1
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Wang CR, McFarlane LO, Pukala TL. Exploring Snake Venoms Beyond the Primary Sequence: from Proteoforms to Protein-Protein Interactions. Toxicon 2024:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomics workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia.
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3
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Shaw J, Harvey SR, Du C, Xu Z, Edgington RM, Olmedillas E, Saphire EO, Wysocki VH. Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583498. [PMID: 38496594 PMCID: PMC10942452 DOI: 10.1101/2024.03.07.583498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We illustrate the utility of native mass spectrometry (nMS) combined with a fast, tunable gas-phase charge reduction, electron capture charge reduction (ECCR), for the characterization of protein complex topology and glycoprotein heterogeneity. ECCR efficiently reduces the charge states of tetradecameric GroEL, illustrating Orbitrap m/z measurements to greater than 100,000 m/z. For pentameric C-reactive protein and tetradecameric GroEL, our novel device combining ECCR with surface induced dissociation (SID) reduces the charge states and yields more topologically informative fragmentation. This is the first demonstration that ECCR yields more native-like SID fragmentation. ECCR also significantly improved mass and glycan heterogeneity measurements of heavily glycosylated SARS-CoV-2 spike protein trimer and thyroglobulin dimer. Protein glycosylation is important for structural and functional properties and plays essential roles in many biological processes. The immense heterogeneity in glycosylation sites and glycan structure poses significant analytical challenges that hinder a mechanistic understanding of the biological role of glycosylation. Without ECCR, average mass determination of glycoprotein complexes is available only through charge detection mass spectrometry or mass photometry. With narrow m/z selection windows followed by ECCR, multiple glycoform m/z values are apparent, providing quick global glycoform profiling and providing a future path for glycan localization on individual intact glycoforms.
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4
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Nurrohman DT, Chiu NF, Hsiao YS, Lai YJ, Nanda HS. Advances in Nanoplasmonic Biosensors: Optimizing Performance for Exosome Detection Applications. BIOSENSORS 2024; 14:307. [PMID: 38920611 PMCID: PMC11201745 DOI: 10.3390/bios14060307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024]
Abstract
The development of sensitive and specific exosome detection tools is essential because they are believed to provide specific information that is important for early detection, screening, diagnosis, and monitoring of cancer. Among the many detection tools, surface-plasmon resonance (SPR) biosensors are analytical devices that offer advantages in sensitivity and detection speed, thereby making the sample-analysis process faster and more accurate. In addition, the penetration depth of the SPR biosensor, which is <300 nm, is comparable to the size of the exosome, making the SPR biosensor ideal for use in exosome research. On the other hand, another type of nanoplasmonic sensor, namely a localized surface-plasmon resonance (LSPR) biosensor, has a shorter penetration depth of around 6 nm. Structural optimization through the addition of supporting layers and gap control between particles is needed to strengthen the surface-plasmon field. This paper summarizes the progress of the development of SPR and LSPR biosensors for detecting exosomes. Techniques in signal amplification from two sensors will be discussed. There are three main parts to this paper. The first two parts will focus on reviewing the working principles of each sensor and introducing several methods that can be used to isolate exosomes. This article will close by explaining the various sensor systems that have been developed and the optimizations carried out to obtain sensors with better performance. To illustrate the performance improvements in each sensor system discussed, the parameters highlighted include the detection limit, dynamic range, and sensitivity.
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Affiliation(s)
- Devi Taufiq Nurrohman
- Laboratory of Nano-Photonics and Biosensors, Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
| | - Nan-Fu Chiu
- Laboratory of Nano-Photonics and Biosensors, Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan;
| | - Yu-Sheng Hsiao
- Department of Materials Science and Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Road, Da-an District, Taipei 10607, Taiwan;
| | - Yun-Ju Lai
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan;
| | - Himansu Sekhar Nanda
- Biomedical Engineering and Technology Laboratory, Mechanical Engineering Discipline, PDPM Indian Institute of Information Technology, Design & Manufacturing, Jabalpur 482005, India;
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5
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Meldrum KL, Swansiger AK, Daniels MM, Hale WA, Kirmiz Cody C, Qiu X, Knierman M, Sausen J, Prell JS. Gábor Transform-Based Signal Isolation, Rapid Deconvolution, and Quantitation of Intact Protein Ions with Mass Spectrometry. Anal Chem 2024; 96:9512-9523. [PMID: 38788216 DOI: 10.1021/acs.analchem.4c00978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
High-resolution mass spectrometry (HRMS) is a powerful technique for the characterization and quantitation of complex biological mixtures, with several applications including clinical monitoring and tissue imaging. However, these medical and pharmaceutical applications are pushing the analytical limits of modern HRMS techniques, requiring either further development in instrumentation or data processing methods. Here, we demonstrate new developments in the interactive Fourier-transform analysis for mass spectrometry (iFAMS) software including the first application of Gábor transform (GT) to protein quantitation. Newly added automation tools detect signals from minimal user input and apply thresholds for signal selection, deconvolution, and baseline correction to improve the objectivity and reproducibility of deconvolution. Additional tools were added to improve the deconvolution of highly complex or congested mass spectra and are demonstrated here for the first time. The "Gábor Slicer" enables the user to explore trends in the Gábor spectrogram with instantaneous ion mass estimates accurate to 10 Da. The charge adjuster allows for easy visual confirmation of accurate charge state assignments and quick adjustment if necessary. Deconvolution refinement utilizes a second GT of isotopically resolved data to remove common deconvolution artifacts. To assess the quality of deconvolution from iFAMS, several comparisons are made to deconvolutions using other algorithms such as UniDec and an implementation of MaxEnt in Agilent MassHunter BioConfirm. Lastly, the newly added batch processing and quantitation capabilities of iFAMS are demonstrated and compared to a common extracted ion chromatogram approach.
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Affiliation(s)
- Kayd L Meldrum
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Meghan M Daniels
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Wendi A Hale
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Crystal Kirmiz Cody
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Xi Qiu
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Michael Knierman
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - John Sausen
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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Spesyvyi A, Žabka J, Polášek M, Malečková M, Khawaja N, Schmidt J, Kempf S, Postberg F, Charvat A, Abel B. Selected ice nanoparticle accelerator hypervelocity impact mass spectrometer (SELINA-HIMS): features and impacts of charged particles. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230208. [PMID: 38736336 DOI: 10.1098/rsta.2023.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
The selected ice nanoparticle accelerator, SELINA, was used to prepare beams of single ice particles with positive or negative charge. Positively charged particles were prepared from deionized water and 0.05-0.2 molar solutions of sodium chloride in water, and negatively charged ice particles were generated from water without salt. Depending on the electrospray source configuration, the measured particles vary from 50 to 1000 nm in diameter. The kinetic energy per charge for all particles was set to 200 eV by the collisional equilibration in quadrupoles, which resulted in primary velocities up to 600 m/s for the lowest m/z particles. The electrospray ionization and thus particle formation from SELINA become less efficient with increasing salt concentration, resulting in a lower detected particle frequency and size. Good instrument operation is achievable for concentrations below 0.2 M. After we have verified and characterized positively and negatively charged ice particles, we have combined SELINA with a target and time-of-flight spectrometer for a 'proof-of-principle' post acceleration of 120 nm particles towards hypervelocity (v ~ 3000 m/s) and detection of fragments from the particle impact (SELINA-HIMS). General conditions are discussed for the acceleration of particles between 50 and 1000 nm to velocities well above 3000 m/s with SELINA-HIMS instrument. This article is part of the theme issue 'Dust in the Solar System and beyond'.
