retain underwater superhydrophobicity for at least 60 days. As a demonstration, the air layer thickness is also monitored in real time when titrating water with low surface tension liquids. Among several topographies tested, a superhydrophobic surface exhibiting hierarchical topography and a high roughness ratio is able to retain a stable air layer when submersed in liquids with surface tension down to 44 mN m −1 .

Hierarchical micro-nanostructured surfaces are key components of ‘smart’ multifunctional materials, used to control wetting, adhesion, tactile, friction, optical, antifogging, antibacterial, and many more surface properties. Hierarchical surfaces comprise random or ordered structures ranked by their length scale spanning the range from a few nanometers to a few micrometers, with the larger microstructures typically embedding smaller nanostructures. Despite the importance of hierarchical surfaces, there have been few studies on their precise and controlled fabrication or their quantitative characterization, and they usually involve multiple and complex fabrication steps. Here, we present a new plasma nanotechnology, which we term ‘nanoinhibit’, and a new plasma reactor for producing in one facile process-step-controlled hierarchy at will on polymeric surfaces. We couple the new plasma nanotechnology with detailed computational nanometrology based on the analysis of scanning electron microscopy images and targeted to specific functionality. We showcase the potential of ‘nanoinhibit’ for functional surface fabrication by controlling the wetting and optical functionality of the fabricated hierarchical surfaces and showing its dependence on surface morphology metrics. Finally, we observe that ‘nanoinhibit’ produces a new class of ‘strong hierarchical’ surfaces exhibiting spatially separated periodic and fractal-like components.

In this work, we present plasma etching alone as a directed assembly method to both create the nanodot pattern on an etched polymeric (PMMA) film and transfer it to a silicon substrate for the fabrication of silicon nanopillars or cone-like nanostructuring. By using a shield to control sputtering from inside the plasma reactor, the size and shape of the resulting nanodots can be better controlled by varying plasma parameters as the bias power. The effect of the shield on inhibitor deposition on the etched surfaces was investigated by time-of-flight secondary ion mass spectroscopy (ToF-SIMS) measurements. The fabrication of quasi-ordered PMMA nanodots of a diameter of 25 nm and period of 54 nm is demonstrated. Pattern transfer to the silicon substrate using the same plasma reactor was performed in two ways: (a) a mixed fluorine-fluorocarbon-oxygen nanoscale etch plasma process was employed to fabricate silicon nanopillars with a diameter of 25 nm and an aspect ratio of 5.6, which show the same periodicity as the nanodot pattern, and (b) high etch rate cryogenic plasma process was used for pattern transfer. The result is the nanostructuring of Si by high aspect ratio nanotip or nanocone-like features that show excellent antireflective properties.

We present the concept of the combined synthesis of organic-inorganic nanocomposite coatings and atmospheric pressure plasma etching/nanotexturing for tailoring the surface topography and fabricating multifunctional surfaces. As demonstration, we fabricated super-hydrophobic ZnO/poly(methyl methacrylate) (PMMA) nanocomposite coatings. Composite coatings differing in ZnO content were synthesized and plasma etched in a dielectric barrier discharge operating in He/O-2 in an open-air environment. The phase selective plasma etching of organic over inorganic matter resulted in the gradual revealing of the inorganic ZnO particles, which were multisized due to agglomeration during the synthesis and plasma etching process. The creation of hierarchical topography led to the fabrication of roll-off superhydrophobic surfaces with water contact angle similar to 158 degrees and sliding angle similar to 3 degrees after the application of a low-pressure plasma deposited Teflon-like film. Moreover, we studied the optical properties of the superhydrophobic, atmospheric plasma nanotextured surfaces in terms of reflectance measurements (total, diffuse, and specular) to evaluate their possible use as antireflective surfaces.

We propose a new route for pattern formation based on atmospheric pressure plasma directed assembly during photoresist removal. Atmospheric plasma etching of AZ5214E resist coated on Silicon leads to the formation of periodic, oxygen-plasma resistant residuals on the underlying substrate. The O-2 content in the He/O-2 gas feed was found to play significant role on the size and density of the formed structures. Fourier analysis of the spatial morphology of surfaces confirmed quantitatively the approximate periodicity and its dependence on O-2 content. XPS analysis revealed the formation of sulfur-containing compounds coming from DNQ molecules of AZ5214E, which organize to etching-resistant molecules due to the synergistic effect of etching and radiation from the radio frequency (RF) discharge. Finally, we applied anisotropic plasma etching based on a pulsed-gas alternating plasma process in low pressure to transfer the atmospheric plasma induced pattern on the underlying Silicon substrate fabricating quasi-ordered Si pillars. The results show the potential of atmospheric plasma directed assembly for uniform, large-area and open-air pattern definition for application in modern nanofabrication.

A photovoltaic device based on radial p(+)n junction, plasma-etched silicon nanowires (SiNWs) is demonstrated. Cryogenic Si plasma etching after colloidal lithography is employed for the fabrication of ordered, high aspect ratio and perpendicular to the substrate nanowires. Radial junction is established by boron rapid thermal diffusion from spin-on dopants (SOD) solution. We study the effect of SOD annealing process conditions and show that shallow p(+)n junctions with depth of a few tens of nanometers and high dopant concentration are formed. Structural and electrical study of the final device is performed by current-voltage characterization under illumination, and compared to a planar Si photovoltaic device with similar p(+)n junction characteristics. Short-circuit current density of 12.3 mA cm(-2), open-circuit voltage of 430 mV, fill factor of 0.64 and power conversion efficiency of 3.69% were obtained for the radial SiNW photovoltaic devices, significantly improved compared to the related figures for the corresponding planar device being 8.13 mA cm(-2), 384 mV, 0.72 and 2.24%, respectively.

