Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators

A Hybrid Orbitrap-Nanoelectromechanical Systems Approach for the Analysis of Individual, Intact Proteins in Real Time

Nanoelectromechanical systems (NEMS)-based mass spectrometry (MS) is an emerging technique that enables determination of the mass of individual adsorbed particles by driving nanomechanical devices at resonance and monitoring the real-time changes in their resonance frequencies induced by each single molecule adsorption event. We incorporate NEMS into an Orbitrap mass spectrometer and report our progress towards leveraging the single-molecule capabilities of the NEMS to enhance the dynamic range of conventional MS instrumentation and to offer new capabilities for performing deep proteomic analysis of clinically relevant samples. We use the hybrid instrument to deliver E. coli GroEL molecules (801 kDa) to the NEMS devices in their native, intact state. Custom ion optics are used to focus the beam down to 40 μm diameter with a maximum flux of 25 molecules/second. The mass spectrum obtained with NEMS-MS shows good agreement with the known mass of GroEL.

Flexural-Mode Piezoelectric Resonators: Structure, Performance, and Emerging Applications in Physical Sensing Technology, Micropower Systems, and Biomedicine

Piezoelectric material-based devices have garnered considerable attention from scientists and engineers due to their unique physical characteristics, resulting in numerous intriguing and practical applications. Among these, flexural-mode piezoelectric resonators (FMPRs) are progressively gaining prominence due to their compact, precise, and efficient performance in diverse applications. FMPRs, resonators that utilize one- or two-dimensional piezoelectric materials as their resonant structure, vibrate in a flexural mode. The resonant properties of the resonator directly influence its performance, making in-depth research into the resonant characteristics of FMPRs practically significant for optimizing their design and enhancing their performance. With the swift advancement of micro-nano electronic technology, the application range of FMPRs continues to broaden. These resonators, representing a domain of piezoelectric material application in micro-nanoelectromechanical systems, have found extensive use in the field of physical sensing and are starting to be used in micropower systems and biomedicine. This paper reviews the structure, working principle, resonance characteristics, applications, and future prospects of FMPRs.

Simultaneous Optical and Mechanical Sensing Based on Optomechanical Resonators

Optical and mechanical resonators have each been abundantly employed in sensing applications, albeit following separate development. Here we show that bringing together optical and mechanical resonances in a unique sensing device significantly improves the sensor performance. To that purpose, we employ nanoscale optomechanical disk resonators that simultaneously support high quality optical and mechanical modes localized in tiny volumes, which provide extraordinary sensitivities. We perform environmental sensing, but the conclusions of our work extend to other sensing applications. First, we determine optical and mechanical responsivities to temperature and relative humidity changes. Second, by characterizing mechanical and optical frequency stabilities, we determine the corresponding limits of detection. Mechanical modes appear more sensitive to relative humidity changes, while optical modes appear more sensitive to temperature ones, reaching, respectively, 0.05% and 0.6 mK of independent resolution. We then prove that simultaneous optical and mechanical monitoring enables disentangling both effects and demonstrates 0.1% and 1 mK resolution, even considering that both parameters may change at the same time. Finally, we highlight the importance of actively tracking the optical mode when optomechanical sensor devices. Not doing so enforces tedious independent calibration, influences the device sensitivity during the experiment, and shortens the sensing range. The present work hence clarifies the requirements for the optimal operation of optomechanical sensors, which will be of importance for chemical and biological sensing.

Nanomaterials Based Micro/Nanoelectromechanical System (MEMS and NEMS) Devices

The micro- and nanoelectromechanical system (MEMS and NEMS) devices based on two-dimensional (2D) materials reveal novel functionalities and higher sensitivity compared to their silicon-base counterparts. Unique properties of 2D materials boost the demand for 2D material-based nanoelectromechanical devices and sensing. During the last decades, using suspended 2D membranes integrated with MEMS and NEMS emerged high-performance sensitivities in mass and gas sensors, accelerometers, pressure sensors, and microphones. Actively sensing minute changes in the surrounding environment is provided by means of MEMS/NEMS sensors, such as sensing in passive modes of small changes in momentum, temperature, and strain. In this review, we discuss the materials preparation methods, electronic, optical, and mechanical properties of 2D materials used in NEMS and MEMS devices, fabrication routes besides device operation principles.

Quantitative Detection of Biological Nanovesicles in Drops of Saliva Using Microcantilevers

Extracellular nanovesicles (EVs) are lipid-based vesicles secreted by cells and are present in all bodily fluids. They play a central role in communication between distant cells and have been proposed as potential indicators for the early detection of a wide range of diseases, including different types of cancer. However, reliable quantification of a specific subpopulation of EVs remains challenging. The process is typically lengthy and costly and requires purification of relatively large quantities of biopsy samples. Here, we show that microcantilevers operated with sufficiently small vibration amplitudes can successfully quantify a specific subpopulation of EVs directly from a drop (0.1 mL) of unprocessed saliva in less than 20 min. Being a complex fluid, saliva is highly non-Newtonian, normally precluding mechanical sensing. With a combination of standard rheology and microrheology, we demonstrate that the non-Newtonian properties are scale-dependent, enabling microcantilever measurements with a sensitivity identical to that in pure water when operating at the nanoscale. We also address the problem of unwanted sensor biofouling by using a zwitterionic coating, allowing efficient quantification of EVs at concentrations down to 0.1 μg/mL, based on immunorecognition of the EVs' surface proteins. We benchmark the technique on model EVs and illustrate its potential by quantifying populations of natural EVs commonly present in human saliva. The method effectively bypasses the difficulty of targeted detection in non-Newtonian fluids and could be used for various applications, from the detection of EVs and viruses in bodily fluids to the detection of molecular clusters or nanoparticles in other complex fluids.