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Affiliation(s)
- Anatolii Spesyvyi
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Prague 18223, Czechia
| | - Ján Žabka
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Prague 18223, Czechia
| | - Miroslav Polášek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Prague 18223, Czechia
| | - Michaela Malečková
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Prague 18223, Czechia
| | - Nozair Khawaja
- Institute of Geological Sciences, Freie Universität Berlin , Berlin, 12249, Germany
| | - Jürgen Schmidt
- Institute of Geological Sciences, Freie Universität Berlin , Berlin, 12249, Germany
| | - Sascha Kempf
- Laboratory for Atmospheric and Space Physics, University of Colorado , Boulder, CO, 80303, USA
| | - Frank Postberg
- Institute of Geological Sciences, Freie Universität Berlin , Berlin, 12249, Germany
| | - Ales Charvat
- Institute of Chemical Technology and Wilhelm Ostwald-Institute of Physical and Theoretical Chemistry , Leipzig, 04103, Germany
- Leibniz Institute of Surface Engineering , Leipzig, 04318, Germany
| | - Bernd Abel
- Institute of Chemical Technology and Wilhelm Ostwald-Institute of Physical and Theoretical Chemistry , Leipzig, 04103, Germany
- Leibniz Institute of Surface Engineering , Leipzig, 04318, Germany
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7
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Burke SE, Continetti RE. Submicrometer Particle Impact Dynamics and Chemistry. Annu Rev Phys Chem 2024; 75:67-88. [PMID: 38941529 DOI: 10.1146/annurev-physchem-083122-122157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Experimental studies of the collision phenomena of submicrometer particles is a developing field. This review examines the range of phenomena that can be observed with new experimental approaches. The primary focus is on single-particle impact studies enabled by charge detection mass spectrometry (CDMS) implemented using the Aerosol Impact Spectrometer (AIS) at the University of California, San Diego. The AIS combines electrospray ionization, aerodynamic lens techniques, CDMS, and an electrostatic linear accelerator to study the dynamics of particle impact over a wide range of incident velocities. The AIS has been used for single-particle impact experiments on positively charged particles of diverse composition, including polystyrene latex spheres, tin particles, and ice grains, over a wide range of impact velocities. Detection schemes based on induced charge measurements and time-of-flight mass spectrometry have enabled measurements of the impact inelasticity through the determination of the coefficient of restitution, measurements of the angular distributions of scattered submicrometer particles, and the chemical composition and dissociation of solute molecules in hypervelocity ice grain impacts.
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Affiliation(s)
- Sally E Burke
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; ,
| | - Robert E Continetti
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; ,
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8
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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9
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Pizzala NJ, Bhanot JS, Carrick IJ, Dziekonski ET, McLuckey SA. Ion parking in native mass spectrometry. Analyst 2024; 149:2966-2977. [PMID: 38600834 PMCID: PMC11089522 DOI: 10.1039/d4an00242c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
A forced, damped harmonic oscillator model for gas-phase ion parking using single-frequency resonance excitation is described and applied to high-mass ions of relevance to native mass spectrometry. Experimental data are provided to illustrate key findings revealed by the modelling. These include: (i) ion secular frequency spacings between adjacent charge states of a given protein are essentially constant and decrease with the mass of the protein (ii) the mechanism for ion parking of high mass ions is the separation of the ion clouds of the oppositely-charged ions with much less influence from an increase in the relative ion velocity due to resonance excitation, (iii) the size of the parked ion cloud ultimately limits ion parking at high m/z ratio, and (iv) the extent of ion parking of off-target ions is highly sensitive to the bath gas pressure in the ion trap. The model is applied to ions of 17 kDa, 467 kDa, and 2 MDa while experimental data are also provided for ions of horse skeletal muscle myoglobin (≈17 kDa) and β-galactosidase (≈467 kDa). The model predicts and data show that it is possible to effect ion parking on a 17 kDa protein to the 1+ charge state under trapping conditions that are readily accessible with commercially available ion traps. It is also possible to park β-galactosidase efficiently to a roughly equivalent m/z ratio (i.e., the 26+ charge state) under the same trapping conditions. However, as charge states decrease, analyte ion cloud sizes become too large to allow for efficient ion trapping. The model allows for a semi-quantitative prediction of ion trapping performance as a function of ion trapping, resonance excitation, and pressure conditions.
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Affiliation(s)
- Nicolas J Pizzala
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Jay S Bhanot
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Ian J Carrick
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Eric T Dziekonski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
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10
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Liang SY, Cua Estayan MI, Hsieh LW, Pan MC, Li KX, Chang HC, Peng WP. Real-Time Monitoring of the Evaporation and Fission of Electrospray-Ionized Polystyrene Beads and Bacterial Pellets at Elevated Temperatures. Anal Chem 2024; 96:7179-7186. [PMID: 38661266 DOI: 10.1021/acs.analchem.4c00763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
This study uses real-time monitoring, at microsecond time scales, with a charge-sensing particle detector to investigate the evaporation and fission processes of methanol/micrometer-sized polystyrene beads (PS beads) droplets and bacterial particles droplets generated via electrospray ionization (ESI) under elevated temperatures. By incrementally raising capillary temperatures, the solvent, such as methanol on 0.75 μm PS beads, experiences partial evaporation. Further temperature increase induces fission, and methanol molecules continue to evaporate until PS ions are detected after this range. Similar partial evaporation is observed on 3 μm PS beads. However, the shorter period of the fission temperature range is necessary compared to 0.75 μm PS beads. For the spherical-shaped bacterium, Staphylococcus aureus, the desolvation process shows a similar fission period as compared to 0.75 μm PS beads. Comparably, the rod-shaped bacteria, Escherichia coli EC11303, and E. coli strain W have shorter fission periods than S. aureus. This research provides insights into the evaporation and fission mechanisms of ESI droplets containing different sizes and shapes of micrometer-sized particles, contributing to a better understanding of gaseous macroion formation.
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Affiliation(s)
- Shao-Yu Liang
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401
| | - Mhar Ian Cua Estayan
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401
- Department of Mathematics and Physics, University of Santo Tomas, Manila 1008, Philippines
| | - Li-Wei Hsieh
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401
| | - Meng-Cheng Pan
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401
| | - Kai-Xiang Li
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401
| | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan 10617
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401
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11
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Hrabovsky D, Argence B, Lesage D, Colomby P, Surugue M, Cole RB. Charge Detection Mass Spectrometry for Megadalton Polymer Characterization and Measurement of Electrospray-Generated Charged Droplet Dynamics with a New "Direct Visualization of the Rayleigh Limit" Approach to Aid in m/ z Calibration. Anal Chem 2024; 96:6986-6994. [PMID: 38652037 DOI: 10.1021/acs.analchem.4c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
A charge detector has been constructed and mounted inside the vacuum housing of a commercial mass spectrometer (Micromass-Waters Quattro I, Waters Corp., Manchester, UK). The in-house built single-pass charge detector is composed of a designed, complete electronics system that includes a low-noise charge amplifier. Communication to the data acquisition system was enabled, and analog and digital filters were devised, followed by their tuning and programming. Data treatment scripts for data analysis and plotting were automated, and the assembled system was calibrated and tested. The instrument has an acquisition speed of ∼200 detection events/s, and it permits detection down to ∼510 charges (= three times RMS noise) for a single measured particle. The charge detector was employed to determine the oligomer distribution of a megadalton polymer, polyethylene glycol (PEG). The PEG size distribution exhibits a maximum at ∼ m/z 5910 with the oligomeric population mass distribution peaking near 4.45 MDa. In studies of methanol droplet dynamics, "charge vs time-of-flight" plots enabled clear visualization of the zone near the Rayleigh limit to droplet charging. The highest population of methanol droplets near the Rayleigh limit carried 5000-7000 charges. This corresponds to droplet weights of 10-20 GDa, with the high-end tail extending above 70 GDa. This visualization of the most highly charged droplets (that bear numbers of charges near those defined by the Rayleigh equation) was exploited as a calibration aid for our charge detector, which lacks a means of precisely defining ion energy. A maximum m/z error of -12.3% was calculated for the method, i.e., less than the potential error in assigning the true level of charging of the most highly charged droplets relative to the Rayleigh limit. With these limitations in mind, the introduced method will provide a new means for aiding the calibration of m/z values in charge detectors.
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Affiliation(s)
- David Hrabovsky
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Université-Faculté des Sciences et Ingénierie, 4 Place Jussieu, Paris 75252, Cedex 05, France
| | - Bérengère Argence
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Université-Faculté des Sciences et Ingénierie, 4 Place Jussieu, Paris 75252, Cedex 05, France
| | - Denis Lesage
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Université-Faculté des Sciences et Ingénierie, 4 Place Jussieu, Paris 75252, Cedex 05, France
| | - Philippe Colomby
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Université-Faculté des Sciences et Ingénierie, 4 Place Jussieu, Paris 75252, Cedex 05, France
| | - Michel Surugue
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Université-Faculté des Sciences et Ingénierie, 4 Place Jussieu, Paris 75252, Cedex 05, France
| | - Richard B Cole
- Institut Parisien de Chimie Moléculaire, UMR 8232, Sorbonne Université-Faculté des Sciences et Ingénierie, 4 Place Jussieu, Paris 75252, Cedex 05, France
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12
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Wesdemiotis C, Williams-Pavlantos KN, Keating AR, McGee AS, Bochenek C. Mass spectrometry of polymers: A tutorial review. MASS SPECTROMETRY REVIEWS 2024; 43:427-476. [PMID: 37070280 DOI: 10.1002/mas.21844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Ever since the inception of synthetic polymeric materials in the late 19th century, the number of studies on polymers as well as the complexity of their structures have only increased. The development and commercialization of new polymers with properties fine-tuned for specific technological, environmental, consumer, or biomedical applications requires powerful analytical techniques that permit the in-depth characterization of these materials. One such method with the ability to provide chemical composition and structure information with high sensitivity, selectivity, specificity, and speed is mass spectrometry (MS). This tutorial review presents and exemplifies the various MS techniques available for the elucidation of specific structural features in a synthetic polymer, including compositional complexity, primary structure, architecture, topology, and surface properties. Key to every MS analysis is sample conversion to gas-phase ions. This review describes the fundamentals of the most suitable ionization methods for synthetic materials and provides relevant sample preparation protocols. Most importantly, structural characterizations via one-step as well as hyphenated or multidimensional approaches are introduced and demonstrated with specific applications, including surface sensitive and imaging techniques. The aim of this tutorial review is to illustrate the capabilities of MS for the characterization of large, complex polymers and emphasize its potential as a powerful compositional and structural elucidation tool in polymer chemistry.
