A mechanical nanomembrane detector for time-of-flight mass spectrometry

Field Emission from Carbon Nanotubes on Titanium Nitride-Coated Planar and 3D-Printed Substrates

Carbon nanotubes (CNTs) are well known for their outstanding field emission (FE) performance, facilitated by their unique combination of electrical, mechanical, and thermal properties. However, if the substrate of choice is a poor conductor, the electron supply towards the CNTs can be limited, restricting the FE current. Furthermore, ineffective heat dissipation can lead to emitter-substrate bond degradation, shortening the field emitters' lifetime. Herein, temperature-stable titanium nitride (TiN) was deposited by plasma-enhanced atomic layer deposition (PEALD) on different substrate types prior to the CNT growth. A turn-on field reduction of up to 59% was found for the emitters that were generated on TiN-coated bulk substrates instead of on pristine ones. This observation was attributed exclusively to the TiN layer as no significant change in the emitter morphology could be identified. The fabrication route and, consequently, improved FE properties were transferred from bulk substrates to free-standing, electrically insulating nanomembranes. Moreover, 3D-printed, polymeric microstructures were overcoated by atomic layer deposition (ALD) employing its high conformality. The results of our approach by combining ALD with CNT growth could assist the future fabrication of highly efficient field emitters on 3D scaffold structures regardless of the substrate material.

Thermally Driven Field Emission from Zinc Oxide Wires on a Nanomembrane Used as a Detector for Time-of-Flight Mass Spectrometry

Mass spectrometry is a crucial technology in numerous applications, but it places stringent requirements on the detector to achieve high resolution across a broad spectrum of ion masses. Low-dimensional nanostructures offer opportunities to tailor properties and achieve performance not reachable in bulk materials. Here, an array of sharp zinc oxide wires was directly grown on a 30 nm thin, free-standing silicon nitride nanomembrane to enhance its field emission (FE). The nanomembrane was subsequently used as a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry detector. When ionized biomolecules impinge on the backside of the surface-modified nanomembrane, the current-emitted from the wires on the membrane's front side-is amplified by the supplied thermal energy, which allows for the detection of the ions. An extensive simulation framework was developed based on a combination of lateral heat diffusion in the nanomembrane, heat diffusion along the wires, and FE, including Schottky barrier lowering, to investigate the impact of wire length and diameter on the FE. Our theoretical model suggests a significant improvement in the overall FE response of the nanomembrane by growing wires on top. Specifically, long thin wires are ideal to enhance the magnitude of the FE signal and to shorten its duration for the fastest response simultaneously, which could facilitate the future application of detectors in mass spectrometry with properties improved by low-dimensional nanostructures.

Development of a High-Field "Brick" Mass Spectrometer with Extended Mass Range and Capable of Characterizing Native Proteins

One of the main challenges of analyzing intact proteins on an ion trap mass spectrometer is the mass range limitation, especially for miniature mass spectrometers. In this study, a high-field frequency scanning ion trap miniature mass spectrometer, namely the high-field "Brick" mass spectrometer, was developed to analyze intact proteins. A high-voltage broadband radio frequency (rf) amplifier was designed with a maximum output of 900 Vp-p over a frequency range of 130-700 kHz. Compared to the 600 Vp-p rf amplifier equipped in the conventional "Brick" mass spectrometer, the mass range of the instrument could be extended from 2000 to over 8000 Th. Sensitivity and mass resolution for native protein analyses were also evaluated and compared. Various proteins as well as their mixtures were analyzed on the high-field "Brick" mass spectrometer. The noncovalent interaction between protein-ligand complexes, lysozyme with triN-acetylchitotriose, was also analyzed. In addition, a hybrid ion scan mode was explored to further expand the mass range of the instrument at both low- and high-mass ends. In the hybrid ion scan mode, both rf frequency and amplitude were tuned, and a mass range from 100 to 12,000 Th was realized. As a result, both small drugs and proteins could be analyzed in a single mass scan. As proof-of-concept demonstrations, a mixture of atenolol and bovine serum albuminand oligomers of transferrin were analyzed.