Antigen self-anchoring onto bacteriophage T5 capsid-like particles for vaccine design

The promises of vaccines based on virus-like particles stimulate demand for universal non-infectious virus-like platforms that can be efficiently grafted with large antigens. Here, we harnessed the modularity and extreme affinity of the decoration protein pb10 for the capsid of bacteriophage T5. SPR experiments demonstrated that pb10 fused to mCherry or to the model antigen ovalbumin (Ova) retained picomolar affinity for DNA-free T5 capsid-like particles (T5-CLPs), while cryo-EM studies attested to the full occupancy of the 120 capsid binding sites. Mice immunization with CLP-bound pb10-Ova chimeras elicited strong long-lasting anti-Ova humoral responses involving a large panel of isotypes, as well as CD8+ T cell responses, without any extrinsic adjuvant. Therefore, T5-CLP constitutes a unique DNA-free bacteriophage capsid able to display a regular array of large antigens through highly efficient chemical-free anchoring. Its ability to elicit robust immune responses paves the way for further development of this novel vaccination platform.

The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions

Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.

Vibrational Anharmonicity and Energy Relaxation in Nanoscale Acoustic Resonators

The fundamental and n = 3 overtones of Au nanoplate thickness vibrations have been studied by transient absorption microscopy. The frequencies of the n = 3 overtone are less than 3× the frequency of the fundamental. This anharmonicity is explained through a continuum mechanics model that includes organic layers on top of the nanoplate and between the nanoplate and the glass substrate. In this model, anharmonicity arises from coupling between the vibrations of the nanoplate and the organic layers, which creates avoided crossings that reduce the overtone frequencies compared to the fundamental. Comparison of the experimental and calculated quality factors shows that coupling occurs to the top organic layer. Good agreement between the measured and calculated quality factors is obtained by introducing internal damping for the nanoplate. These results show that engineering layers of soft material around metal nanostructures can be used to control the vibrational lifetimes.

Characterization of Mechanical Oscillations in Bismuth Selenide Nanowires at Low Temperatures

A single transistor preamplifier circuit was designed to facilitate electrical detection of mechanical oscillations in nanoelectromechanical systems (NEMSs) at low temperatures. The amplifier was integrated in the close vicinity of the nanowire inside the cryostat to minimize cabling load and interference. The function of the circuit was impedance conversion for current flow measurements in NEMSs with a high internal resistance. The circuit was tested to operate at temperatures as low as 5 K and demonstrated the ability to detect oscillations in double-clamped bismuth selenide nanowires upon excitation by a 0.1 MHz-10 MHz AC signal applied to a mechanically separated gate electrode. A strong resonance frequency dependency on temperature was observed. A relatively weak shift in the oscillation amplitude and resonance frequency was measured when a DC bias voltage was applied to the gate electrode at a constant temperature.

Atmospheric-Pressure Mass Spectrometry by Single-Mode Nanoelectromechanical Systems

Weighing particles above the megadalton mass range has been a persistent challenge in commercial mass spectrometry. Recently, nanoelectromechanical systems-based mass spectrometry (NEMS-MS) has shown remarkable performance in this mass range, especially with the advance of performing mass spectrometry under entirely atmospheric conditions. This advance reduces the overall complexity and cost while increasing the limit of detection. However, this technique required the tracking of two mechanical modes and the accurate knowledge of mode shapes that may deviate from their ideal values, especially due to air damping. Here, we used a NEMS architecture with a central platform, which enables the calculation of mass by single-mode measurements. Experiments were conducted using polystyrene and gold nanoparticles to demonstrate the successful acquisition of mass spectra using a single mode with an improved areal capture efficiency. This advance represents a step forward in NEMS-MS, bringing it closer to becoming a practical application for the mass sensing of nanoparticles.

Real-time detection of virus antibody interaction by label-free common-path interferometry

Viruses have a profound influence on all forms of life, motivating the development of rapid and minimally invasive methods for virus detection. In this study, we present a novel methodology that enables quantitative measurement of the interaction between individual biotic nanoparticles and antibodies in solution. Our approach employs a label-free, full-field common-path interferometric technique to detect and track biotic nanoparticles and their interactions with antibodies. It is based on the interferometric detection of light scattered by viruses in aqueous samples for the detection of individual viruses. We employ single-particle tracking analysis to characterize the size and properties of the detected nanoparticles, and to monitor the changes in their diffusive mobility resulting from interactions. To validate the sensitivity of our detection approach, we distinguish between particles having identical diffusion coefficients but different scattering signals, using DNA-loaded and DNA-devoid capsids of the Escherichia coli T5 virus phage. In addition, we have been able to monitor, in real time, the interaction between the bacteriophage T5 and purified antibodies targeting its major capsid protein pb8, as well as between the phage SPP1 and nonpurified anti-SPP1 antibodies present in rabbit serum. Interestingly, these virus-antibody interactions are observed within minutes. Finally, by estimating the number of viral particles interacting with antibodies at different concentrations, we successfully quantify the dissociation constant K d of the virus-antibody reaction using single-particle tracking analysis.

