Determination of iron content and dispersity of intact ferritin by superconducting tunnel junction cryodetection mass spectrometry

Stochastic assembly of biomacromolecular complexes: impact and implications on charge interpretation in native mass spectrometry

Native mass spectrometry is a potent method for characterizing biomacromolecular assemblies. A critical aspect to extracting accurate mass information is the correct inference of the ion ensemble charge states. While a variety of experimental strategies and algorithms have been developed to facilitate this, virtually all approaches rely on the implicit assumption that any peaks in a native mass spectrum can be directly attributed to an underlying charge state distribution. Here, we demonstrate that this paradigm breaks down for several types of macromolecular protein complexes due to the intrinsic heterogeneity induced by the stochastic nature of their assembly. Utilizing several protein assemblies of adeno-associated virus capsids and ferritin, we demonstrate that these particles can produce a variety of unexpected spectral appearances, some of which appear superficially similar to a resolved charge state distribution. When interpreted using conventional charge inference strategies, these distorted spectra can lead to substantial errors in the calculated mass (up to ∼5%). We provide a novel analytical framework to interpret and extract mass information from these spectra by combining high-resolution native mass spectrometry, single particle Orbitrap-based charge detection mass spectrometry, and sophisticated spectral simulations based on a stochastic assembly model. We uncover that these mass spectra are extremely sensitive to not only mass heterogeneity within the subunits, but also to the magnitude and width of their charge state distributions. As we postulate that many protein complexes assemble stochastically, this framework provides a generalizable solution, further extending the usability of native mass spectrometry in the characterization of biomacromolecular assemblies.

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.

Anatomy of Protein Electrospray Ionization Mass Spectra by Superconducting Tunnel Junction Mass and Energy Spectrometry

Cryogenic superconducting tunnel junction (STJ) detectors have the advantage of single-particle sensitivity, high quantum efficiency, low noise, and the ability to detect the time and relative impact energy of deposited ions. This makes them attractive for use in mass spectrometry (MS) and as a form of energy spectrometry. STJ cryodetectors have been coupled to time-of-flight (TOF) mass spectrometers equipped with a matrix-assisted laser desorption ionization (MALDI) source and to an electrospray ionization (ESI) TOF mass spectrometer. Here, a lab-made linear quadrupole ion trap (LIT) mass spectrometer system was coupled to an ESI source and a 16-channel Nb-STJ array with improved readout electronics. The goal was to investigate fundamentals of ESI-generated protein ions by further exploiting the advantage of resolving these ions in a third dimension of the relative energy deposited into the STJs. The proteins equine cytochrome c, bovine carbonic anhydrase, bovine serum albumin, and murine immunoglobulin G were studied using this ESI-LIT-STJ-MS instrument. Multiply charged monomers, multimers, and fragments from metastable ions were resolved from monomer peaks by differences in ion deposition energy even when these ions have the same mass-to-charge ratio as the corresponding monomer. The determination of a fragment mass from metastable decomposition is accomplished without knowing the charge state of the fragment. The average charge state of the multimers is reduced with each addition of a protein which is presumed to be a direct reflection of the surface area available for charging. Multiply charged in-source fragments have also been observed and distinguished in the mass spectrum of carbonic anhydrase by using the differences in the energy deposited in the STJs.

Mass Spectrometry of Au10(4-tert-butylbenzenethiolate)10 Nanoclusters Using Superconducting Tunnel Junction Cryodetection Reveals Distinct Metastable Fragmentation

Cryodetection mass spectrometry (MS) was used to study the Au₁₀(TBBT)₁₀ (TBBT = 4-tert-butylbenzenethiolate) catenane nanocluster. The matrix-assisted laser desorption ionization (MALDI) process generates distinct fragments that can be arranged into two distinct regimes: (i) in-source fragmentation, which occurs rapidly in a relatively short (<170 ns) time frame, and (ii) metastable fragmentation, which occurs postacceleration during a time-of-flight (TOF) mass analysis over a longer time frame (>170 ns-250 μs). Using MALDI-TOF MS with superconducting tunnel junction (STJ) cryodetection, distinct metastable nanocluster fragments were resolved at lower energies deposited into the detector. The results also demonstrated that STJ cryodetection MS can be used to acquire multiple (>10), simultaneous tandem mass spectra in a single experiment. Simulated fragmentation of the Au₁₀ nanocluster using ab initio molecular dynamics (AIMD) revealed the different fragmentation processes and confirmed the MS results. Using both the empirical MS data and AIMD calculations, fragmentation pathways are proposed for Au₁₀(TBBT)₁₀, which terminate with two small, stable ringed species.