Booster-microchannel plate (BMCP) detector for signal amplification in MALDI-TOF mass spectrometry for ions beyond m/z 50 000

Top-down proteomics deals with the characterization of intact biomolecules, which reduces the sample complexity and facilitates the detection of modifications at the protein level. The combination of the matrix-assisted laser desorption/ionization (MALDI) technique with time-of-flight (TOF) mass analysis allows for the generation of gaseous ions in low charge states from high-mass biomolecules, followed by their mass-to-charge ratio (m/z) separation, as high-mass ions drift down the flight tube more slowly than lighter ones. However, the detection efficiency of conventional microchannel plate (MCP) detectors is strongly reduced with decreasing ion velocity-corresponding to an increase in ion mass-which impedes the reliable detection of high-mass biomolecules. Herein, we present a simple modification of the MCP detector that allows for the amplification of the signal from ionized proteins of up to m/z 150 000. Two circular electrodes were assembled in front of the conventional detector and set to negative electrical voltages to affect the positively charged ions directly before they impinge on the MCP, possibly through a combination of a velocity boost and ion optical effects. In the present study, three booster electrode configurations were experimentally tested to maximize the signal intensification. Compared to the conventional MCP assembly, the signal intensity was amplified in a proof-of-concept experiment by a factor of 24.3 and of 10.7 for the singly charged BSA ion (m/z 66 400) and for the singly charged IgG ion (m/z 150 000), respectively, by applying the booster-MCP (BMCP) detector.

Subtractive Low-Temperature Preparation Route for Porous SiO2 Used for the Catalyst-Assisted Growth of ZnO Field Emitters

The possibility to gradually increase the porosity of thin films facilitates a variety of applications, such as anti-reflective coatings, diffusion membranes, and the herein investigated tailored nanostructuring of a substrate for subsequent self-assembly processes. A low-temperature (<160 °C) preparation route for porous silicon oxide (porSiO2) thin films with porosities of about 60% and effective refractive indices down to 1.20 is tailored for bulk as well as free-standing membranes. Subsequently, both substrate types are successfully employed for the catalyst-assisted growth of nanowire-like zinc oxide (ZnO) field emitters by metal organic chemical vapor deposition. ZnO nanowires can be grown with a large aspect ratio and exhibit a good thermal and chemical stability, which makes them excellent candidates for field emitter arrays. We present a method that allows for the direct synthesis of nanowire-like ZnO field emitters on free-standing membranes using a porSiO2 template. Besides the application of porSiO2 for the catalyst-assisted growth of nanostructures and their use as field emission devices, the herein presented general synthesis route for the preparation of low refractive index films on other than bulk substrates-such as on free-standing, ultra-thin membranes-may pave the way for the employment of porSiO2 in micro-electro-mechanical systems.

Development of a miniature protein mass spectrometer capable of analyzing native proteins

Current miniature mass spectrometers were usually designed for the detection of small and medium size molecules, including volatile (semi-volatile) compounds, drugs and lipids. In this study, a miniature protein mass spectrometer was developed in this work, which could serve as a biosensor for the rapid identification of proteins as well as their conformations. A linear ion trap with a field radius of 2.5 mm was designed to extend mass range of the instrument to over 6500 Th. Mass resolution and sensitivity of the instrument were also optimized for protein ions by increasing the buffer gas pressure and using a high-gain Faraday detector. It is then demonstrated that the mass spectra of native proteins, such as IgG1, could be acquired by coupling the instrument with a soft electrospray ionization source. As a proof-of-concept demonstration, results suggest that the current instrument could be used to identify target proteins and probe/distinguish their conformations in solutions.

