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Jordan JS, Harper CC, Zhang F, Kofman E, Li M, Sathiyamoorthy K, Zaragoza JP, Fayadat-Dilman L, Williams ER. Charge Detection Mass Spectrometry Reveals Conformational Heterogeneity in Megadalton-Sized Monoclonal Antibody Aggregates. J Am Chem Soc 2024; 146:23297-23305. [PMID: 39110484 DOI: 10.1021/jacs.4c05885] [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: 08/22/2024]
Abstract
Aggregation of protein-based therapeutics can occur during development, production, or storage and can lead to loss of efficacy and potential toxicity. Native mass spectrometry of a covalently linked pentameric monoclonal antibody complex with a mass of ∼800 kDa reveals several distinct conformations, smaller complexes, and abundant higher-order aggregates of the pentameric species. Charge detection mass spectrometry (CDMS) reveals individual oligomers up to the pentamer mAb trimer (15 individual mAb molecules; ∼2.4 MDa) whereas intermediate aggregates composed of 6-9 mAb molecules and aggregates larger than the pentameric dimer (1.6 MDa) were not detected/resolved by standard mass spectrometry, size exclusion chromatography (SEC), capillary electrophoresis (CE-SDS), or by mass photometry. Conventional quadrupole time-of-flight mass spectrometry (QTOF MS), mass photometry, SEC, and CE-SDS did not resolve partially or more fully unfolded conformations of each oligomer that were readily identified using CDMS by their significantly higher extents of charging. Trends in the charge-state distributions of individual oligomers provides detailed insight into how the structures of compact and elongated mAb aggregates change as a function of aggregate size. These results demonstrate the advantages of CDMS for obtaining accurate masses and information about the conformations of large antibody aggregates despite extensive overlapping m/z values. These results open up the ability to investigate structural changes that occur in small, soluble oligomers during the earliest stages of aggregation for antibodies or other proteins.
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Affiliation(s)
- Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Conner C Harper
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Fan Zhang
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., 213 E Grand Ave., South San Francisco, California 94080, United States
| | - Esther Kofman
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., 213 E Grand Ave., South San Francisco, California 94080, United States
| | - Mandy Li
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., 213 E Grand Ave., South San Francisco, California 94080, United States
| | - Karthik Sathiyamoorthy
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., 213 E Grand Ave., South San Francisco, California 94080, United States
| | - Jan Paulo Zaragoza
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., 213 E Grand Ave., South San Francisco, California 94080, United States
| | - Laurence Fayadat-Dilman
- Discovery Biologics, Protein Sciences, Merck & Co., Inc., 213 E Grand Ave., South San Francisco, California 94080, United States
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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2
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Harper CC, Jordan JS, Papanu S, Williams ER. Characterization of Mass, Diameter, Density, and Surface Properties of Colloidal Nanoparticles Enabled by Charge Detection Mass Spectrometry. ACS NANO 2024; 18:17806-17814. [PMID: 38913932 DOI: 10.1021/acsnano.4c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
A variety of scattering-based, microscopy-based, and mobility-based methods are frequently used to probe the size distributions of colloidal nanoparticles with transmission electron microscopy (TEM) often considered to be the "gold standard". Charge detection mass spectrometry (CDMS) is an alternative method for nanoparticle characterization that can rapidly measure the mass and charge of individual nanoparticle ions with high accuracy. Two low polydispersity, ∼100 nm diameter nanoparticle size standards with different compositions (polymethyl methacrylate/polystyrene copolymer and 100% polystyrene) were characterized using both TEM and CDMS to explore the merits and complementary aspects of both methods. Mass and diameter distributions are rapidly obtained from CDMS measurements of thousands of individual ions of known spherical shape, requiring less time than TEM sample preparation and image analysis. TEM image-to-image variations resulted in a ∼1-2 nm range in the determined mean diameters whereas the CDMS mass precision of ∼1% in these experiments leads to a diameter uncertainty of just 0.3 nm. For the 100% polystyrene nanoparticles with known density, the CDMS and TEM particle diameter distributions were in excellent agreement. For the copolymer nanoparticles with unknown density, the diameter from TEM measurements combined with the mass from CDMS measurements enabled an accurate measurement of nanoparticle density. Differing extents of charging for the two nanoparticle standards measured by CDMS show that charging is sensitive to nanoparticle surface properties. A mixture of the two samples was separated based on their different extents of charging despite having overlapping mass distributions centered at 341.5 and 331.0 MDa.