Protein-Based Nanoparticles for the Imaging and Treatment of Solid Tumors: The Case of Ferritin Nanocages, a Narrative Review

Protein nanocages have been studied extensively, due to their unique architecture, exceptional biocompatibility and highly customization capabilities. In particular, ferritin nanocages (FNs) have been employed for the delivery of a vast array of molecules, ranging from chemotherapeutics to imaging agents, among others. One of the main favorable characteristics of FNs is their intrinsic targeting efficiency toward the Transferrin Receptor 1, which is overexpressed in many tumors. Furthermore, genetic manipulation can be employed to introduce novel variants that are able to improve the loading capacity, targeting capabilities and bio-availability of this versatile drug delivery system. In this review, we discuss the main characteristics of FN and the most recent applications of this promising nanotechnology in the field of oncology with a particular emphasis on the imaging and treatment of solid tumors.

Direct detection of iron clusters in L ferritins through ESI-MS experiments

Human cytoplasmic ferritins are heteropolymers of H and L subunits containing a catalytic ferroxidase center and a nucleation site for iron biomineralization, respectively. Here, ESI-MS successfully detected labile metal-protein interactions revealing the formation of tetra- and octa-iron clusters bound to L subunits, as previously underscored by X-ray crystallography.

RECENT ADVANCES IN INSTRUMENTAL APPROACHES TO TIME-OF-FLIGHT MASS SPECTROMETRY

Time-of-flight mass spectrometry (TOFMS) is one of the simplest and most powerful approaches for mass spectrometry. Realization of the advantages inherent in TOFMS requires innovation in the theory and practice of the technique. Instrumental developments, in turn, create new capabilities that enable applications in chemical measurement. This review focuses on the recent advances in TOFMS instrumentation. New strategies for ion acceleration, multiplexed detection, miniaturized TOFMS instruments, approaches to extend the length of ion flight, and novel ion detection technologies are reviewed. Techniques that change the basic paradigm of TOFMS by measuring m/z based on ion flight distance are considered, as are applications at the frontiers of instrumental performance. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Mass spectrometry for multi-dimensional characterization of natural and synthetic materials at the nanoscale

Characterization of materials at the nanoscale plays a crucial role in in-depth understanding the nature and processes of the substances. Mass spectrometry (MS) has characterization capabilities for nanomaterials (NMs) and nanostructures by offering reliable multi-dimensional information consisting of accurate mass, isotopic, and molecular structural information. In the last decade, MS has emerged as a powerful nano-characterization technique. This review comprehensively summarizes the capabilities of MS in various aspects of nano-characterization that greatly enrich the toolbox of nano research. Compared with other characterization techniques, MS has unique capabilities for real-time monitoring and tracking reaction intermediates and by-products. Moreover, MS has shown application potential in some novel aspects, such as MS imaging of the biodistribution and fate of NMs in animals and humans, stable isotopic tracing of NMs, and risk assessment of NMs, which deserve update and integration into the current knowledge framework of nano-characterization.

Higher Resolution Charge Detection Mass Spectrometry

Charge detection mass spectrometry is a single particle technique where the masses of individual ions are determined from simultaneous measurements of each ion's m/z ratio and charge. The ions pass through a conducting cylinder, and the charge induced on the cylinder is detected. The cylinder is usually placed inside an electrostatic linear ion trap so that the ions oscillate back and forth through the cylinder. The resulting time domain signal is analyzed by fast Fourier transformation; the oscillation frequency yields the m/z, and the charge is determined from the magnitudes. The mass resolving power depends on the uncertainties in both quantities. In previous work, the mass resolving power was modest, around 30-40. In this work we report around an order of magnitude improvement. The improvement was achieved by coupling high-accuracy charge measurements (obtained with dynamic calibration) with higher resolution m/z measurements. The performance was benchmarked by monitoring the assembly of the hepatitis B virus (HBV) capsid. The HBV capsid assembly reaction can result in a heterogeneous mixture of intermediates extending from the capsid protein dimer to the icosahedral T = 4 capsid with 120 dimers. Intermediates of all possible sizes were resolved, as well as some overgrown species. Despite the improved mass resolving power, the measured peak widths are still dominated by instrumental resolution. Heterogeneity makes only a small contribution. Resonances were observed in some of the m/z spectra. They result from ions with different masses and charges having similar m/z values. Analogous resonances are expected whenever the sample is a heterogeneous mixture assembled from a common building block.

Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin

X-ray structures of homopolymeric human L-ferritin and horse spleen ferritin were solved by freezing protein crystals at different time intervals after exposure to a ferric salt and revealed the growth of an octa-nuclear iron cluster on the inner surface of the protein cage with a key role played by some glutamate residues. An atomic resolution view of how the cluster formation develops starting from a (μ³ -oxo)tris[(μ² -glutamato-κO:κO')](glutamato-κO)(diaquo)triiron(III) seed is provided. The results support the idea that iron biomineralization in ferritin is a process initiating at the level of the protein surface, capable of contributing coordination bonds and electrostatic guidance.

Implementation of a Charge-Sensitive Amplifier without a Feedback Resistor for Charge Detection Mass Spectrometry Reduces Noise and Enables Detection of Individual Ions Carrying a Single Charge

Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. Electrical noise limits the accuracy of the charge measurement and the smallest charge that can be detected. Thermal noise in the feedback resistor is a major source of electrical noise. We describe the implementation of a charge-sensitive amplifier without a feedback resistor. The design has significantly reduced 1/f noise facilitating the detection of high m/z ions and substantially reducing the measurement time required to achieve almost perfect charge accuracy. With the new design we have been able to detect individual ions carrying a single charge. This is an important milestone in the development of CDMS.

Characterizing the iron loading pattern of ferritin using high-mass matrix-assisted laser desorption ionization mass spectrometry

RATIONALE

Ferritin is an iron storage protein assembly, usually formed by a 24-subunit protein shell and an iron core. The ferritin shell has been well studied using various structural biology tools such as X-ray diffraction and cryo-electron microscopy, whereas the iron status of ferritin is less studied and no well-established method exists for characterizing the distribution of the iron loading of ferritin. Recent advances in mass spectrometry (MS) have expanded the observable m/z range, making the measurement of ferritin possible with MS. In this study, matrix-assisted laser desorption ionization (MALDI)-MS was employed to quantify the iron content of ferritin.

METHODS

The iron content of ferritin was quantified using a MALDI-MS system coupled with a commercially available ion conversions dynode high-mass detector. IgG1 antibody and its aggregates were used as external mass calibrants. The stability of HoloFt and ApoFt was also assessed in this study under different conditions, including various buffer pH, crosslinking agents and MALDI laser intensities.

RESULTS

The differences in peak width of HoloFt, ApoFt and IgG1 indicate the existence of mineral adducts in both HoloFt and ApoFt, and the mineral loading is heterogeneous among the HoloFt and ApoFt population. An average of 2773 ± 1584 iron atoms were determined for a commercial HoloFt sample. The iron core inside the ferritin complex is shown to stabilize and maintain the intact globular complex structure of ferritin.

CONCLUSIONS

This work introduces a MALDI-MS-based workflow for characterizing the ferritin iron loading pattern, which is meaningful for clinical analysis of iron deficiency/overload. In addition, the stability of ferritin is examined under various conditions, providing a guideline for further method development related to ferritin complex.

Dramatic Improvement in Sensitivity with Pulsed Mode Charge Detection Mass Spectrometry

Charge detection mass spectrometry (CDMS) is emerging as a valuable tool to determine mass distributions for heterogeneous and high-mass samples. It is a single-particle technique where masses are determined for individual ions from simultaneous measurements of their mass-to-charge ratio (m/z) and charge. Ions are trapped in an electrostatic linear ion trap (ELIT) and oscillate back and forth through a detection cylinder. The trap is open and able to trap ions for a small fraction of the total measurement time so most of the ions (>99.8%) in a continuous ion beam are lost. Here, we implement an ion storage scheme where ions are accumulated and stored in a hexapole and then injected into the ELIT at the right time for them to be trapped. This pulsed mode of operation increases the sensitivity of CDMS by more than 2 orders of magnitude, which allows much lower titer samples to be analyzed. A limit of detection of 3.3 × 10⁸ particles/mL was obtained for hepatitis B virus T = 4 capsids with a 1.3 μL sample. The hexapole where the ions are accumulated and stored is a significant distance from the ion trap so ions are dispersed in time by their m/z values as they travel between the hexapole and the ELIT. By varying the delay time between ion release and trapping, different windows of m/z values can be trapped.