Resonant Tunneling Induced Enhancement of Electron Field Emission by Ultra-Thin Coatings

The emission of electrons from the surface of a material into vacuum depends strongly on the material’s work function, temperature, and the intensity of electric field. The combined effects of these give rise to a multitude of related phenomena, including Fowler-Nordheim tunneling and Schottky emission, which, in turn, enable several families of devices, ranging from vacuum tubes, to Schottky diodes, and thermionic energy converters. More recently, nanomembrane-based detectors have found applications in high-resolution mass spectrometry measurements in proteomics. Progress in all the aforementioned applications critically depends on discovering materials with effective low surface work functions. We show that a few atomic layer deposition (ALD) cycles of zinc oxide onto suspended diamond nanomembranes, strongly reduces the threshold voltage for the onset of electron field emission which is captured by resonant tunneling from the ZnO layer. Solving the Schroedinger equation, we obtain an electrical field- and thickness-dependent population of the lowest few subbands in the thin ZnO layer, which results in a minimum in the threshold voltage at a thickness of 1.08 nm being in agreement with the experimentally determined value. We conclude that resonant tunneling enables cost-effective ALD coatings that lower the effective work function and enhance field emission from the device.

Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) provides a unique in situ chemical profile that can include drugs, nucleic acids, metabolites, lipids, and proteins. MSI of individual cells (of a known cell type) affords a unique insight into normal and disease-related processes and is a prerequisite for combining the results of MSI and other single-cell modalities (e.g. mass cytometry and next-generation sequencing). Technological barriers have prevented the high-throughput assignment of MSI spectra from solid tissue preparations to their cell type. These barriers include obtaining a suitable cell-identifying image (e.g. immunohistochemistry) and obtaining sufficiently accurate registration of the cell-identifying and MALDI-MS images. This study introduces a technique that overcame these barriers by assigning cell type directly from mass spectra. We hypothesized that, in MSI from mice with a defined fluorescent protein expression pattern, the fluorescent protein's molecular ion could be used to identify cell cohorts. A method was developed for the purification of enhanced yellow fluorescent protein (EYFP) from mice. To determine EYFP's molecular mass for MSI studies, we performed intact mass analysis and characterized the protein's primary structure and post-translational modifications through various techniques. MALDI-MSI methods were developed to enhance the detection of EYFP in situ, and by extraction of EYFP's molecular ion from MALDI-MS images, automated, whole-image assignment of cell cohorts was achieved. This method was validated using a well-characterized mouse line that expresses EYFP in motor and sensory neurons and should be applicable to hundreds of commercially available mice (and other animal) strains comprising a multitude of cell-specific fluorescent labels.

Single-molecule mass spectrometry

In single-molecule mass spectrometry, the mass of each ion is measured individually; making it suitable for the analysis of very large, heterogeneous objects that cannot be analyzed by conventional means. A range of single-molecule mass spectrometry techniques has been developed, including time-of-flight with cryogenic detectors, a quadrupole ion trap with optical detection, single-molecule Fourier transform ion cyclotron resonance, charge detection mass spectrometry, quadrupole ion traps coupled to charge detector plates, and nanomechanical oscillators. In addition to providing information on mass and heterogeneity, these techniques have been used to study impact craters from cosmic dust, monitor the assembly of viruses, elucidate the fluorescence dynamics of quantum dots, and much more. This review focuses on the merits of each of these technologies, their limitations, and their applications. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:715-733, 2017.

Selective High-Frequency Mechanical Actuation Driven by the VO2 Electronic Instability

Relaxation oscillators consist of periodic variations of a physical quantity triggered by a static excitation. They are a typical consequence of nonlinear dynamics and can be observed in a variety of systems. VO₂ is a correlated oxide with a solid-state phase transition above room temperature, where both electrical resistance and lattice parameters undergo a drastic change in a narrow temperature range. This strong nonlinear response allows to realize spontaneous electrical oscillations in the megahertz range under a DC voltage bias. These electrical oscillations are employed to set into mechanical resonance a microstructure without the need of any active electronics, with small power consumption and with the possibility to selectively excite specific flexural modes by tuning the value of the DC electrical bias in a range of few hundreds of millivolts. This actuation method is robust and flexible and can be implemented in a variety of autonomous DC-powered devices.