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Affiliation(s)
- Conner C Harper
- 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
| | - Steven Papanu
- Colloidal Metrics Corporation, 2520 Wyandotte Street Suite F, Mountain View, California 94083-2381, United States
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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3
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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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4
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McPartlan MS, Harper CC, Hanozin E, Williams ER. Ion emission from 1-10 MDa salt clusters: individual charge state resolution with charge detection mass spectrometry. Analyst 2024; 149:735-744. [PMID: 38189568 DOI: 10.1039/d3an01913f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Salt cluster ions produced by electrospray ionization are used for mass calibration and fundamental investigations into cluster stability and charge separation processes. However, previous studies have been limited to relatively small clusters owing to the heterogeneity associated with large, multiply-charged clusters that leads to unresolved signals in conventional m/z spectra. Here, charge detection mass spectrometry is used to measure both the mass and charge distributions of positively charged clusters of KCl, CaCl2, and LaCl3 with masses between ∼1 and 10 MDa by dynamically measuring the energy per charge, m/z, charge, and mass of simultaneously trapped individual ions throughout a 1 s trapping time. The extent of remaining hydration on the clusters, determined from the change in the frequency of ion motion with time as a result of residual water loss, follows the order KCl < CaCl2 < LaCl3, and is significantly lower than that of a pure water nanodrop, consistent with tighter water binding to the more highly charged cations in these clusters. The number of ion emission events from these clusters also follows this same trend, indicating that water at the cluster surface facilitates charge loss. A new frequency-based method to determine the magnitude of the charge loss resulting from individual ion emission events clearly resolves losses of +1 and +2 ions. Achieving this individual charge state resolution for ion emission events is an important advance in obtaining information about the late stages of bare gaseous ions formation. Future experiments on more hydrated clusters are expected to lead to a better understanding of ion formation in electrospray ionization.
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Affiliation(s)
- Matthew S McPartlan
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Conner C Harper
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Emeline Hanozin
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
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5
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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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6
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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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7
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Hanozin E, Harper CC, McPartlan MS, Williams ER. Dynamics of Rayleigh Fission Processes in ∼100 nm Charged Aqueous Nanodrops. ACS CENTRAL SCIENCE 2023; 9:1611-1622. [PMID: 37637724 PMCID: PMC10451037 DOI: 10.1021/acscentsci.3c00323] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Indexed: 08/29/2023]
Abstract
Fission of micron-size charged droplets has been observed using optical methods, but little is known about fission dynamics and breakup of smaller nanosize droplets that are important in a variety of natural and industrial processes. Here, spontaneous fission of individual aqueous nanodrops formed by electrospray is investigated using charge detection mass spectrometry. Fission processes ranging from formation of just two progeny droplets in 2 ms to production of dozens of progeny droplets over 100+ ms are observed for nanodrops that are charged above the Rayleigh limit. These results indicate that Rayleigh fission is a continuum of processes that produce progeny droplets that vary widely in charge, mass, and number.