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Affiliation(s)
| | | | - Addie R Keating
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Andrew S McGee
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Calum Bochenek
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
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13
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Xiong C, Pan Y, Fan J, Li Y, Wang J, Nie Z. Accurate and High-Resolution Particle Mass Measurement Using a Peak Filtering Algorithm. Anal Chem 2024; 96:6511-6516. [PMID: 38634936 DOI: 10.1021/acs.analchem.3c04217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Charge detection quadrupole ion trap mass spectrometry (CD-QIT MS) is an effective way of achieving the mass analysis of microparticles with ultrahigh mass. However, its mass accuracy and resolution are still poor. To enhance the performance of CD-QIT MS, the resolution Rpeak of each peak in the mass spectra resulting from an individual particle was assessed, and a peak filtering algorithm that can filter out particle adducts and clusters with a lower Rpeak was proposed. By using this strategy, more accurate mass information about the analyzed particles could be obtained, and the mass resolution of CD-QIT MS was improved by nearly 2-fold, which was demonstrated by using the polystyrene (PS) particle size standards and red blood cells (RBCs). Benefiting from these advantages of the peak filtering algorithm, the baseline separation and relative quantification of 3 and 4 μm PS particles were achieved. To prove the application value of this algorithm in a biological system, the mass of yeast cells harvested at different times was measured, and it was found that the mixed unbudded and budded yeast cells, which otherwise would not be differentiable, were distinguished and quantified with the algorithm.
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Affiliation(s)
- Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Pan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghan Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
| | - Jiyun Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Deslignière E, Yin VC, Ebberink EHTM, Rolland AD, Barendregt A, Wörner TP, Nagornov KO, Kozhinov AN, Fort KL, Tsybin YO, Makarov AA, Heck AJR. Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry. Nat Methods 2024; 21:619-622. [PMID: 38443506 DOI: 10.1038/s41592-024-02207-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
Orbitrap-based charge detection mass spectrometry utilizes single-molecule sensitivity to enable mass analysis of even highly heterogeneous, high-mass macromolecular assemblies. For contemporary Orbitrap instruments, the accessible ion detection (recording) times are maximally ~1-2 s. Here by modifying a data acquisition method on an Orbitrap ultrahigh mass range mass spectrometer, we trapped and monitored individual (single) ions for up to 25 s, resulting in a corresponding and huge improvement in signal-to-noise ratio (×5 compared with 1 s), mass resolution (×25) and accuracy in charge and mass determination of Orbitrap-based charge detection mass spectrometry.
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Affiliation(s)
- Evolène Deslignière
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Victor C Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands.
| | - Eduard H T M Ebberink
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Amber D Rolland
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | | | | | | | - Kyle L Fort
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | - Alexander A Makarov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands.
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15
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Jarrold MF. Single-Ion Mass Spectrometry for Heterogeneous and High Molecular Weight Samples. J Am Chem Soc 2024; 146:5749-5758. [PMID: 38394699 DOI: 10.1021/jacs.3c08139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In charge detection mass spectrometry (CD-MS) the mass of each individual ion is determined from the measurement of its mass to charge ratio (m/z) and charge. Performing this measurement for thousands of ions allows mass distributions to be measured for heterogeneous and high mass samples that cannot be analyzed by conventional mass spectrometry (MS). CD-MS opens the door to accurate mass measurements for samples into the giga-Dalton regime, vastly expanding the reach of MS and allowing mass distributions to be determined for viruses, gene therapies, and vaccines. Following the success of CD-MS, single-ion mass measurements have recently been performed on an Orbitrap. CD-MS and Orbitrap individual ion mass spectrometry (I2MS) are described. Illustrative examples are provided, and the prospects for higher resolution measurements discussed. In the case of CD-MS, computer simulations indicate that much higher resolving powers are within reach. The ability to perform high-resolution CD-MS analysis of heterogeneous samples will be enabling and disruptive in top-down MS as high-resolution m/z and accurate charge measurements will allow very complex m/z spectra to be unraveled.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
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16
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Parikh RA, Draper BE, Jarrold MF. Multiple Ion Charge Extraction (MICE) for High-Throughput Charge Detection Mass Spectrometry. Anal Chem 2024. [PMID: 38329825 DOI: 10.1021/acs.analchem.3c05087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Charge detection mass spectrometry (CD-MS) is a single-particle technique, where the masses of individual ions are determined from simultaneous measurements of their mass-to-charge ratio (m/z) and charge. The ions are trapped in an electrostatic linear ion trap (ELIT) and oscillate back and forth through a conducting cylinder connected to a charge-sensitive amplifier. The oscillating ions generate a periodic signal that is processed with fast Fourier transforms (FFTs) to obtain the oscillation frequency (which is related to m/z) and magnitude (which is proportional to the charge). The simultaneous trapping of two or more ions is a way to increase throughput. However, when multiple ions are trapped, it is possible that some of them have overlapping oscillation frequencies, which can lead to an error in the charge determination. To avoid this error, results from overlapping ions are usually discarded. When measurements are performed with many trapped ions, the most abundant m/z species are discarded at a higher rate, which affects the relative abundances in the mass distribution. Here, we report the development of a post-processing method called multiple ion charge extraction (MICE) that uses a statistical approach to assign charges to ions with overlapping frequencies. MICE recovers single-ion information from high signal measurements and makes the relative abundances more resilient to the signal intensity. This approach corrects for high signal m/z biasing, allowing analysis to be faster and more reliable. Using MICE, CD-MS measurements were made at rates of 120 ions/s with little m/z biasing.
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Affiliation(s)
- Raj A Parikh
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
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17
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Yang R, Ko YH, Li F, Lokareddy RK, Hou CFD, Kim C, Klein S, Antolínez S, Marín JF, Pérez-Segura C, Jarrold MF, Zlotnick A, Hadden-Perilla JA, Cingolani G. Structural basis for nuclear import of hepatitis B virus (HBV) nucleocapsid core. SCIENCE ADVANCES 2024; 10:eadi7606. [PMID: 38198557 PMCID: PMC10780889 DOI: 10.1126/sciadv.adi7606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an intact particle, hijacking human importins in a reaction stimulated by host kinases. This paper describes the mechanisms of HBV capsid recognition by importins. We found that importin α1 binds a nuclear localization signal (NLS) at the far end of the HBV coat protein Cp183 carboxyl-terminal domain (CTD). This NLS is exposed to the capsid surface through a pore at the icosahedral quasi-sixfold vertex. Phosphorylation at serine-155, serine-162, and serine-170 promotes CTD compaction but does not affect the affinity for importin α1. The binding of 30 importin α1/β1 augments HBV capsid diameter to ~620 angstroms, close to the maximum size trafficable through the NPC. We propose that phosphorylation favors CTD externalization and prompts its compaction at the capsid surface, exposing the NLS to importins.
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Affiliation(s)
- Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ravi K. Lokareddy
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Christine Kim
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | - Shelby Klein
- Department of Chemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | - Santiago Antolínez
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Juan F. Marín
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, IN 47405, USA
| | | | - Gino Cingolani
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
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18
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Kaltashov IA, Ivanov DG, Yang Y. Mass spectrometry-based methods to characterize highly heterogeneous biopharmaceuticals, vaccines, and nonbiological complex drugs at the intact-mass level. MASS SPECTROMETRY REVIEWS 2024; 43:139-165. [PMID: 36582075 PMCID: PMC10307928 DOI: 10.1002/mas.21829] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The intact-mass MS measurements are becoming increasingly popular in characterization of a range of biopolymers, especially those of interest to biopharmaceutical industry. However, as the complexity of protein therapeutics and other macromolecular medicines increases, the new challenges arise, one of which is the high levels of structural heterogeneity that are frequently exhibited by such products. The very notion of the molecular mass measurement loses its clear and intuitive meaning when applied to an extremely heterogenous system that cannot be characterized by a unique mass, but instead requires that a mass distribution be considered. Furthermore, convoluted mass distributions frequently give rise to unresolved ionic signal in mass spectra, from which little-to-none meaningful information can be extracted using standard approaches that work well for homogeneous systems. However, a range of technological advances made in the last decade, such as the hyphenation of intact-mass MS measurements with front-end separations, better integration of ion mobility in MS workflows, development of an impressive arsenal of gas-phase ion chemistry tools to supplement MS methods, as well as the revival of the charge detection MS and its triumphant entry into the field of bioanalysis already made impressive contributions towards addressing the structural heterogeneity challenge. An overview of these techniques is accompanied by critical analysis of the strengths and weaknesses of different approaches, and a brief overview of their applications to specific classes of biopharmaceutical products, vaccines, and nonbiological complex drugs.