High Mass Ion Detection with Charge Detector Coupled to Rectilinear Ion Trap Mass Spectrometer

Conventional linear ion trap mass analyzers (LIT-MS) provide high ion capacity and show their MS ⁿ ability; however, the detection of high mass ions is still challenging because LIT-MS with secondary electron detectors (SED) cannot detect high mass ions. To detect high mass ions, we coupled a charge detector (CD) to a rectilinear ion trap mass spectrometer (RIT-MS). Immunoglobulin G ions (m/z ~150,000) are measured successfully with controlled ion kinetic energy. In addition, when mass-to-charge (m/z) ratios of singly charged ions exceed 10 kTh, the detection efficiency of CD is found to be greater than that of SED. The CD can be coupled to LIT-MS to extend the detection mass range and provide the potential to perform MS ⁿ of high mass ions inside the ion trap. Graphical Abstract ᅟ.

Top-down Proteomics: Technology Advancements and Applications to Heart Diseases

INTRODUCTION

Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood.

AREAS COVERED

Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.

Mechanical Modulation of Phonon-Assisted Field Emission in a Silicon Nanomembrane Detector for Time-of-Flight Mass Spectrometry

We demonstrate mechanical modulation of phonon-assisted field emission in a free-standing silicon nanomembrane detector for time-of-flight mass spectrometry of proteins. The impacts of ion bombardment on the silicon nanomembrane have been explored in both mechanical and electrical points of view. Locally elevated lattice temperature in the silicon nanomembrane, resulting from the transduction of ion kinetic energy into thermal energy through the ion bombardment, induces not only phonon-assisted field emission but also a mechanical vibration in the silicon nanomembrane. The coupling of these mechanical and electrical phenomenon leads to mechanical modulation of phonon-assisted field emission. The thermal energy relaxation through mechanical vibration in addition to the lateral heat conduction and field emission in the silicon nanomembrane offers effective cooling of the nanomembrane, thereby allowing high resolution mass analysis.

Top-down proteomics in health and disease: challenges and opportunities

Proteomics is essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in human disease; however, the unique characteristics of the human proteome, which include a high dynamic range of protein expression and extreme complexity due to a plethora of PTMs and sequence variations, make such analyses challenging. An emerging "top-down" MS-based proteomics approach, which provides a "bird's eye" view of all proteoforms, has unique advantages for the assessment of PTMs and sequence variations. Recently, a number of studies have showcased the potential of top-down proteomics for the unraveling of disease mechanisms and discovery of new biomarkers. Nevertheless, the top-down approach still faces significant challenges in terms of protein solubility, separation, and the detection of large intact proteins, as well as underdeveloped data analysis tools. Consequently, new technological developments are urgently needed to advance the field of top-down proteomics. Herein, we intend to provide an overview of the recent applications of top-down proteomics in biomedical research. Moreover, we will outline the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases.

Spatial mapping of multimode Brownian motions in high-frequency silicon carbide microdisk resonators

High-order and multiple modes in high-frequency micro/nanomechanical resonators are attractive for empowering signal processing and sensing with multi-modalities, yet many challenges remain in identifying and manipulating these modes, and in developing constitutive materials and structures that efficiently support high-order modes. Here we demonstrate high-frequency multimode silicon carbide microdisk resonators and spatial mapping of the intrinsic Brownian thermomechanical vibrations, up to the ninth flexural mode, with displacement sensitivities of ~7-14 fm Hz(-1/2). The microdisks are made in a 500-nm-carbide on 500-nm-oxide thin-film technology that facilitates ultrasensitive motion detection via scanning laser interferometry with high spectral and spatial resolutions. Mapping of these thermomechanical vibrations vividly visualizes the shapes and textures of high-order Brownian motions in the microdisks. Measurements on devices with varying dimensions provide deterministic information for precisely identifying the mode sequence and characteristics, and for examining mode degeneracy, spatial asymmetry and other effects, which can be exploited for encoding information with increasing complexity.