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Affiliation(s)
- Emeline Hanozin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Conner C. Harper
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew S. McPartlan
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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8
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Harper CC, Avadhani VS, Hanozin E, Miller ZM, Williams ER. Dynamic Energy Measurements in Charge Detection Mass Spectrometry Eliminate Adverse Effects of Ion-Ion Interactions. Anal Chem 2023; 95:10077-10086. [PMID: 37343124 PMCID: PMC10389283 DOI: 10.1021/acs.analchem.3c01520] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Ion-ion interactions in charge detection mass spectrometers that use electrostatic traps to measure masses of individual ions have not been reported previously, although ion trajectory simulations have shown that these types of interactions affect ion energies and thereby degrade measurement performance. Here, examples of interactions between simultaneously trapped ions that have masses ranging from ca. 2 to 350 MDa and ca. 100 to 1000 charges are studied in detail using a dynamic measurement method that makes it possible to track the evolution of the mass, charge, and energy of individual ions over their trapping lifetimes. Signals from ions that have similar oscillation frequencies can have overlapping spectral leakage artifacts that result in slightly increased uncertainties in the mass determination, but these effects can be mitigated by the careful choice of parameters used in the short-time Fourier transform analysis. Energy transfers between physically interacting ions are also observed and quantified with individual ion energy measurement resolution as high as ∼950. The mass and charge of interacting ions do not change, and their corresponding measurement uncertainties are equivalent to ions that do not undergo physical interactions. Simultaneous trapping of multiple ions in CDMS can greatly decrease the acquisition time necessary to accumulate a statistically meaningful number of individual ion measurements. These results demonstrate that while ion-ion interactions can occur when multiple ions are trapped, they have negligible effects on mass accuracy when using the dynamic measurement method.
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Affiliation(s)
- Conner C. Harper
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Veena S. Avadhani
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Emeline Hanozin
- 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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9
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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: 14] [Impact Index Per Article: 14.0] [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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10
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Miller ZM, Harper CC, Lee H, Bischoff AJ, Francis MB, Schaffer DV, Williams ER. Apodization Specific Fitting for Improved Resolution, Charge Measurement, and Data Analysis Speed in Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2129-2137. [PMID: 36173188 PMCID: PMC10389282 DOI: 10.1021/jasms.2c00213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Short-time Fourier transforms with short segment lengths are typically used to analyze single ion charge detection mass spectrometry (CDMS) data either to overcome effects of frequency shifts that may occur during the trapping period or to more precisely determine the time at which an ion changes mass or charge, or enters an unstable orbit. The short segment lengths can lead to scalloping loss unless a large number of zero-fills are used, making computational time a significant factor in real-time analysis of data. Apodization specific fitting leads to a 9-fold reduction in computation time compared to zero-filling to a similar extent of accuracy. This makes possible real-time data analysis using a standard desktop computer. Rectangular apodization leads to higher resolution than the more commonly used Gaussian or Hann apodization and makes it possible to separate ions with similar frequencies, a significant advantage for experiments in which the masses of many individual ions are measured simultaneously. Equally important is a >20% increase in S/N obtained with rectangular apodization compared to Gaussian or Hann, which directly translates to a corresponding improvement in accuracy of both charge measurements and ion energy measurements that rely on the amplitudes of the fundamental and harmonic frequencies. Combined with computing the fast Fourier transform in a lower-level language, this fitting procedure eliminates computational barriers and should enable real-time processing of CDMS data on a laptop computer.
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Affiliation(s)
- Zachary M. Miller
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Conner C. Harper
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Hyuncheol Lee
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720-1460, United States
| | - Amanda J. Bischoff
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
| | - Matthew B. Francis
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
| | - David V. Schaffer
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
| | - Evan R. Williams
- College of Chemistry, University of California, Berkeley, California, 94720-1460, United States
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11
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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: 12] [Impact Index Per Article: 6.0] [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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12
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA 97403-1252
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13
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Rusinov A, Ding L, Smirnov S, Knight P, Andrzejewski R, Waki H. Protein Analysis by Electrospray-Orbital Frequency Analyzer with Charge Detection Mass Spectrometry Algorithm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1145-1154. [PMID: 33872500 DOI: 10.1021/jasms.0c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Orbital frequency analyzer (OFA) is one of the electrostatic ion trap mass analysers for FTMS, which offers ultrahigh mass resolution and high ion charge capacity. In order to analyze multiply charged proteins and other large biological particles by means of charge detection mass spectrometry, a data processing algorithm was created to suit the image charge signal of nonharmonic waveform nature. The algorithm is capable of detecting collisions between ions and residual gas molecules, to determine lifetime of ions, and to evaluate the charge and mass values for ions having lifetime above a threshold. With the filtering of the lifetime and charge value, the chemical noise from small molecules and protein fragments can be eliminated in the reconstructed spectrum, facilitating measurement of protein content at a very low concentration, down to tens of nanomolars. The standard deviation of charge measurement is between 1.1 to 1.8 e for ions with oscillation lifetimes from 1 to 0.4 s, and this in turn determines the CDMS spectrum mass peak width. It has been found that the lower voltage setting of the OFA results in a larger population of ions surviving for longer times and thus produces narrower mass peak width. While OFA is able to run multiplexed CDMS without ion motion interference, coexisting ions of the same or very close m/z can cause interference between their image charge signals, which increases the error in charge determination.