Self-Assembly of Ferritin: Structure, Biological Function and Potential Applications in Nanotechnology

Protein cages are normally formed by the self-assembly of multiple protein subunits and ferritin is a typical example of a protein cage structure. Ferritin is a ubiquitous multi-subunit iron storage protein formed by 24 polypeptide chains that self-assemble into a hollow, roughly spherical protein cage. Ferritin has external and internal diameters of approximately 12 nm and 8 nm, respectively. Functionally, ferritin performs iron sequestration and is highly conserved in evolution. The interior cavity of ferritin provides a unique reaction vessel to carry out reactions separated from the exterior environment. In nature, the cavity is utilized for sequestration of iron and bio-mineralization as a mechanism to render iron inert and safe from the external environment. Material scientists have been inspired by this system and exploited a range of ferritin superfamily proteins as supramolecular templates to encapsulate different carrier molecules ranging from cancer drugs to therapeutic proteins, in addition to using ferritin proteins as well-defined building blocks for fabrication. Besides the interior cavity, the exterior surface and sub-unit interface of ferritin can be modified without affecting ferritin assembly.

Cancer cell death induced by ferritins and the peculiar role of their labile iron pool

Cellular uptake of human H-ferritin loaded with 50 or 350 iron ions results in significant cytotoxicity on HeLa cells at submicromolar concentrations. Conversely, Horse Spleen Ferritin, that can be considered a model of L-cages, as it contains only about 10% of H subunits, even when loaded with 1000 iron ions, is toxic only at >1 order of magnitude higher protein concentrations. We propose here that the different cytotoxicity of the two ferritin cages originates from the presence in H-ferritin of a pool of non-biomineralized iron ions bound at the ferroxidase catalytic sites of H-ferritin subunits. This iron pool is readily released during the endosomal-mediated H-ferritin internalization.

Characterization of Mega-Dalton-Sized Nanoparticles by Superconducting Tunnel Junction Cryodetection Mass Spectrometry

The characterization of nanomaterials is critical to understand the size/structure-dependent properties of these particles. In this report, a form of heavy ion mass spectrometry, namely, superconducting tunnel junction (STJ) cryodetection mass spectrometry (MS) is used to characterize quantum dot semiconductor nanocrystals and gold nanoparticles. The nanoparticles studied ranged in mass from 200 kDa to >1.5 MDa and included lead sulfide quantum dots, various cadmium selenide and/or telluride-based core-shell quantum dots coated with different ligands, and gold nanoparticles. Nanoparticles were ionized by both matrix-assisted laser desorption ionization (MALDI) and laser desorption ionization (LDI), shot with an aimed ion gun into a flight tube, mass separated by time-of-flight (TOF), and detected by an energy-sensitive STJ cryodetector. STJ cryodetection MS can be used to analyze intact heterogeneous nanoparticles, allowing determination of average particle mass, dispersity, and ligand loading. Some nanoparticles, however, do undergo fragmentation during the MALDI or LDI-TOF mass analyses. The measurement of the energy deposited into the detector was found to be different for different types of particles. Metastable fragments from these nanoparticles were observed at lower energies. The lower energies deposited for metastable fragments can provide insight into the stability and surface compositions of these materials. Cadmium selenide core-shell quantum dots (655 nm emission) conjugated to biomacromolecules, such as cholera toxin B and human serum transferrin, were also analyzed. When compared to unconjugated particles by mass, it was determined that ∼96 cholera toxin B and ∼14 transferrin proteins were attached to the surface of these nanoparticles.

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.

Unsaturated Long-Chain Fatty Acids Are Preferred Ferritin Ligands That Enhance Iron Biomineralization

Ferritin is a ubiquitous nanocage protein, which can accommodate up to thousands of iron atoms inside its cavity. Aside from its iron storage function, a new role as a fatty acid binder has been proposed for this protein. The interaction of apo horse spleen ferritin (HoSF) with a variety of lipids has been here investigated through NMR spectroscopic ligand-based experiments, to provide new insights into the mechanism of ferritin-lipid interactions, and the link with iron mineralization. 1D ¹ H, diffusion (DOSY) and saturation-transfer difference (STD) NMR experiments provided evidence for a stronger interaction of ferritin with unsaturated fatty acids compared to saturated fatty acids, detergents, and bile acids. Mineralization assays showed that oleate c aused the most efficient increase in the initial rate of iron oxidation, and the highest formation of ferric species in HoSF. The comprehension of the factors inducing a faster biomineralization is an issue of the utmost importance, given the association of ferritin levels with metabolic syndromes, such as insulin resistance and diabetes, characterized by fatty acid concentration dysregulation. The human ferritin H-chain homopolymer (HuHF), featuring ferroxidase activity, was also tested for its fatty acid binding capabilities. Assays show that oleate can bind with high affinity to HuHF, without altering the reaction rates at the ferroxidase site.