Compact and modular system architecture for a nano-resonator-mass spectrometer

Mass measurements in the mega-to giga-Dalton range are essential for the characterization of natural and synthetic nanoparticles, but very challenging to perform using conventional mass spectrometers. Nano-electro-mechanical system (NEMS) based MS has demonstrated unique capabilities for the analysis of ultra-high mass analytes. Yet, system designs to date included constraints transferred from conventional MS instruments, such as ion guides and high vacuum requirements. Encouraged by other reports, we investigated the influence of pressure on the performances of the NEMS sensor and the aerodynamic focusing lens that equipped our first-generation instrument. We thus realized that the NEMS spectrometer could operate at significantly higher pressures than anticipated without compromising particle focusing nor mass measurement quality. Based on these observations, we designed and constructed a new NEMS-MS prototype considerably more compact than our original system, and which features an improved aerodynamic lens alignment concept, yielding superior particle focusing. We evaluated this new prototype by performing nanoparticle deposition to characterize aerodynamic focusing, and mass measurements of calibrated gold nanoparticles samples. The particle capture efficiency showed nearly two orders of magnitude improvement compared to our previous prototype, while operating at two orders of magnitude greater pressure, and without compromising mass resolution.

Mode specific dynamics for the acoustic vibrations of a gold nanoplate

The vibrational modes of semiconductor and metal nanostructures occur in the MHz to GHz frequency range, depending on dimensions. These modes are at the heart of nano-optomechanical devices, and understanding how they dissipate energy is important for applications of the devices. In this paper ultrafast transient absorption microscopy has been used to examine the breathing modes of a single gold nanoplate, where up to four overtones were observed. Analysis of the frequencies and amplitudes of the modes using a simple continuum mechanics model shows that the system behaves as a free plate, even though it is deposited onto a surface with no special preparation. The overtones decay faster than the fundamental mode, which is not predicted by continuum mechanics calculations of mode damping due to radiation of sound waves. Possible reasons for this effect include frequency dependent thermoelastic effects in the nanoplate, and/or flow of acoustic energy out of the excitation region.

Efficient Focusing of Aerosol Particles in the Microchannel under Reverse External Force: A Numerical Simulation Study

Focusing aerosol particles efficiently is of great significance for high-precision aerosol jet printing and detection of the airborne target. A new method was proposed herein to achieve the efficient focusing of aerosol particles in the microchannel by using a reverse external force. Considering the slip at the interface between the gas and the aerosol particle, a numerical model of the particle movement in the microchannel was established and simulations were conducted on the gas-particle two-phase flow in the microchannel under the effect of the reverse external force. The results showed that a suitable reverse external force in a similar order of magnitude to the Stokes force can dramatically increase the velocity difference between the particle and the gas, which significantly enhances the Saffman lift force exerted on the aerosol particle. Eventually, the aerosol particle can be efficiently focused at the center of the microchannel in a short channel length. In addition, the influence of the channel geometry, the magnitude, and the direction of the external force on the particle focusing was also studied. This work is of great significance for the precise detection of aerosol particles and the design of nozzles for aerosol jet printing.

Graphene nano-electromechanical mass sensor with high resolution at room temperature

The inherent properties of 2D materials-light mass, high out-of-plane flexibility, and large surface area-promise great potential for precise and accurate nanomechanical mass sensing, but their application is often hampered by surface contamination. Here we demonstrate a tri-layer graphene nanomechanical resonant mass sensor with sub-attogram resolution at room temperature, fabricated by a bottom-up process. We found that Joule-heating is effective in cleaning the graphene membrane surface, which results in a large improvement in the stability of the resonance frequency. We characterized the sensor by depositing Cr metal using a stencil mask and found a mass-resolution that is sufficient to weigh very small particles, like large proteins and protein complexes, with potential applications in the fields of nanobiology and medicine.

Protein adsorption by nanomechanical mass spectrometry: Beyond the real-time molecular weighting

During past decades, enormous progress in understanding the mechanisms of the intermolecular interactions between the protein and surface at the single-molecule level has been achieved. These advances could only be possible by the ongoing development of highly sophisticated experimental methods such as atomic force microscopy, optical microscopy, surface plasmon resonance, ellipsometry, quartz crystal microbalance, conventional mass spectrometry, and, more recently, the nanomechanical systems. Here, we highlight the main findings of recent studies on the label-free single-molecule (protein) detection by nanomechanical systems including those focusing on the protein adsorption on various substrate surfaces. Since the nanomechanical techniques are capable of detecting and manipulating proteins even at the single-molecule level, therefore, they are expected to open a new way of studying the dynamics of protein functions. It is noteworthy that, in contrast to other experimental methods, where only given protein properties like molecular weight or protein stiffness can be determined, the nanomechanical systems enable a real-time measurement of the multiple protein properties (e.g., mass, stiffness, and/or generated surface stress), making them suitable for the study of protein adsorption mechanisms. Moreover, we also discuss the possible future trends in label-free detection and analysis of dynamics of protein complexes with these nanomechanical systems.

Time-Resolved Imaging of High Mass Proteins and Metastable Fragments Using Matrix-Assisted Laser Desorption/Ionization, Axial Time-of-Flight Mass Spectrometry, and TPX3CAM

The Timepix (TPX) is a position- and time-sensitive pixelated charge detector that can be coupled with time-of-flight mass spectrometry (TOF MS) in combination with microchannel plates (MCPs) for the spatially and temporally resolved detection of biomolecules. Earlier generation TPX detectors used in previous studies were limited by a moderate time resolution (at best 10 ns) and single-stop detection for each pixel that hampered the detection of ions with high mass-to-charge (m/z) values at high pixel occupancies. In this study, we have coupled an MCP-phosphor screen-TPX3CAM detection assembly that contains a silicon-coated TPX3 chip to a matrix-assisted laser desorption/ionization (MALDI)-axial TOF MS. A time resolution of 1.5625 ns, per-pixel multihit functionality, simultaneous measurement of TOF and time-over-threshold (TOT) values, and kHz readout rates of the TPX3 extended the m/z detection range of the TPX detector family. The detection of singly charged intact Immunoglobulin M ions of m/z value approaching 1 × 10⁶ Da has been demonstrated. We also discuss the utilization of additional information on impact coordinates and TOT provided by the TPX3 compared to conventional MS detectors for the enhancement of the quality of the mass spectrum in terms of signal-to-noise (S/N) ratio. We show how the reduced dead time and event-based readout in TPX3 compared to the TPX improves the sensitivity of high m/z detection in both low and high mass measurements (m/z range: 757-970,000 Da). We further exploit the imaging capabilities of the TPX3 detector for the spatial and temporal separation of neutral fragments generated by metastable decay at different locations along the field-free flight region by simultaneous application of deflection and retarding fields.