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Affiliation(s)
- Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst MA 01003
| | - Daniil G. Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst MA 01003
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19
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Onishi T, Nonaka M, Maruno T, Yamaguchi Y, Fukuhara M, Torisu T, Maeda M, Abbatiello S, Haris A, Richardson K, Giles K, Preece S, Yamano-Adachi N, Omasa T, Uchiyama S. Enhancement of recombinant adeno-associated virus activity by improved stoichiometry and homogeneity of capsid protein assembly. Mol Ther Methods Clin Dev 2023; 31:101142. [PMID: 38027055 PMCID: PMC10663676 DOI: 10.1016/j.omtm.2023.101142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023]
Abstract
Studies of recombinant adeno-associated virus (rAAV) revealed the mixture of full particles with different densities in rAAV. There are no conclusive results because of the lack of quantitative stoichiometric viral proteins, encapsidated DNA, and particle level analyses. We report the first comprehensive characterization of low- and high-density rAAV serotype 2 particles. Capillary gel electrophoresis showed high-density particles possessing a designed DNA encapsidated in the capsid composed of (VP1 + VP2)/VP3 = 0.27, whereas low-density particles have the same DNA but with a different capsid composition of (VP1 + VP2)/VP3 = 0.31, supported by sedimentation velocity-analytical ultracentrifugation and charge detection-mass spectrometry. In vitro analysis demonstrated that the low-density particles had 8.9% higher transduction efficacy than that of the particles before fractionation. Further, based on our recent findings of VP3 clip, we created rAAV2 single amino acid variants of the transcription start methionine of VP3 (M203V) and VP3 clip (M211V). The rAAV2-M203V variant had homogeneous particles with higher (VP1+VP2)/VP3 values (0.35) and demonstrated 24.7% higher transduction efficacy compared with the wild type. This study successfully provided highly functional rAAV by the extensive fractionation from the mixture of rAAV2 full particles or by the single amino acid replacement.
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Affiliation(s)
- Takayuki Onishi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Michika Nonaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- U-Medico Inc, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsuko Fukuhara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- U-Medico Inc, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuo Torisu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaharu Maeda
- Osaka Consolidated Laboratory, Manufacturing Technology Association of Biologics, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | - Keith Richardson
- Waters Corporation (Micromass UK Ltd), Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | | | - Steve Preece
- Waters Corporation (Micromass UK Ltd), Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Noriko Yamano-Adachi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Omasa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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20
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Ryan JP, Kostelic MM, Hsieh CC, Powers J, Aspinwall C, Dodds JN, Schiel JE, Marty MT, Baker ES. Characterizing Adeno-Associated Virus Capsids with Both Denaturing and Intact Analysis Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2811-2821. [PMID: 38010134 DOI: 10.1021/jasms.3c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Adeno-associated virus (AAV) capsids are among the leading gene delivery platforms used to treat a vast array of human diseases and conditions. AAVs exist in a variety of serotypes due to differences in viral protein (VP) sequences with distinct serotypes targeting specific cells and tissues. As the utility of AAVs in gene therapy increases, ensuring their specific composition is imperative for the correct targeting and gene delivery. From a quality control perspective, current analytical tools are limited in their selectivity for viral protein (VP) subunits due to their sequence similarities, instrumental difficulties in assessing the large molecular weights of intact capsids, and the uncertainty in distinguishing empty and filled capsids. To address these challenges, we combined two distinct analytical workflows that assess the intact capsids and VP subunits separately. First, a selective temporal overview of resonant ion (STORI)-based charge detection-mass spectrometry (CD-MS) was applied for characterization of the intact capsids. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations were then used for the capsid denaturing measurements. This multimethod combination was applied to three AAV serotypes (AAV2, AAV6, and AAV8) to evaluate their intact empty and filled capsid ratios and then examine the distinct VP sequences and modifications present.
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Affiliation(s)
- Jack P Ryan
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| | - Marius M Kostelic
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Joshua Powers
- Institute for Bioscience and Biotechnology Research (NIST), Gaithersburg Maryland 20899, United States
- North Carolina State University, Biomanufacturing Training and Education Center (BTEC), Raleigh, North Carolina 27695, United States
| | - Craig Aspinwall
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - James N Dodds
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
| | - John E Schiel
- Institute for Bioscience and Biotechnology Research (NIST), Gaithersburg Maryland 20899, United States
| | - Michael T Marty
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, Arizona 85721, United States
| | - Erin S Baker
- University of North Carolina, Department of Chemistry, Chapel Hill, North Carolina 27599, United States
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21
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Westphall MS, Lee KW, Salome AZ, Coon JJ, Grant T. Mass spectrometers as cryoEM grid preparation instruments. Curr Opin Struct Biol 2023; 83:102699. [PMID: 37703606 PMCID: PMC11019453 DOI: 10.1016/j.sbi.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Structure determination by single-particle cryoEM has matured into a core structural biology technique. Despite many methodological advancements, most cryoEM grids are still prepared using the plunge-freezing method developed ∼40 years ago. Embedding samples in thin films and exposing them to the air-water interface often leads to sample damage and preferential orientation of the particles. Using native mass spectrometry to create cryoEM samples, potentially avoids these problems and allows the use of mass spectrometry sample isolation techniques during EM grid creation. We review the recent publications that have demonstrated protein complexes can be ionized, flown through the mass spectrometer, gently landed onto EM grids, imaged, and reconstructed in 3D. Although many uncertainties and challenges remain, the combination of cryoEM and MS has great potential.
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Affiliation(s)
- Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Kenneth W Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
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22
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Harper CC, Miller ZM, Williams ER. Combined Multiharmonic Frequency Analysis for Improved Dynamic Energy Measurements and Accuracy in Charge Detection Mass Spectrometry. Anal Chem 2023; 95:16659-16667. [PMID: 37917546 DOI: 10.1021/acs.analchem.3c03160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The ability to determine ion energies in electrostatic ion-trap-based charge detection mass spectrometry (CDMS) experiments is important for the accurate measurement of individual ion m/z, charge, and mass. Dynamic energy measurements throughout the time an ion is trapped take advantage of the relationship between ion energy and the harmonic amplitude ratio (HAR) composed from the fundamental and second harmonic amplitudes in the Fourier transform of the ion signal. This method eliminates the need for energy-filtering optics in CDMS and makes it possible to measure energy lost in collisions and changes in ion masses due to dissociation. However, the accuracy of the energy measurement depends on the signal-to-noise ratio (S/N) of the amplitudes used to determine the HAR. Here, a major improvement to this HAR-based dynamic energy measurement method is achieved using HARs composed of higher-order harmonics in addition to the fundamental and second harmonic to determine ion energies. This combined harmonic amplitude ratios for precision energy refinement (CHARPER) method is applied to the analysis of a 103 nm polystyrene nanoparticle ion (359.7 MDa, m/z = 308,300) and the energy resolution (3140) and effective mass resolution (730) achieved are the best yet demonstrated in electrostatic ion-trap-based CDMS. The CHARPER method applied to an ensemble of several thousand adeno-associated virus ion signals also results in higher mass resolution compared to the basic HAR method, making it possible to resolve additional features in the composite mass histogram.
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Affiliation(s)
- Conner C Harper
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Zachary M Miller
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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23
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Lai YH, Wang YS. Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions. MASS SPECTROMETRY REVIEWS 2023; 42:2426-2445. [PMID: 35686331 DOI: 10.1002/mas.21790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.
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Affiliation(s)
- Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National United University, Miaoli, Taiwan, R.O.C
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, R.O.C
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
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24
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Du C, Cleary SP, Kostelic MM, Jones BJ, Kafader JO, Wysocki VH. Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes. Anal Chem 2023; 95:13889-13896. [PMID: 37672632 PMCID: PMC10874503 DOI: 10.1021/acs.analchem.3c02185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc.) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogeneous assemblies that are not readily obtained by traditional MS measurements.