Detection of large ions in time-of-flight mass spectrometry: effects of ion mass and acceleration voltage on microchannel plate detector response

In time-of-flight mass spectrometry (TOF-MS), ion detection is typically accomplished by the generation and amplification of secondary electrons produced by ions colliding with a microchannel plate (MCP) detector. Here, the response of an MCP detector as a function of ion mass and acceleration voltage is characterized, for singly charged peptide/protein ions ranging from 1 to 290 kDa in mass, and for acceleration voltages from 5 to 25 kV. A nondestructive inductive charge detector (ICD) employed in parallel with MCP detection provides a reliable reference signal to allow accurate calibration of the MCP response. MCP detection efficiencies were very close to unity for smaller ions at high acceleration voltages (e.g., angiotensin, 1046.5 Da, at 25 kV acceleration voltage), but decreased to ~11% for the largest ions examined (immunoglobulin G (IgG) dimer, 290 kDa) even at the highest acceleration voltage employed (25 kV). The secondary electron yield γ (average number of electrons produced per ion collision) is found to be proportional to mv(3.1) (m: ion mass, v: ion velocity) over the entire mass range examined, and inversely proportional to the square root of m in TOF-MS analysis. The results indicate that although MCP detectors indeed offer superlative performance in the detection of smaller peptide/protein species, their performance does fall off substantially for larger proteins, particularly under conditions of low acceleration voltage.

Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques

Mass spectrometric techniques can measure the masses and fragments of large biomolecules and bioparticles.

A silicon nanomembrane detector for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of large proteins

We describe a MALDI-TOF ion detector based on freestanding silicon nanomembrane technology. The detector is tested in a commercial MALDI-TOF mass spectrometer with equimolar mixtures of proteins. The operating principle of the nanomembrane detector is based on phonon-assisted field emission from these silicon nanomembranes, in which impinging ion packets excite electrons in the nanomembrane to higher energy states. Thereby the electrons can overcome the vacuum barrier and escape from the surface of the nanomembrane via field emission. Ion detection is demonstrated of apomyoglobin (16,952 Da), aldolase (39,212 Da), bovine serum albumin (66,430 Da), and their equimolar mixtures. In addition to the three intact ions, a large number of fragment ions are also revealed by the silicon nanomembrane detector, which are not observable with conventional detectors.

Mass discrimination in high-mass MALDI-MS

In high-mass matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), the accessible m/z range is limited by the detector used. Therefore, special high-mass detectors based on ion conversion dynodes (ICDs) have been developed. Recently, we have found that mass bias may exist when such ICD detectors are used [Weidmann et al., Anal. Chem. 85(6), 3425-3432 (2013)]. In this contribution, the mass-dependent response of an ICD detector was systematically studied, the response factors for proteins with molecular weights from 35.9 to 129.9 kDa were determined, and the reasons for mass bias were identified. Compared with commonly employed microchannel plate detectors, we found that the mass discrimination is less pronounced, although ions with higher masses are weakly favored when using an ICD detector. The relative response was found to depend on the laser power used for MALDI; low-mass ions are discriminated against with higher laser power. The effect of mutual ion suppression in dependence of the proteins used and their molar ratio is shown. Mixtures consisting of protein oligomers that only differ in mass show less mass discrimination than mixtures consisting of different proteins with similar masses. Furthermore, mass discrimination increases for molar ratios far from 1. Finally, we present clear guidelines that help to choose the experimental parameters such that the response measured matches the actual molar fraction as closely as possible.