High-throughput determination of dry mass of single bacterial cells by ultrathin membrane resonators

How bacteria are able to maintain their size remains an open question. Techniques that can measure the biomass (dry mass) of single cells with high precision and high-throughput are demanded to elucidate this question. Here, we present a technological approach that combines the transport, guiding and focusing of individual bacteria from solution to the surface of an ultrathin silicon nitride membrane resonator in vacuum. The resonance frequencies of the membrane undergo abrupt variations at the instants where single cells land on the membrane surface. The resonator design displays a quasi-symmetric rectangular shape with an extraordinary capture area of 0.14 mm², while maintaining a high mass resolution of 0.7 fg (1 fg = 10⁻¹⁵g) to precisely resolve the dry mass of single cells. The small rectangularity of the membrane provides unprecedented frequency density of vibration modes that enables to retrieve the mass of individual cells with high accuracy by specially developed inverse problem theory. We apply this approach for profiling the dry mass distribution in Staphylococcus epidermidis and Escherichia coli cells. The technique allows the determination of the dry mass of single bacterial cells with an accuracy of about 1% at an unparalleled throughput of 20 cells/min. Finally, we revisit Koch & Schaechter model developed during 60 s to assess the intrinsic sources of stochasticity that originate cell size heterogeneity in steady-state populations. The results reveal the importance of mass resolution to correctly describe these mechanisms.

A technological approach combines transport, guiding and focusing of individual bacteria from solution to ultrathin membrane resonators for dry mass determination of single cells with accuracy within 1% and throughput of 20 cells/min.

Nanomechanical Resonators: Toward Atomic Scale

The quest for realizing and manipulating ever smaller man-made movable structures and dynamical machines has spurred tremendous endeavors, led to important discoveries, and inspired researchers to venture to previously unexplored grounds. Scientific feats and technological milestones of miniaturization of mechanical structures have been widely accomplished by advances in machining and sculpturing ever shrinking features out of bulk materials such as silicon. With the flourishing multidisciplinary field of low-dimensional nanomaterials, including one-dimensional (1D) nanowires/nanotubes and two-dimensional (2D) atomic layers such as graphene/phosphorene, growing interests and sustained effort have been devoted to creating mechanical devices toward the ultimate limit of miniaturization─genuinely down to the molecular or even atomic scale. These ultrasmall movable structures, particularly nanomechanical resonators that exploit the vibratory motion in these 1D and 2D nano-to-atomic-scale structures, offer exceptional device-level attributes, such as ultralow mass, ultrawide frequency tuning range, broad dynamic range, and ultralow power consumption, thus holding strong promises for both fundamental studies and engineering applications. In this Review, we offer a comprehensive overview and summary of this vibrant field, present the state-of-the-art devices and evaluate their specifications and performance, outline important achievements, and postulate future directions for studying these miniscule yet intriguing molecular-scale machines.

Recent Advances in Nanomechanical Membrane-Type Surface Stress Sensors towards Artificial Olfaction

Nanomechanical sensors have gained significant attention as powerful tools for detecting, distinguishing, and identifying target analytes, especially odors that are composed of a complex mixture of gaseous molecules. Nanomechanical sensors and their arrays are a promising platform for artificial olfaction in combination with data processing technologies, including machine learning techniques. This paper reviews the background of nanomechanical sensors, especially conventional cantilever-type sensors. Then, we focus on one of the optimized structures for static mode operation, a nanomechanical Membrane-type Surface stress Sensor (MSS), and discuss recent advances in MSS and their applications towards artificial olfaction.

Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool

Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.

Mechanospray Ionization MS of Proteins Including in the Folded State and Polymers

Mechanospray ionization (MoSI) is a technique that produces ions directly from solution-like electrospray ionization (ESI) but without the need of a high voltage. In MoSI, mechanical vibrations aerosolize solution phase analytes, whereby the resulting microdroplets can be directed into the inlet orifice of a mass spectrometer. In this work, MoSI is applied to biomolecules up to 80 kDa in mass in both denatured and native conditions as well as polymers up to 12 kDa in mass. The various MoSI devices used in these analyses were all comprised of a piezoelectric annulus attached to a central metallic disk containing an array of 4 to 7 μm diameter holes. The devices vibrated in the 100-170 kHz range to generate a beam of microdroplets that ultimately resulted in ion formation. A linear quadrupole ion trap (LIT) and orbitrap mass spectrometer were used in the analysis to investigate higher mass proteins at both native (folded) and denatured (unfolded) conditions. MoSI native mass spectra of proteins acquired on the orbitrap and LIT instrument demonstrated that proteins could remain intact and in a folded state. In the case of native MS of holomyoglobin, the intact folded protein remained mostly bound noncovalently to the heme group, and typically, the spectra showed reduced loss of the heme group by MoSI as compared to ESI. In both non-native and native protein analyses examples, broader often multimodal distributions to lower charge states were observed. When using the LIT instrument, a significant increase in the relative abundance of dimers was observed by MoSI as compared to ESI. The softness of the MoSI technique was evidenced by the lack of fragmentation, the formation of dimers as also noted by others ( J. Mass Spectrom. 2016, 424-429) and under native conditions, the retention of proteins in one or more presumed folded structures and for holomyoglobin the high retention of the heme group. When analyzing polyethylene glycol (PEG) and polypropylene glycol (PPG), MoSI also generated a broader distribution to lower charge states than ESI. By using the improved separation of peaks at lower charge states and all the charge states available, MoSI data should provide an improved ionization method to obtain more accurate mass and dispersity values for some polymers.