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Affiliation(s)
- Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sean P Cleary
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Marius M Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jared O Kafader
- Departments of Chemistry, Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Yin V, Devine PWA, Saunders JC, Barendregt A, Cusdin F, Ristani A, Hines A, Shepherd S, Dembek M, Dobson CL, Snijder J, Bond NJ, Heck AJR. Stochastic assembly of biomacromolecular complexes: impact and implications on charge interpretation in native mass spectrometry. Chem Sci 2023; 14:9316-9327. [PMID: 37712025 PMCID: PMC10498669 DOI: 10.1039/d3sc03228k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023] Open
Abstract
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.
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Affiliation(s)
- Victor Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Paul W A Devine
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Janet C Saunders
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Fiona Cusdin
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Alexandra Ristani
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Alistair Hines
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Sam Shepherd
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Marcin Dembek
- Purification Process Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Claire L Dobson
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
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26
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Reynaud A, Trzpil W, Dartiguelongue L, Çumaku V, Fortin T, Sansa M, Hentz S, Masselon C. Compact and modular system architecture for a nano-resonator-mass spectrometer. Front Chem 2023; 11:1238674. [PMID: 37841207 PMCID: PMC10569461 DOI: 10.3389/fchem.2023.1238674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 10/17/2023] Open
Abstract
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.
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Affiliation(s)
| | | | - Louis Dartiguelongue
- Université Grenoble Alpes, CEA, Institut de Recherche Interdisciplinaire de Grenoble, Grenoble, France
- INSERM UA13 Biosciences et bioingénérie pour la santé, Grenoble, France
| | - Vaitson Çumaku
- Université Grenoble Alpes, CEA, Institut de Recherche Interdisciplinaire de Grenoble, Grenoble, France
- INSERM UA13 Biosciences et bioingénérie pour la santé, Grenoble, France
| | - Thomas Fortin
- Université Grenoble Alpes, CEA, Institut de Recherche Interdisciplinaire de Grenoble, Grenoble, France
- INSERM UA13 Biosciences et bioingénérie pour la santé, Grenoble, France
| | - Marc Sansa
- Université Grenoble Alpes, CEA-Leti, Grenoble, France
| | | | - Christophe Masselon
- Université Grenoble Alpes, CEA, Institut de Recherche Interdisciplinaire de Grenoble, Grenoble, France
- INSERM UA13 Biosciences et bioingénérie pour la santé, Grenoble, France
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27
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Botamanenko DY, Reitenbach DW, Miller LM, Jarrold MF. Electrostatic Linear Ion Trap Optimization Strategy for High Resolution Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1731-1740. [PMID: 37466262 PMCID: PMC10842736 DOI: 10.1021/jasms.3c00177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Single ion mass measurements allow mass distributions to be recorded for heterogeneous samples that cannot be analyzed by conventional mass spectrometry. In charge detection mass spectrometry (CD-MS), ions are detected using a conducting cylinder coupled to a charge sensitive amplifier. For optimum performance, the detection cylinder is embedded in an electrostatic linear ion trap (ELIT) where trapped ions oscillate between end-caps that act as opposing ion mirrors. The oscillating ions generate a periodic signal that is analyzed by fast Fourier transforms. The frequency yields the m/z, and the magnitude provides the charge. With a charge precision of 0.2 elementary charges, ions can be assigned to their correct charge states with a low error rate, and the m/z resolving power determines the mass resolving power. Previously, the best mass resolving power achieved with CD-MS was 300. We have recently increased the mass resolving power to 700, through the better optimization of the end-cap potentials. To make a more dramatic improvement in the m/z resolving power, it is necessary to find an ELIT geometry and end-cap potentials that can simultaneously make the ion oscillation frequency independent of both the ion energy and ion trajectory (angular divergence and radial offset) of the entering ion. We describe an optimization strategy that allows these conditions to be met while also adjusting the signal duty cycle to 50% to maximize the signal-to-noise ratio for the charge measurement. The optimized ELIT provides an m/z resolving power of over 300 000 in simulations. Coupled with the high precision charge determination available with CD-MS, this will yield a mass resolving power of 300 000. Such a high mass resolving power will be transformative for the analysis of heterogeneous samples.
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Affiliation(s)
- Daniel Y Botamanenko
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
- Megadalton Solutions Inc., 3750 E Bluebird Lane, Bloomington, Indiana 47401
| | - David W Reitenbach
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
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28
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Fernandez de la Mora J, Almazán F, Rodríguez JM. Spontaneous Interconversion between Different Narrowly Defined Shapes of Rotavirus Double-Layered Particles Studied in Real Time by High-Resolution Mobility Analysis. Anal Chem 2023; 95:11483-11490. [PMID: 37463035 DOI: 10.1021/acs.analchem.3c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Rotavirus double-layered particles (DLPs) are studied in the gas phase with a high-resolution differential mobility analyzer (DMA). DLPs were transferred to 10 mM aqueous ammonium acetate, electrosprayed into the gas phase, converted into primarily singly charged particles, and DMA-analyzed. Up to seven slightly different conformations were resolved, whose apparently random, fast (minutes), and reversible interconversions were followed in real time. They sometimes evolved into just two distinct structures, with periods of one dominating over the other and vice versa. Differences between the DLP structures in solution and in the gas phase are clearly revealed by the smaller DLP diameter found here (60 versus 70 nm). Nevertheless, we argue that the multiple gas-phase conformers observed originate in as many conformations pre-existing in solution. We further hypothesize that these conformers correspond to incomplete DLPs having lost some of the VP6 trimer quintets surrounding each of the 12 5-fold axes. Instances of this peculiar loss have been previously documented by cryoelectron microscopy for the rotavirus Wa strain, as well as via charge detection mass spectrometry for five other rotavirus strains included in the RotaTec vaccine. Evidence of this loss systematically found for all 7 rotavirus types so far studied in aqueous ammonium acetate may be a special feature of this electrolyte.
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Affiliation(s)
- Juan Fernandez de la Mora
- Department of Mechanical Engineering and Materials Science, Yale University, 9 Hillhouse Avenue, New Haven, Connecticut 06520-8286, United States
| | - Fernando Almazán
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
| | - Javier M Rodríguez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
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29
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Nguyen HA, Dixon G, Dou FY, Gallagher S, Gibbs S, Ladd DM, Marino E, Ondry JC, Shanahan JP, Vasileiadou ES, Barlow S, Gamelin DR, Ginger DS, Jonas DM, Kanatzidis MG, Marder SR, Morton D, Murray CB, Owen JS, Talapin DV, Toney MF, Cossairt BM. Design Rules for Obtaining Narrow Luminescence from Semiconductors Made in Solution. Chem Rev 2023. [PMID: 37311205 DOI: 10.1021/acs.chemrev.3c00097] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Solution-processed semiconductors are in demand for present and next-generation optoelectronic technologies ranging from displays to quantum light sources because of their scalability and ease of integration into devices with diverse form factors. One of the central requirements for semiconductors used in these applications is a narrow photoluminescence (PL) line width. Narrow emission line widths are needed to ensure both color and single-photon purity, raising the question of what design rules are needed to obtain narrow emission from semiconductors made in solution. In this review, we first examine the requirements for colloidal emitters for a variety of applications including light-emitting diodes, photodetectors, lasers, and quantum information science. Next, we will delve into the sources of spectral broadening, including "homogeneous" broadening from dynamical broadening mechanisms in single-particle spectra, heterogeneous broadening from static structural differences in ensemble spectra, and spectral diffusion. Then, we compare the current state of the art in terms of emission line width for a variety of colloidal materials including II-VI quantum dots (QDs) and nanoplatelets, III-V QDs, alloyed QDs, metal-halide perovskites including nanocrystals and 2D structures, doped nanocrystals, and, finally, as a point of comparison, organic molecules. We end with some conclusions and connections, including an outline of promising paths forward.