Characterization of ZnO Nanoparticles using Superconducting Tunnel Junction Cryodetection Mass Spectrometry

Zinc oxide (ZnO) nanoparticles coated with either n-octylamine (OA) or α-amino poly(styrene-co-acrylonitrile) (PSAN) ligands (L) have been analyzed using laser desorption/ionization and matrix assisted laser desorption/ionization (MALDI) time-of-flight (TOF) superconducting tunnel junction (STJ) cryodetection mass spectrometry. STJ cryodetection has the advantage of high m/z detection and allows for the determination of average molecular weights and dispersities for 500-600 kDa ZnO-L nanoparticles. The ability to detect the relative energies deposited into the STJs has allowed for investigation of ZnO-L metastable fragmentation. ZnO-L precursor ions gain enough internal energy during the MALDI process to undergo metastable fragmentation in the flight tube. These fragments produced a lower energy peak, which was assigned as ligand-stripped ZnO cores whereas the individual ligands were at too low of an energy to be observed. From these STJ energy resolved peaks, the average weight percentage of inorganic material making up the nanoparticle was determined, where ZnO-OA and ZnO-PSAN nanoparticles are comprised of ~62% and ~68% wt ZnO, respectively. In one example, grafting densities were calculated based on the metastable fragmentation of ligands from the core to be 16 and 1.1 nm^-2 for ZnO-OA and ZnO-PSAN, respectively, and compared with values determined by thermogravimetric analysis (TGA) and transmission electron microscopy (TEM). Graphical Abstract ᅟ.

Single Particle Analyzer of Mass: A Charge Detection Mass Spectrometer with a Multi-Detector Electrostatic Ion Trap

A new charge detection mass spectrometer that combines array detection and electrostatic ion trapping to repeatedly measure the masses of single ions is described. This instrument has four detector tubes inside an electrostatic ion trap with conical electrodes (cone trap) to provide multiple measurements of an ion on each pass through the trap resulting in a signal gain over a conventional trap with a single detection tube. Simulations of a cone trap and a dual ion mirror trap design indicate that more passes through the trap per unit time are possible with the latter. However, the cone trap has the advantages that ions entering up to 2 mm off the central axis of the trap are still trapped, the trapping time is less sensitive to the background pressure, and only a narrow range of energies are trapped so it can be used for energy selection. The capability of this instrument to obtain information about the molecular weight distributions of heterogeneous high molecular weight samples is demonstrated with 8 MDa polyethylene glycol (PEG) and 50 and 100 nm amine modified polystyrene nanoparticle samples. The measured mass distribution of the PEG sample is centered at 8 MDa. The size distribution obtained from mass measurements of the 100 nm nanoparticle sample is similar to the size distribution obtained from transmission electron microscopy (TEM) images, but most of the smaller nanoparticles observed in TEM images of the 50 nm nanoparticles do not reach a sufficiently high charge to trigger the trap on a single pass and be detected by the mass spectrometer. With the maximum trapping time set to 100 ms, the charge uncertainty is as low as ±2 charges and the mass uncertainty is approximately 2% for PEG and polystyrene ions.

Native Mass Spectrometry: What is in the Name?

Electrospray ionization mass spectrometry (ESI-MS) is nowadays one of the cornerstones of biomolecular mass spectrometry and proteomics. Advances in sample preparation and mass analyzers have enabled researchers to extract much more information from biological samples than just the molecular weight. In particular, relevant for structural biology, noncovalent protein-protein and protein-ligand complexes can now also be analyzed by MS. For these types of analyses, assemblies need to be retained in their native quaternary state in the gas phase. This initial small niche of biomolecular mass spectrometry, nowadays often referred to as "native MS," has come to maturation over the last two decades, with dozens of laboratories using it to study mostly protein assemblies, but also DNA and RNA-protein assemblies, with the goal to define structure-function relationships. In this perspective, we describe the origins of and (re)define the term native MS, portraying in detail what we meant by "native MS," when the term was coined and also describing what it does (according to us) not entail. Additionally, we describe a few examples highlighting what native MS is, showing its successes to date while illustrating the wide scope this technology has in solving complex biological questions. Graphical Abstract ᅟ.