Atmospheric Pressure Mass Spectrometry of Single Viruses and Nanoparticles by Nanoelectromechanical Systems

Mass spectrometry of intact nanoparticles and viruses can serve as a potent characterization tool for material science and biophysics. Inaccessible by widespread commercial techniques, the mass of single nanoparticles and viruses (>10MDa) can be readily measured by nanoelectromechanical systems (NEMS)-based mass spectrometry, where charged and isolated analyte particles are generated by electrospray ionization (ESI) in air and transported onto the NEMS resonator for capture and detection. However, the applicability of NEMS as a practical solution is hindered by their miniscule surface area, which results in poor limit-of-detection and low capture efficiency values. Another hindrance is the necessity to house the NEMS inside complex vacuum systems, which is required in part to focus analytes toward the miniscule detection surface of the NEMS. Here, we overcome both limitations by integrating an ion lens onto the NEMS chip. The ion lens is composed of a polymer layer, which charges up by receiving part of the ions incoming from the ESI tip and consequently starts to focus the analytes toward an open window aligned with the active area of the NEMS electrostatically. With this integrated system, we have detected the mass of gold and polystyrene nanoparticles under ambient conditions and with two orders-of-magnitude improvement in capture efficiency compared to the state-of-the-art. We then applied this technology to obtain the mass spectrum of SARS-CoV-2 and BoHV-1 virions. With the increase in analytical throughput, the simplicity of the overall setup, and the operation capability under ambient conditions, the technique demonstrates that NEMS mass spectrometry can be deployed for mass detection of engineered nanoparticles and biological samples efficiently.

Frequency chasing of individual megadalton ions in an Orbitrap analyser improves precision of analysis in single-molecule mass spectrometry

To enhance the performance of charge-detection mass spectrometry, we investigated the behaviour of macromolecular single ions on their paths towards and within the Orbitrap analyser. Ions with a mass beyond one megadalton reach a plateau of stability and can be successfully trapped for seconds, travelling a path length of multiple kilometres, thereby enabling precise mass analysis with an effective resolution of greater than 100,000 at a mass-to-charge ratio of 35,000. Through monitoring the frequency of individual ions, we show that these high-mass ions, rather than being lost from the trap, can gradually lose residual solvent molecules and, in rare cases, a single elementary charge. We also demonstrate that the frequency drift of single ions due to desolvation and charge stripping can be corrected, which improves the effective ion sampling 23-fold and gives a twofold improvement in mass precision and resolution.

The mass precision and resolution in charge-detection mass spectrometry can be improved by correcting frequency drifts of single ions. Now, chasing these individual ions for seconds in an Orbitrap mass spectrometer has revealed the exceptional stability of ultra-high-mass ions, culminating in an effective resolution of greater than 100,000 at m/z = 35,000.

Real-Time Sensing with Multiplexed Optomechanical Resonators

Nanoelectromechanical resonators have been successfully used for a variety of sensing applications. Their extreme resolution comes from their small size, which strongly limits their capture area. This leads to a long analysis time and the requirement for large sample quantity. Moreover, the efficiency of the electrical transductions commonly used for silicon resonators degrades with increasing frequency, limiting the achievable mechanical bandwidth and throughput. Multiplexing a large number of high-frequency resonators appears to be a solution, but this is complex with electrical transductions. We propose here a route to solve these issues, with a multiplexing scheme for very high-frequency optomechanical resonators. We demonstrate the simultaneous frequency measurement of three silicon microdisks fabricated with a 200 mm wafer large-scale process. The readout architecture is simple and does not degrade the sensing resolutions. This paves the way toward the realization of sensors for multiparametric analysis with an extremely low limit of detection and response time.

Multimode Optomechanical Weighting of a Single Nanoparticle

We demonstrate multimode optomechanical sensing of individual nanoparticles with a radius between 75 and 150 nm. A semiconductor optomechanical disk resonator is optically driven and detected under ambient conditions, as nebulized nanoparticles land on it. Multiple mechanical and optical resonant signals of the disk are tracked simultaneously, providing access to several pieces of physical information about the landing analyte in real time. Thanks to a fast camera registering the time and position of landing, these signals can be employed to weight each nanoparticle with precision. Sources of error and deviation are discussed and modeled, indicating a path to evaluate the elasticity of the nanoparticles on top of their mere mass. The device is optimized for the future investigation of biological particles in the high megadalton range, such as large viruses.

Particles in Biopharmaceutical Formulations, Part 2: An Update on Analytical Techniques and Applications for Therapeutic Proteins, Viruses, Vaccines and Cells

Particles in biopharmaceutical formulations remain a hot topic in drug product development. With new product classes emerging it is crucial to discriminate particulate active pharmaceutical ingredients from particulate impurities. Technical improvements, new analytical developments and emerging tools (e.g., machine learning tools) increase the amount of information generated for particles. For a proper interpretation and judgment of the generated data a thorough understanding of the measurement principle, suitable application fields and potential limitations and pitfalls is required. Our review provides a comprehensive overview of novel particle analysis techniques emerging in the last decade for particulate impurities in therapeutic protein formulations (protein-related, excipient-related and primary packaging material-related), as well as particulate biopharmaceutical formulations (virus particles, virus-like particles, lipid nanoparticles and cell-based medicinal products). In addition, we review the literature on applications, describe specific analytical approaches and illustrate advantages and drawbacks of currently available techniques for particulate biopharmaceutical formulations.