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Affiliation(s)
- Hao A Nguyen
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Grant Dixon
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Florence Y Dou
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Shaun Gallagher
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Stephen Gibbs
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Dylan M Ladd
- Department of Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Emanuele Marino
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Via Archirafi 36, 90123 Palermo, Italy
| | - Justin C Ondry
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - James P Shanahan
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Eugenia S Vasileiadou
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stephen Barlow
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Daniel R Gamelin
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - David S Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - David M Jonas
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Mercouri G Kanatzidis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Seth R Marder
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Daniel Morton
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Christopher B Murray
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jonathan S Owen
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Michael F Toney
- Department of Materials Science and Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Brandi M Cossairt
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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30
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Miller LM, Draper BE, Barnes LF, Ofoegbu PC, Jarrold MF. Analysis of Megadalton-Sized DNA by Charge Detection Mass Spectrometry: Entropic Trapping and Shearing in Nanoelectrospray. Anal Chem 2023. [PMID: 37267126 DOI: 10.1021/acs.analchem.3c01027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The analysis of nucleic acids by conventional mass spectrometry is complicated by counter ions which cause mass heterogeneity and limit the size of the DNA that can be analyzed. In this work, we overcome this limitation using charge detection mass spectrometry to analyze megadalton-sized DNA. Using positive mode electrospray, we find two dramatically different charge distributions for DNA plasmids. A low charge population that charges like compact DNA origami and a much higher charge population, with charges that extend over a broad range. For the high-charge population, the deviation between the measured mass and mass expected from the DNA sequence is consistently around 1%. For the low-charge population, the deviation is larger and more variable. The high-charge population is attributed to the supercoiled plasmid in a random coil configuration, with the broad charge distribution resulting from the rich variety of geometries the random coil can adopt. High-resolution measurements show that the mass distribution shifts to slightly lower mass with increasing charge. The low-charge population is attributed to a condensed form of the plasmid. We suggest that the condensed form results from entropic trapping where the random coil must undergo a geometry change to squeeze through the Taylor cone and enter an electrospray droplet. For the larger plasmids, shearing (mechanical breakup) occurs during electrospray or in the electrospray interface. Shearing is reduced by lowering the salt concentration.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions Inc, 3750 E Bluebird Ln, Bloomington, Indiana 47401, United States
| | - Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Polycarp C Ofoegbu
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
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31
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Kwan V, Ballaney P, Consta S. Limitations of Atomistic Molecular Dynamics to Reveal Ejection of Proteins from Charged Nanodroplets. J Phys Chem B 2023. [PMID: 37216215 DOI: 10.1021/acs.jpcb.3c01313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Atomistic molecular dynamics (MD) is frequently used to unravel the mechanisms of macroion release from electrosprayed droplets. However, atomistic MD is currently feasible for only the smallest window of droplet sizes appearing at the end steps of a droplet's lifetime. The relevance of the observations made to the actual droplet evolution, which is much longer than the simulated sizes, has not been addressed yet in the literature. Here, we perform a systematic study of the desolvation mechanisms of poly(ethylene glycol) (PEG), protonated peptides of different compositions, and proteins, to (a) obtain insight into the charging mechanism of macromolecules in larger droplets than those that are currently amenable to atomistic MD and (b) examine whether currently used atomistic MD modeling can establish the extrusion mechanism of proteins from droplets. To mimic larger droplets that are not amenable to MD modeling, we scale down the systems, by simulating a large droplet size relative to the macromolecule. MD of PEG charging reveals that, above a critical droplet size, ions are available near the backbone of the macromolecule, but charging occurs only transiently by transfer of ions from the solvent to the macroion, while below the critical size, the capture of the ion from PEG has a lifetime sufficiently long for the extrusion of a charged PEG from the aqueous droplet. This is the first report of the role of droplet curvature in the relation between macroion conformation and charging. Simulations of protonated peptides with a high degree of hydrophobicity show that partial extrusion of a peptide from the droplet surface is rare relative to desolvation by drying-out. Different from what has been presented in the literature, we argue that atomistic MD simulations have not sufficiently established the extrusion mechanism of proteins from droplets and their charging mechanism. We also argue that release of highly charged proteins can occur at an earlier stage of a droplet's lifetime than predicted by atomistic MD. In this earlier stage, we emphasize the key role of jets emanating from a droplet at the point of charge-induced instability in the release of proteins.
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Affiliation(s)
- Victor Kwan
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Pranav Ballaney
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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32
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Spesyvyi A, Žabka J, Polášek M, Charvat A, Schmidt J, Postberg F, Abel B. Charged Ice Particle Beams with Selected Narrow Mass and Kinetic Energy Distributions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:878-892. [PMID: 37018538 DOI: 10.1021/jasms.2c00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Small ice particles play an important role in atmospheric and extraterrestrial chemistry. Circumplanetary ice particles that are encountered by space probes at hypervelocities play a critical role in the determination of surface and subsurface properties of their source bodies. Here we present an apparatus for the generation of low-intensity beams of single mass-selected charged ice particles under vacuum. They are produced via electrospray ionization of water at atmospheric pressure and undergo evaporative cooling when transferred to vacuum through an atmospheric vacuum interface. m/z selection is achieved through two subsequent quadrupole mass filters operated in the variable-frequency mode within a range of m/z values between 8 × 104 and 3 × 107. Velocity and charge of the selected particles are measured using a nondestructive single-pass image charge detector. From the known electrostatic acceleration potentials and settings of the quadrupoles the particle masses could be obtained and be accurately controlled. It has been shown that the droplets are frozen within the transit time of the apparatus such that ice particles are present after the quadrupole stages and finally detected. The demonstrated correspondence between particle mass and specific quadrupole potentials in this device allows preparation of beams of single particles with a repetition rate between 0.1 and 1 Hz with various diameter distributions from 50 to 1000 nm at 30-250 eV of kinetic energy per charge. This corresponds to velocities and particle masses quickly available between 600 m/s (80 nm) and 50 m/s (900 nm) and particle charge numbers (positive) between 103 and 104[e], depending upon size.
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Affiliation(s)
- Anatolii Spesyvyi
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 18223 Prague 8, Czech Republic
| | - Ján Žabka
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 18223 Prague 8, Czech Republic
| | - Miroslav Polášek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 2155/3, 18223 Prague 8, Czech Republic
| | - Ales Charvat
- Institute of Chemical Technology and Wilhelm-Ostwald-Institute of Physical and Theoretical Chemistry, Linnestrasse 3, D-04103 Leipzig, Germany
- Leibniz Institute of Surface Engineering, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Jürgen Schmidt
- Institute of Geological Sciences, Freie Universität Berlin, Malteserstraße 74-100, D-12249 Berlin, Germany
| | - Frank Postberg
- Institute of Geological Sciences, Freie Universität Berlin, Malteserstraße 74-100, D-12249 Berlin, Germany
| | - Bernd Abel
- Institute of Chemical Technology and Wilhelm-Ostwald-Institute of Physical and Theoretical Chemistry, Linnestrasse 3, D-04103 Leipzig, Germany
- Leibniz Institute of Surface Engineering, Permoserstrasse 15, D-04318 Leipzig, Germany
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33
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Harper CC, Miller ZM, McPartlan MS, Jordan JS, Pedder RE, Williams ER. Accurate Sizing of Nanoparticles Using a High-Throughput Charge Detection Mass Spectrometer without Energy Selection. ACS NANO 2023; 17:7765-7774. [PMID: 37027782 PMCID: PMC10389270 DOI: 10.1021/acsnano.3c00539] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The sizes and shapes of nanoparticles play a critical role in their chemical and material properties. Common sizing methods based on light scattering or mobility lack individual particle specificity, and microscopy-based methods often require cumbersome sample preparation and image analysis. A promising alternative method for the rapid and accurate characterization of nanoparticle size is charge detection mass spectrometry (CDMS), an emerging technique that measures the masses of individual ions. A recently constructed CDMS instrument designed specifically for high acquisition speed, efficiency, and accuracy is described. This instrument does not rely on an ion energy filter or estimates of ion energy that have been previously required for mass determination, but instead uses direct, in situ measurements. A standardized sample of ∼100 nm diameter polystyrene nanoparticles and ∼50 nm polystyrene nanoparticles with amine-functionalized surfaces are characterized using CDMS and transmission electron microscopy (TEM). Individual nanoparticle masses measured by CDMS are transformed to diameters, and these size distributions are in close agreement with distributions measured by TEM. CDMS analysis also reveals dimerization of ∼100 nm nanoparticles in solution that cannot be determined by TEM due to the tendency of nanoparticles to agglomerate when dried onto a surface. Comparing the acquisition and analysis times of CDMS and TEM shows particle sizing rates up to ∼80× faster are possible using CDMS, even when samples ∼50× more dilute were used. The combination of both high-accuracy individual nanoparticle measurements and fast acquisition rates by CDMS represents an important advance in nanoparticle analysis capabilities.