Phonon-assisted field emission in silicon nanomembranes for time-of-flight mass spectrometry of proteins

Time-of-flight (TOF) mass spectrometry has been considered as the method of choice for mass analysis of large intact biomolecules, which are ionized in low charge states by matrix-assisted-laser-desorption/ionization (MALDI). However, it remains predominantly restricted to the mass analysis of biomolecules with a mass below about 50,000 Da. This limitation mainly stems from the fact that the sensitivity of the standard detectors decreases with increasing ion mass. We describe here a new principle for ion detection in TOF mass spectrometry, which is based upon suspended silicon nanomembranes. Impinging ion packets on one side of the suspended silicon nanomembrane generate nonequilibrium phonons, which propagate quasi-diffusively and deliver thermal energy to electrons within the silicon nanomembrane. This enhances electron emission from the nanomembrane surface with an electric field applied to it. The nonequilibrium phonon-assisted field emission in the suspended nanomembrane connected to an effective cooling of the nanomembrane via field emission allows mass analysis of megadalton ions with high mass resolution at room temperature. The high resolution of the detector will give better insight into high mass proteins and their functions.

Detection systems for mass spectrometry imaging: a perspective on novel developments with a focus on active pixel detectors

Instrumental developments for imaging and individual particle detection for biomolecular mass spectrometry (imaging) and fundamental atomic and molecular physics studies are reviewed. Ion-counting detectors, array detection systems and high mass detectors for mass spectrometry (imaging) are treated. State-of-the-art detection systems for multi-dimensional ion, electron and photon detection are highlighted. Their application and performance in three different imaging modes--integrated, selected and spectral image detection--are described. Electro-optical and microchannel-plate-based systems are contrasted. The analytical capabilities of solid-state pixel detectors--both charge coupled device (CCD) and complementary metal oxide semiconductor (CMOS) chips--are introduced. The Medipix/Timepix detector family is described as an example of a CMOS hybrid active pixel sensor. Alternative imaging methods for particle detection and their potential for future applications are investigated.

Challenges for nanomechanical sensors in biological detection

Nanomechanical biosensing relies on changes in the movement and deformation of micro- and nanoscale objects when they interact with biomolecules and other biological targets. This field of research has provided ever-increasing records in the sensitivity of label-free detection but it has not yet been established as a practical alternative for biological detection. We analyze here the latest advancements in the field, along with the challenges remaining for nanomechanical biosensors to become a commonly used tool in biology and biochemistry laboratories.

Quasi-dynamic mode of nanomembranes for time-of-flight mass spectrometry of proteins

Mechanical resonators realized on the nano-scale by now offer applications in mass-sensing of biomolecules with extraordinary sensitivity. The general idea is that perfect mechanical biosensors should be of extremely small size to achieve zeptogram sensitivity in weighing single molecules similar to a balance. However, the small scale and long response time of weighing biomolecules with a cantilever restrict their usefulness as a high-throughput method. Commercial mass spectrometry (MS) such as electro-spray ionization (ESI)-MS and matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-MS are the gold standards to which nanomechanical resonators have to live up to. These two methods rely on the ionization and acceleration of biomolecules and the following ion detection after a mass selection step, such as time-of-flight (TOF). Hence, the spectrum is typically represented in m/z, i.e. the mass to ionization charge ratio. Here, we describe the feasibility and mass range of detection of a new mechanical approach for ion detection in time-of-flight mass spectrometry, the principle of which is that the impinging ion packets excite mechanical oscillations in a silicon nitride nanomembrane. These mechanical oscillations are henceforth detected via field emission of electrons from the nanomembrane. Ion detection is demonstrated in MALDI-TOF analysis over a broad range with angiotensin, bovine serum albumin (BSA), and an equimolar protein mixture of insulin, BSA, and immunoglobulin G (IgG). We find an unprecedented mass range of operation of the nanomembrane detector.