The Human Proteoform Project: Defining the human proteome

Proteins are the primary effectors of function in biology, and thus, complete knowledge of their structure and properties is fundamental to deciphering function in basic and translational research. The chemical diversity of proteins is expressed in their many proteoforms, which result from combinations of genetic polymorphisms, RNA splice variants, and posttranslational modifications. This knowledge is foundational for the biological complexes and networks that control biology yet remains largely unknown. We propose here an ambitious initiative to define the human proteome, that is, to generate a definitive reference set of the proteoforms produced from the genome. Several examples of the power and importance of proteoform-level knowledge in disease-based research are presented along with a call for improved technologies in a two-pronged strategy to the Human Proteoform Project.

Requirements and attributes of nano-resonator mass spectrometry for the analysis of intact viral particles

When studying viruses, the most prevalent aspects that come to mind are their structural and functional features, but this leaves in the shadows a quite universal characteristic: their mass. Even if approximations can be derived from size and density measurements, the multi MDa to GDa mass range, featuring a majority of viruses, has so far remained largely unexplored. Recently, nano-electromechanical resonator-based mass spectrometry (NEMS-MS) has demonstrated the ability to measure the mass of intact DNA filled viral capsids in excess of 100 MDa. However, multiple factors have to be taken in consideration when performing NEMS-MS measurements. In this article, phenomena influencing NEMS-MS mass estimates are listed and discussed, including some particle's extraneous physical properties (size, aspect ratio, stiffness), and the influence of frequency noise and device fabrication defects. These factors being accounted for, we could begin to notice subtler effects linked with (e.g.) particle desolvation as a function of operating parameters. Graphical abstract.

The Recent Progress of MEMS/NEMS Resonators

MEMS/NEMS resonators are widely studied in biological detection, physical sensing, and quantum coupling. This paper reviews the latest research progress of MEMS/NEMS resonators with different structures. The resonance performance, new test method, and manufacturing process of single or double-clamped resonators, and their applications in mass sensing, micromechanical thermal analysis, quantum detection, and oscillators are introduced in detail. The material properties, resonance mode, and application in different fields such as gyroscope of the hemispherical structure, microdisk structure, drum resonator are reviewed. Furthermore, the working principles and sensing methods of the surface acoustic wave and bulk acoustic wave resonators and their new applications such as humidity sensing and fast spin control are discussed. The structure and resonance performance of tuning forks are summarized. This article aims to classify resonators according to different structures and summarize the working principles, resonance performance, and applications.

The emerging landscape of single-molecule protein sequencing technologies

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

Single virus inductively coupled plasma mass spectroscopy analysis: A comprehensive study

The characterisation of individual nanoparticles by single particle ICP-MS (SP-ICP-MS) has paved the way for the analysis of smallest biological systems. This study suggests to adapting this method for single viruses (SV) identification and counting. With high resolution multi-channel sector field (MC SF) ICP-MS records in SV detection mode, the counting of master and key ions can allow analysis and identification of single viruses. The counting of 2-500 virial units can be performed in 20 s. Analyses are proposed to be carried out in Ar torch for master ions: ¹²C⁺, ¹³C⁺, ¹⁴N⁺, ¹⁵N⁺, and key ions ³¹P⁺, ³²S⁺, ³³S⁺ and ³⁴S⁺. All interferences are discussed in detail. The use of high resolution SF ICP-MS is recommended while options with anaerobic/aerobic atmospheres are explored to upgrade the analysis when using quadrupole ICP-MS. Application for two virus types (SARS-COV2 and bacteriophage T5) is investigated using time scan and fixed mass analysis for the selected virus ions allowing characterisation of the species using the N/C, P/C and S/C molar ratio's and quantification of their number concentration.

Superconducting Nanoelectromechanical Transducer Resilient to Magnetic Fields

Nanoscale electromechanical coupling provides a unique route toward control of mechanical motions and microwave fields in superconducting cavity electromechanical devices. However, conventional devices composed of aluminum have presented severe constraints on their operating conditions due to the low superconducting critical temperature (1.2 K) and magnetic field (0.01 T) of aluminum. To enhance their potential in device applications, we fabricate a superconducting electromechanical device employing niobium and demonstrate a set of cavity electromechanical dynamics, including back-action cooling and amplification, and electromechanically induced reflection at 4.2 K and in strong magnetic fields up to 0.8 T. Niobium-based electromechanical transducers operating at this temperature could potentially be employed to realize compact, nonreciprocal microwave devices in place of conventional isolators and cryogenic amplifiers. Moreover, with their resilience to magnetic fields, niobium devices utilizing the electromechanical back-action effects could be used to study spin-phonon interactions for nanomechanical spin-sensing.

A dynamical approach to generate chaos in a micromechanical resonator

Chaotic systems, presenting complex and nonreproducible dynamics, may be found in nature, from the interaction between planets to the evolution of weather, but can also be tailored using current technologies for advanced signal processing. However, the realization of chaotic signal generators remains challenging due to the involved dynamics of the underlying physics. In this paper, we experimentally and numerically present a disruptive approach to generate a chaotic signal from a micromechanical resonator. This technique overcomes the long-established complexity of controlling the buckling in micro/nanomechanical structures by modulating either the amplitude or the frequency of the driving force applied to the resonator in the nonlinear regime. The experimental characteristic parameters of the chaotic regime, namely, the Poincaré sections and Lyapunov exponents, are directly comparable to simulations for different configurations. These results confirm that this dynamical approach is transposable to any kind of micro/nanomechanical resonator, from accelerometers to microphones. We demonstrate a direct application exploiting the mixing properties of the chaotic regime by transforming an off-the-shelf microdiaphragm into a true random number generator conforming to the National Institute of Standards and Technology specifications. The versatility of this original method opens new paths to combine the unique properties of chaos with the exceptional sensitivity of microstructures, leading to emergent microsystems.