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Affiliation(s)
- Conner C Harper
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Zachary M Miller
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Matthew S McPartlan
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Randall E Pedder
- Ardara Technologies LP, Ardara, Pennsylvania 15615, United States
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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34
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Patil AA, Liu ZX, Chiu YP, Lại TKL, Chou SW, Cheng CY, Su WM, Liao HT, Agcaoili JBA, Peng WP. Development of a linear ion trap mass spectrometer capable of analyzing megadalton MALDI ions. Talanta 2023; 259:124555. [PMID: 37088041 DOI: 10.1016/j.talanta.2023.124555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Detecting megadalton matrix-assisted laser desorption/ionization (MALDI) ions in an ion trap mass spectrometer is a technical challenge. In this study, megadalton protein and polymer ions were successfully measured by MALDI linear ion trap mass spectrometer (LIT-MS) for the first time. The LIT-MS is comprised of a Thermo linear ion trap mass analyzer and a highly sensitive charge-sensing particle detector (CSPD). A newly designed radio frequency (rf) scan mode with dipolar resonance ejection techniques is proposed to extend the mass range of LIT-MS up to one million Thomson (Th). We analyze high mass ions with mass-to charge (m/z) ratios ranging from 100 kTh to 1 MTh, including thyroglobulin, alpha-2-macroglobulin, immunoglobulins (e.g., IgG and IgM), and polymer (∼ 940 kTh) ions. Besides, it is also very challenging for ion trap mass spectrometry to detect megadalton ions at low concentrations. By adopting high affinity carboxylated/oxidized detonation nanodiamonds (oxDNDs) to enrich IgM molecules and form antibody-nanodiamond conjugates, we have successfully reached ∼ 5 nM (5 μg/mL) concentration which is better than that by the other techniques.
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Affiliation(s)
- Avinash A Patil
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, 97401, Taiwan
| | - Zhe-Xuan Liu
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, 97401, Taiwan
| | - Yi-Pang Chiu
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, 97401, Taiwan
| | - Thị Khánh Ly Lại
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, 97401, Taiwan
| | - Szu-Wei Chou
- AcroMass Technologies Inc., Hukou, Hsinchu, 30352, Taiwan
| | - Chun-Yen Cheng
- AcroMass Technologies Inc., Hukou, Hsinchu, 30352, Taiwan
| | - Wen-Min Su
- Department of Life Science, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Hong-Ting Liao
- Department of Life Science, National Dong Hwa University, Hualien, 97401, Taiwan
| | | | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, 97401, Taiwan.
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35
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Chang Y, Wang Y, Li W, Wei Z, Tang S, Chen R. Mechanisms, Techniques and Devices of Airborne Virus Detection: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085471. [PMID: 37107752 PMCID: PMC10138381 DOI: 10.3390/ijerph20085471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Airborne viruses, such as COVID-19, cause pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods, actually resulting in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, influenza and other airborne transmission viruses.
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Affiliation(s)
- Yuqing Chang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Yuqian Wang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Wen Li
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (W.L.); (Z.W.)
| | - Shichuan Tang
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
| | - Rui Chen
- Beijing Key Laboratory of Occupational Safety and Health, Institute of Urban Safety and Environmental Science, Beijing Academy of Science and Technology, Beijing 100054, China; (Y.C.); (Y.W.); (S.T.)
- Correspondence:
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36
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Miller LM, Jarrold MF. Charge detection mass spectrometry for the analysis of viruses and virus-like particles. Essays Biochem 2023; 67:315-323. [PMID: 36062529 PMCID: PMC10842916 DOI: 10.1042/ebc20220101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022]
Abstract
Heterogeneity usually restricts conventional mass spectrometry to molecular weights less than around a megadalton. As a single-particle technique, charge detection mass spectrometry (CDMS) overcomes this limitation. In CDMS, the mass-to-charge (m/z) ratio and charge are measured simultaneously for individual ions, giving a direct mass measurement for each ion. Recent applications include the analysis of viruses, virus-like particles, vaccines, heavily glycosylated proteins, and gene therapy vectors.
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Affiliation(s)
- Lohra M Miller
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington 47401, Indiana
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington 47401, Indiana
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Role of Omega-Hydroxy Ceramides in Epidermis: Biosynthesis, Barrier Integrity and Analyzing Method. Int J Mol Sci 2023; 24:ijms24055035. [PMID: 36902463 PMCID: PMC10003399 DOI: 10.3390/ijms24055035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/19/2023] [Accepted: 02/25/2023] [Indexed: 03/08/2023] Open
Abstract
Attached to the outer surface of the corneocyte lipid envelope (CLE), omega-hydroxy ceramides (ω-OH-Cer) link to involucrin and function as lipid components of the stratum corneum (SC). The integrity of the skin barrier is highly dependent on the lipid components of SC, especially on ω-OH-Cer. Synthetic ω-OH-Cer supplementation has been utilized in clinical practice for epidermal barrier injury and related surgeries. However, the mechanism discussion and analyzing methods are not keeping pace with its clinical application. Though mass spectrometry (MS) is the primary choice for biomolecular analysis, method modifications for ω-OH-Cer identification are lacking in progress. Therefore, finding conclusions on ω-OH-Cer biological function, as well as on its identification, means it is vital to remind further researchers of how the following work should be done. This review summarizes the important role of ω-OH-Cer in epidermal barrier functions and the forming mechanism of ω-OH-Cer. Recent identification methods for ω-OH-Cer are also discussed, which could provide new inspirations for study on both ω-OH-Cer and skin care development.
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38
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Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of post-transcriptional/post-translational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding molecular heterogeneity of proteins. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Deseree J Reid
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephanie Thibert
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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39
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McGee JP, Senko MW, Jooß K, Des Soye BJ, Compton PD, Kelleher NL, Kafader JO. Automated Control of Injection Times for Unattended Acquisition of Multiplexed Individual Ion Mass Spectra. Anal Chem 2022; 94:16543-16548. [PMID: 36416365 PMCID: PMC9969899 DOI: 10.1021/acs.analchem.2c03495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Charge detection mass spectrometry (CDMS) provides mass domain spectra of large and highly heterogeneous analytes. Over the past few years, we have multiplexed CDMS on Orbitrap instruments, an approach termed Individual Ion Mass Spectrometry (I2MS). Until now, I2MS required manual adjustment of injection times to collect spectra in the individual ion regime. To increase sample adaptability, enable online separations, and reduce the barrier for entry, we report an automated method for adjusting ion injection times in I2MS for image current detectors like the Orbitrap. Automatic Ion Control (AIC) utilizes the density of signals in the m/z domain to adjust an ensemble of ions down to the individual ion regime in real-time. The AIC technique was applied to both denatured and native proteins yielding high quality data without human intervention directly in the mass domain.
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Affiliation(s)
- John P McGee
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California95134, United States
| | - Kevin Jooß
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Benjamin J Des Soye
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Philip D Compton
- Integrated Protein Technologies, Inc., Evanston, Illinois60201, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, Department of Chemical and Biological Engineering, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois60208, United States
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40
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High-throughput determination of dry mass of single bacterial cells by ultrathin membrane resonators. Commun Biol 2022; 5:1227. [PMID: 36369276 PMCID: PMC9651879 DOI: 10.1038/s42003-022-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
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 = 10−15 g) 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.
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41
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Barnes LF, Draper BE, Jarrold MF. Analysis of thermally driven structural changes, genome release, disassembly, and aggregation of recombinant AAV by CDMS. Mol Ther Methods Clin Dev 2022; 27:327-336. [PMID: 36381304 PMCID: PMC9630626 DOI: 10.1016/j.omtm.2022.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/12/2022] [Indexed: 12/13/2022]
Abstract
Charge detection mass spectrometry (CDMS) was used to analyze recombinant adeno-associated virus serotype 8 (rAAV8) vectors after incubation at elevated temperatures. rAAV8 vectors with a range of genomes of interest (GOIs) from 2.22 to 4.84 kb were investigated. For the shorter GOIs, GOI release occurred at surprisingly low temperatures (15 min at 45°C for cytomegalovirus [CMV]-GFP). The released DNA and intermediates with the GOI extruded from the capsid were detected. The temperature required to release the short GOIs is well below the 65°C incubation temperature required to disassemble the empty rAAV8 capsid. The temperature for GOI release increased with its GOI length. With the longer GOIs, the GOI stabilized the capsid so that it remained intact under conditions that would disassemble the empty particle. After incubation at 65°C, the main species in the CDMS mass distributions for the longer GOIs was the vector with the GOI. However, for GOIs longer than the wild-type genome (∼4.7 kb), the stability diminished, and genome release occurred at a lower temperature. Heterogeneous DNA fragments from the host cells or plasmids is released at a lower temperature than the longer GOIs, suggesting that the GOIs have a feature that resists early release.
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Affiliation(s)
- Lauren F. Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Benjamin E. Draper
- Megadalton Solutions, Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F. Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA,Corresponding author Martin F. Jarrold, Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, IN 47405, USA.