A photovoltaic device based on plasma-etched silicon nanopillar (SiNP) arrays is demonstrated. Highly ordered, aligned and perpendicular to the substrate pure crystalline silicon nanopillars, that follow the axial p-n junction geometry, are fabricated by polystyrene colloidal particle self-assembly followed by cryogenic silicon plasma etching. The SiNPs surface electrical passivation by both methyl termination and hydrogen termination is examined and the encapsulation of the pillars by PMMA and transparent conductive oxide is demonstrated. The total reflectance (both specular and diffuse) of SiNP arrays of different period and diameter is measured. The total reflectance of silicon is reduced significantly in a wide range of the optical spectrum. Electrical characterization of bundles of nanowires was performed in terms of I-V measurements under light illumination. A short-circuit current density (Jsc) of 18.9mA/cm2, an open-circuit voltage (Voc) of 367mV and a fill factor (FF) of 0.59 were obtained on such axial p-n SiNP array photovoltaic devices.

In this work we investigate both experimentally and theoretically the optical properties of aligned, perpendicular to the substrate, high aspect ratio (AR), plasma etched Si nanowires (SiNWs) with controlled variability. We focus on the role of imperfections in fabrication, which manifest themselves as dimensional variability of SiNW, lattice defects or positional randomization. SiNW arrays are fabricated by e-beam lithography (perfectly ordered array) or colloidal particle self-assembly (quasi-ordered array) followed by cryogenic Si plasma etching, which offers fast etch rate (up to 3 μm min−1) combined with clean, smooth, and controllable sidewall profile, but induces some dimensional variability on the diameters of the SiNWs. Sub-200 nm diameter SiNWs having AR as high as 37:1 are demonstrated. The total reflectance of SiNWs is below 2% in a wide range of the optical spectrum. We experimentally demonstrate improved light absorption when moving from a perfectly ordered (after e-beam lithography) to a defective and quasi-ordered (after colloidal self-assembly) SiNW array. In addition our measured reflectivity (for both ordered and quasi-ordered SiNWs) is much lower compared to the one predicted theoretically for a perfect SiNWs array, using full-electrodynamic calculations with the layer-multiple-scattering method. To explain such low reflectivity, we model the influence of disorder using the average T-matrix approximation and show that even small dimensional variability (10–20%) leads to dramatic reduction of the reflectance (matching the experimental results) and increased light trapping inside the SiNW justifying their possible application in photovoltaic devices.

Natural evolution over 3.8 billion years has produced a huge diversity of hierarchical micro/nanostructures that have become a source of inspiration for scientists to design and develop the next generation of materials and devices. In this work, a combination of plasma etching techniques and the hydrothermal growth is employed to synthesize in a controllable way bio-inspired, three-dimensional nanoarchitectures of ZnO onto periodic arrays of Si nanowires. It is demonstrated that the proposed methodology offers the ability to tune the length, diameter and density of the ZnO nanostructures resulting in a wide range of nanoarchitectures from plant-like structures to complex three-dimensional interconnected networks.

Plasma nanotexturing, i.e. plasma etching with simultaneous roughening in the nano to micron scale, is used to create roughness on PMMA plates or glass slides coated with PMMA films. Mimicking nature, we use this roughness to create ''smart'' surfaces, with controlled optical and wetting properties. We present results that show combined antireflectivity, superhydrophobicity and superamphiphobicity for optimal plasma treatment time of only one-side of the samples (better results are expected for two-side treatment). In particular, using only 1.5min of plasma nanotexturing and etching of PMMA in oxygen plasma, followed by vacuum deposition of a perfluorinated self-assembled monolayer, a reduction of reflectivity by 30% (compared to its initial value), superhydrophobicity and superamphiphobicity were achieved for liquids with surface tension more than 50mN/m.

We propose a variation of colloidal (microparticle) lithography, which we term “mesh-assisted” colloidal lithography, to improve uniformity and quality of monolayer microparticle assembly over large areas: a square mesh with 200–1000μm open squares (total open-area larger than 75%) and of appropriate height is created/placed on a substrate surface, and acts as template facilitating uniform, monolayer assembly of polystyrene (PS) microparticles with spin-coating. We also study the pattern transfer, the pillar/post formation and their dimensional control on several substrates, namely polymers, silicon and silicon dioxide. Highly ordered nanopillar or nanopost arrays are produced on: (a) PMMA plates by one anisotropic etching step, (b) silicon, and (c) silicon dioxide. The silicon nanopillars and silicon dioxide nanoposts are fabricated by a two step plasma etching: an isotropic oxygen plasma step which shrinks the PS microspheres followed by an anisotropic step to transfer the pattern. The obtained pillars have nanotexture on top of the PS sphere due to plasma roughening, and thus present dual-scale topography, useful for applications such as superhydrophobic surfaces. Our method is thus a combination of photolithography, colloidal lithography, and plasma etching for low-cost, large area nanopost formation.