Multimode Nonlinear Coupling Induced by Internal Resonance in a Microcantilever Resonator

Coupled resonators represent a generic model for many physical systems. In this context, a microcantilever is a multimode resonator clamped at one end, and it finds extensive application in high-precision metrology and is expected to be of great potential use in emerging quantum technologies. Here, we explore the microcantilever as a flexible platform for realizing multimode nonlinear interactions. Multimode nonlinear coupling is achieved by (1:2) internal resonance (IR) and parametric excitation with efficient coherent energy transfer. Specifically, we demonstrate abundant tunable parametric behaviors via frequency and voltage sweeps; these behaviors include mode veering, degenerate four-wave mixing (D4WM) with satellite resonances, partial amplitude suppression, acoustic frequency comb (AFC) generation, mechanically induced transparency (MIT), and normal-mode splitting. The experiments depict a new scheme for manipulating multimode microresonators with IR and parametric excitation.

A Review on Theory and Modelling of Nanomechanical Sensors for Biological Applications

Over the last decades, nanomechanical sensors have received significant attention from the scientific community, as they find plenty of applications in many different research fields, ranging from fundamental physics to clinical diagnosis. Regarding biological applications, nanomechanical sensors have been used for characterizing biological entities, for detecting their presence, and for characterizing the forces and motion associated with fundamental biological processes, among many others. Thanks to the continuous advancement of micro- and nano-fabrication techniques, nanomechanical sensors have rapidly evolved towards more sensitive devices. At the same time, researchers have extensively worked on the development of theoretical models that enable one to access more, and more precise, information about the biological entities and/or biological processes of interest. This paper reviews the main theoretical models applied in this field. We first focus on the static mode, and then continue on to the dynamic one. Then, we center the attention on the theoretical models used when nanomechanical sensors are applied in liquids, the natural environment of biology. Theory is essential to properly unravel the nanomechanical sensors signals, as well as to optimize their designs. It provides access to the basic principles that govern nanomechanical sensors applications, along with their intrinsic capabilities, sensitivities, and fundamental limits of detection.

Microcantilever: Dynamical Response for Mass Sensing and Fluid Characterization

A microcantilever is a suspended micro-scale beam structure supported at one end which can bend and/or vibrate when subjected to a load. Microcantilevers are one of the most fundamental miniaturized devices used in microelectromechanical systems and are ubiquitous in sensing, imaging, time reference, and biological/biomedical applications. They are typically built using micro and nanofabrication techniques derived from the microelectronics industry and can involve microelectronics-related materials, polymeric materials, and biological materials. This work presents a comprehensive review of the rich dynamical response of a microcantilever and how it has been used for measuring the mass and rheological properties of Newtonian/non-Newtonian fluids in real time, in ever-decreasing space and time scales, and with unprecedented resolution.

Single-virus genomics and beyond

Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered. Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.

MASS SPECTROMETRY IN VIROLOGICAL SCIENCES

Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network of interactions between the living world of pro- and eukaryotes and viruses, which delivered "a piece of bad news wrapped in protein" as defined by Peter Medawar, Nobel Prize Laureate, in 1960. However, MS is constantly evolving, and novel approaches allow for a better understanding of interactions in this micro- and nanoworld. Currently, we can investigate the interplay between the virus and the cell by analyzing proteomes, interactomes, virus-cell interactions, and search for the compounds that build viral structures. In addition, by using MS, it is possible to look at the cell from the broader perspective and determine the role of viral infection on the scale of the organism, for example, monitoring the crosstalk between infected tissues and the immune system. In such a way, MS became one of the major tools for the modern virology, allowing us to see the infection in the context of the whole cell or the organism. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.

Weighing synthetic polymers of ultra-high molar mass and polymeric nanomaterials: What can we learn from charge detection mass spectrometry?

Advances in soft ionization techniques for mass spectrometry (MS) of polymeric materials make it possible to determine the masses of intact molecular ions exceeding megadaltons. Interfacing MS with separation and fragmentation methods has additionally led to impressive advances in the ability to structurally characterize polymers. Even if the gap to the megadalton range has been bridged by MS for polymers standards, the MS-based analysis for more complex polymeric materials is still challenging. Charge detection mass spectrometry (CDMS) is a single-molecule method where the mass and the charge of each ion are directly determined from individual measurements. The entire molecular mass distribution of a polymer sample can be thus accurately measured. Described in this perspective paper is how molecular weight distribution as well as charge distribution can provide new insights into the structural and compositional studies of synthetic polymers and polymeric nanomaterials in the megadalton to gigadalton range of molecular weight. The recent multidimensional CDMS studies involving couplings with separation and dissociation techniques will be presented. And, finally, an outlook for the future avenues of the CDMS technique in the field of synthetic polymers of ultra-high molar mass and polymeric nanomaterials will be provided.

Optomechanical mass spectrometry

Nanomechanical mass spectrometry has proven to be well suited for the analysis of high mass species such as viruses. Still, the use of one-dimensional devices such as vibrating beams forces a trade-off between analysis time and mass resolution. Complex readout schemes are also required to simultaneously monitor multiple resonance modes, which degrades resolution. These issues restrict nanomechanical MS to specific species. We demonstrate here single-particle mass spectrometry with nano-optomechanical resonators fabricated with a Very Large Scale Integration process. The unique motion sensitivity of optomechanics allows designs that are impervious to particle position, stiffness or shape, opening the way to the analysis of large aspect ratio biological objects of great significance such as viruses with a tail or fibrils. Compared to top-down beam resonators with electrical read-out and state-of-the-art mass resolution, we show a three-fold improvement in capture area with no resolution degradation, despite the use of a single resonance mode.