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42
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Brown SL, Zenaidee MA, Loo JA, Loo RRO, Donald WA. On the Mechanism of Theta Capillary Nanoelectrospray Ionization for the Formation of Highly Charged Protein Ions Directly from Native Solutions. Anal Chem 2022; 94:13010-13018. [DOI: 10.1021/acs.analchem.2c01654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susannah L. Brown
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
| | - Muhammad A. Zenaidee
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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43
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Harper CC, Miller ZM, Lee H, Bischoff AJ, Francis MB, Schaffer DV, Williams ER. Effects of Molecular Size on Resolution in Charge Detection Mass Spectrometry. Anal Chem 2022; 94:11703-11712. [PMID: 35961005 PMCID: PMC10389281 DOI: 10.1021/acs.analchem.2c02572] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Instrumental resolution of Fourier transform-charge detection mass spectrometry instruments with electrostatic ion trap detection of individual ions depends on the precision with which ion energy is determined. Energy can be selected using ion optic filters or from harmonic amplitude ratios (HARs) that provide Fellgett's advantage and eliminate the necessity of ion transmission loss to improve resolution. Unlike the ion energy-filtering method, the resolution of the HAR method increases with charge (improved S/N) and thus with mass. An analysis of the HAR method with current instrumentation indicates that higher resolution can be obtained with the HAR method than the best resolution demonstrated for instruments with energy-selective optics for ions in the low MDa range and above. However, this gain is typically unrealized because the resolution obtainable with molecular systems in this mass range is limited by sample heterogeneity. This phenomenon is illustrated with both tobacco mosaic virus (0.6-2.7 MDa) and AAV9 (3.7-4.7 MDa) samples where mass spectral resolution is limited by the sample, including salt adducts, and not by instrument resolution. Nevertheless, the ratio of full to empty AAV9 capsids and the included genome mass can be accurately obtained in a few minutes from 1× PBS buffer solution and an elution buffer containing 300+ mM nonvolatile content despite extensive adduction and lower resolution. Empty and full capsids adduct similarly indicating that salts encrust the complexes during late stages of droplet evaporation and that mass shifts can be calibrated in order to obtain accurate analyte masses even from highly salty solutions.
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Affiliation(s)
- Conner C. Harper
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
| | - Zachary M. Miller
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
| | - Hyuncheol Lee
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
| | - Amanda J. Bischoff
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720
| | - Matthew B. Francis
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720
| | - David V. Schaffer
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
| | - Evan R. Williams
- College of Chemistry, University of California, Berkeley, California, 94720-1460
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460
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Woodbury BM, Motwani T, Leroux MN, Barnes LF, Lyktey NA, Banerjee S, Dedeo CL, Jarrold MF, Teschke CM. Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22. Viruses 2022; 14:1400. [PMID: 35891382 PMCID: PMC9320234 DOI: 10.3390/v14071400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
The oligomerization and incorporation of the bacteriophage P22 portal protein complex into procapsids (PCs) depends upon an interaction with scaffolding protein, but the region of the portal protein that interacts with scaffolding protein has not been defined. In herpes simplex virus 1 (HSV-1), conserved tryptophan residues located in the wing domain are required for portal-scaffolding protein interactions. In this study, tryptophan residues (W) present at positions 41, 44, 207 and 211 within the wing domain of the bacteriophage P22 portal protein were mutated to both conserved and non-conserved amino acids. Substitutions at each of these positions were shown to impair portal function in vivo, resulting in a lethal phenotype by complementation. The alanine substitutions caused the most severe defects and were thus further characterized. An analysis of infected cell lysates for the W to A mutants revealed that all the portal protein variants except W211A, which has a temperature-sensitive incorporation defect, were successfully recruited into procapsids. By charge detection mass spectrometry, all W to A mutant portal proteins were shown to form stable dodecameric rings except the variant W41A, which dissociated readily to monomers. Together, these results suggest that for P22 conserved tryptophan, residues in the wing domain of the portal protein play key roles in portal protein oligomerization and incorporation into procapsids, ultimately affecting the functionality of the portal protein at specific stages of virus assembly.
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Affiliation(s)
- Brianna M. Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Tina Motwani
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Makayla N. Leroux
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Lauren F. Barnes
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Nicholas A. Lyktey
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Sanchari Banerjee
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Corynne L. Dedeo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA; (L.F.B.); (N.A.L.); (M.F.J.)
| | - Carolyn M. Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (B.M.W.); (T.M.); (M.N.L.); (S.B.); (C.L.D.)
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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Tsirkou A, Kaczorowski F, Verdurand M, Raffoul R, Pansieri J, Quadrio I, Chauveau F, Antoine R. Charge detection mass spectrometry on human-amplified fibrils from different synucleinopathies. Chem Commun (Camb) 2022; 58:7192-7195. [PMID: 35670578 DOI: 10.1039/d2cc00200k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amyloid fibrils are self-assembled mesoscopic protein aggregates, which can accumulate to form deposits or plaques in the brain. In vitro amplification of fibrils can be achieved with real-time quaking-induced conversion (RT-QuIC). However, this emerging technique would benefit from a complementary method to assess structural properties of the amplification products. This work demonstrates the feasibility of nanospray-charge-detection-mass-spectrometry (CDMS) performed on α-synuclein (αSyn) fibrils amplified from human brains with Parkinson's disease (PD) or Dementia with Lewy bodies (DLB) and its synergistic combination with RT-QuIC.
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Affiliation(s)
- Aikaterini Tsirkou
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Flora Kaczorowski
- Laboratory of Neurobiology and Neurogenetics, Department of Biochemistry and Molecular Biology, Lyon University Hospital, 69677 BRON Cedex, France.,Center for Memory Resources and Research, Lyon University Hospital, Lyon 1 University, Villeurbanne, France.,Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Mathieu Verdurand
- Laboratory of Neurobiology and Neurogenetics, Department of Biochemistry and Molecular Biology, Lyon University Hospital, 69677 BRON Cedex, France.,Center for Memory Resources and Research, Lyon University Hospital, Lyon 1 University, Villeurbanne, France.,Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Rana Raffoul
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
| | - Jonathan Pansieri
- Oxford University, Nuffield Department of Clinical Neurosciences, Oxford University, UK
| | - Isabelle Quadrio
- Laboratory of Neurobiology and Neurogenetics, Department of Biochemistry and Molecular Biology, Lyon University Hospital, 69677 BRON Cedex, France.,Center for Memory Resources and Research, Lyon University Hospital, Lyon 1 University, Villeurbanne, France.,Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Fabien Chauveau
- Univ Lyon, Centre de Recherche en Neurosciences de Lyon, Equipe BIORAN, Inserm U1028 - CNRS UMR5292, Université Claude Bernard Lyon 1, Groupement Hospitalier Est - CERMEP, 69677 BRON Cedex, France.
| | - Rodolphe Antoine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France.
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Yang W, Ivanov DG, Kaltashov IA. Extending the capabilities of intact-mass analyses to monoclonal immunoglobulins of the E-isotype (IgE). MAbs 2022; 14:2103906. [PMID: 35895856 PMCID: PMC9336480 DOI: 10.1080/19420862.2022.2103906] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mass spectrometry (MS) has become an indispensable tool in structural characterization and quality control of monoclonal antibodies (mAbs). Intact-mass analysis is a particularly attractive option that provides a powerful and cost-effective means to not only confirm the structural integrity of the protein, but also probe its interactions with therapeutic targets. To a certain extent, this success can be attributed to relatively modest glycosylation levels exhibited by IgG molecules, which limits their structural heterogeneity and enables straightforward mass measurements at the intact molecule level. The recent surge of interest in expanding the repertoire of mAbs to include other classes of immunoglobulins places a premium on efforts to adapt the IgG-tailored experimental strategies to other classes of antibodies, but their dramatically higher levels of glycosylation may create insurmountable obstacles. The monoclonal murine IgE antibody explored in this work provides a challenging model system, as its glycosylation level exceeds that of conventional IgG mAbs by a factor of nine. The commercial sample, which included various IgE fragments, yields a poorly resolved ionic signal in intact-mass measurements, from which little useful information can be extracted. However, coupling MS measurements with the limited charge reduction of select polycationic species in the gas phase gives rise to well-defined charge ladders, from which both ionic masses and charges can be readily determined. The measurements reveal significant variation of the extent of glycosylation within intact IgE molecules, as well as the presence of low-molecular weight impurities in the commercial IgE sample. Furthermore, incubation of the monoclonal IgE with its antigen (ovalbumin) gives rise to the formation of complexes with varying stoichiometries, which can also be uniquely identified using a combination of native MS, limited charge reduction in the gas phase and data fitting procedures. This work demonstrates that following appropriate modifications, intact-mass analysis measurements can be successfully applied to mAbs beyond the IgG isotype, providing a wealth of information not only on the mass distribution of the intact IgE molecules, but also their large-scale conformational integrity, the integrity of their covalent structure, and their interactions with antigens.
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Affiliation(s)
- Wenhua Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.,College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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