The use of one dimensional devices in nanomechanical mass spectrometry leads to a trade-off between analysis time and resolution. Here, the authors report single-particle mass spectrometry using integrated optomechanical resonators, impervious to particle position, stiffness or shape.

Optomechanical detection of vibration modes of a single bacterium

Low-frequency vibration modes of biological particles, such as proteins, viruses and bacteria, involve coherent collective vibrations at frequencies in the terahertz and gigahertz domains. These vibration modes carry information on their structure and mechanical properties, which are good indicators of their biological state. In this work, we harnessed a particular regime in the physics of coupled mechanical resonators to directly measure these low-frequency mechanical resonances of a single bacterium. We deposit the bacterium on the surface of an ultrahigh frequency optomechanical disk resonator in ambient conditions. The vibration modes of the disk and bacterium hybridize when their associated frequencies are similar. We developed a general theoretical framework to describe this coupling, which allows us to retrieve the eigenfrequencies and mechanical loss of the bacterium low-frequency vibration modes (quality factor). Additionally, we analysed the effect of hydration on these vibrational modes. This work demonstrates that ultrahigh frequency optomechanical resonators can be used for vibrational spectrometry with the unique capability to obtain information on single biological entities.

Suspended Nanochannel Resonator Arrays with Piezoresistive Sensors for High-Throughput Weighing of Nanoparticles in Solution

As the use of nanoparticles is expanding in many industrial sectors, pharmaceuticals, cosmetics among others, flow-through characterization techniques are often required for in-line metrology. Among the parameters of interest, the concentration and mass of nanoparticles can be informative for yield, aggregates formation or even compliance with regulation. The Suspended Nanochannel Resonator (SNR) can offer mass resolution down to the attogram scale precision in a flow-through format. However, since the readout has been based on the optical lever, operating more than a single resonator at a time has been challenging. Here we present a new architecture of SNR devices with piezoresistive sensors that allows simultaneous readout from multiple resonators. To enable this architecture, we push the limits of nanofabrication to create implanted piezoresistors of nanoscale thickness (∼100 nm) and implement an algorithm for designing SNRs with dimensions optimized for maintaining attogram scale precision. Using 8-in. processing technology, we fabricate parallel array SNR devices which contain ten resonators. While maintaining a precision similar to that of the optical lever, we demonstrate a throughput of 40 000 particles per hour-an order of magnitude improvement over a single device with an analogous flow rate. Finally, we show the capability of the SNR array device for measuring polydisperse solutions of gold particles ranging from 20 to 80 nm in diameter. We envision that SNR array devices will open up new possibilities for nanoscale metrology by measuring not only synthetic but also biological nanoparticles such as exosomes and viruses.

Nonvolatile Rewritable Frequency Tuning of a Nanoelectromechanical Resonator Using Photoinduced Doping

Arrays of nanoelectromechanical resonators (NEMS) have shown promise for a suite of applications, from nanomechanical information processing technologies to mass spectrometry. A fundamental challenge toward broader adoption of NEMS arrays is a lack of viable frequency tuning methods, which must simultaneously allow for persistent and reversible control of single resonators while also being scalable to large arrays of devices. In this work, we demonstrate an electro-optic tuning method for graphene-based NEMS where locally photoionized charge tensions a suspended membrane and tunes its resonance frequency. The tuned frequency state persists unchanged for several days in the absence of any external power, and the state can be repeatedly written and erased with a high degree of precision. We show the scalability of this technique by aligning the frequencies of several NEMS devices on the same chip, and we discuss implications of this tuning method for both single devices and programmable NEMS networks.

Mass Sensing for the Advanced Fabrication of Nanomechanical Resonators

We report on a nanomechanical engineering method to monitor matter growth in real time via e-beam electromechanical coupling. This method relies on the exceptional mass sensing capabilities of nanomechanical resonators. Focused electron beam-induced deposition (FEBID) is employed to selectively grow platinum particles at the free end of singly clamped nanotube cantilevers. The electron beam has two functions: it allows both to grow material on the nanotube and to track in real time the deposited mass by probing the noise-driven mechanical resonance of the nanotube. On the one hand, this detection method is highly effective as it can resolve mass deposition with a resolution in the zeptogram range; on the other hand, this method is simple to use and readily available to a wide range of potential users because it can be operated in existing commercial FEBID systems without making any modification. The presented method allows one to engineer hybrid nanomechanical resonators with precisely tailored functionalities. It also appears as a new tool for studying the growth dynamics of ultrathin nanostructures, opening new opportunities for investigating so far out-of-reach physics of FEBID and related methods.

Mass loading effects in the acoustic vibrations of gold nanoplates

The breathing modes of single suspended gold nanoplates have been examined by transient absorption microscopy. These vibrational modes show very high quality factors which means that their frequencies can be accurately measured. Measurements performed before and after removing the organic layer that coats the as synthesized nanoplates show significant increases in frequency, which are consistent with removal of a few nm of organic material from the nanoplate surface. Experiments were also performed after depositing polymer beads on the sample. These measurements show a decrease in frequency in the region of the beads. This implies that adding a localized mass to the nanoplate hybridizes the vibrational normal modes, creating a new breathing mode which has a maximum amplitude at the bead. The nanoplate resonators have a mass sensing detection limit of ca. 10 attograms, which is comparable to the best results that have been achieved with plasmonic nanoparticles.