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Affiliation(s)
| | - Li Ding
- Shimadzu Research Laboratory (Europe) Ltd., Manchester M17 1GP, U.K
- School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Sergey Smirnov
- Shimadzu Research Laboratory (Europe) Ltd., Manchester M17 1GP, U.K
| | - Patrick Knight
- Shimadzu Research Laboratory (Europe) Ltd., Manchester M17 1GP, U.K
| | | | - Hiroaki Waki
- Shimadzu Research Laboratory (Europe) Ltd., Manchester M17 1GP, U.K
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14
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Harper CC, Brauer DD, Francis MB, Williams ER. Direct observation of ion emission from charged aqueous nanodrops: effects on gaseous macromolecular charging. Chem Sci 2021; 12:5185-5195. [PMID: 34168773 PMCID: PMC8179642 DOI: 10.1039/d0sc05707j] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/25/2021] [Indexed: 01/04/2023] Open
Abstract
Mechanistic information about how gaseous ions are formed from charged droplets has been difficult to establish because direct observation of nanodrops in a size range relevant to gaseous macromolecular ion formation by optical or traditional mass spectrometry methods is challenging owing to their small size and heterogeneity. Here, the mass and charge of individual aqueous nanodrops between 1-10 MDa (15-32 nm diameter) with ∼50-300 charges are dynamically monitored for 1 s using charge detection mass spectrometry. Discrete losses of minimally solvated singly charged ions occur, marking the first direct observation of ion emission from aqueous nanodrops in late stages of droplet evaporation relevant to macromolecular ion formation in native mass spectrometry. Nanodrop charge depends on the identity of constituent ions, with pure water nanodrops charged slightly above the Rayleigh limit and aqueous solutions containing alkali metal ions charged progressively below the Rayleigh limit with increasing cation size. MS2 capsid ions (∼3.5 MDa; ∼27 nm diameter) are more highly charged from aqueous ammonium acetate than from its biochemically preferred, 100 mM NaCl/10 mM Na phosphate solution, consistent with ion emission reducing the nanodrop and resulting capsid charge. The extent of charging indicates that the capsid partially collapses inside the nanodrops prior to the charging and formation of the dehydrated gaseous ions. These results demonstrate that ion emission can affect macromolecular charging and that conformational changes to macromolecular structure can occur in nanodrops prior to the formation of naked gaseous ions.
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Affiliation(s)
- Conner C Harper
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Daniel D Brauer
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Matthew B Francis
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
| | - Evan R Williams
- Department of Chemistry, University of California Berkeley California 94720-1460 USA
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15
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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16
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Affiliation(s)
- Tobias
P. Wörner
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Tatiana M. Shamorkina
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of 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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17
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Gustafson EL, Murray HV, Caldwell T, Austin DE. Accurately Mapping Image Charge and Calibrating Ion Velocity in Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2161-2170. [PMID: 32856905 DOI: 10.1021/jasms.0c00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Image charge detection is the foundation of charge detection mass spectrometry (CDMS). The mass-to-charge ratio, m/z, of a highly charged ion or particle is determined by measuring the particle's charge and velocity. Charge is typically determined from a calibrated image charge signal, and the particle velocity is calculated using the peaks from the shaped signal as they relate to the particle position and time-of-flight through a detector of known length. Although much has been done to improve the charge accuracy in CDMS, little has been done to address the inconsistencies in the particle velocity measurements and the interpretation of peak position and effective electrode length. In this work, we combine SIMION ion trajectory software and the Shockley-Ramo theorem to accurately determine the effective electrode length, peak position, and shape of the signal peaks. Six model charge detector geometries were examined with this method and evaluated in laboratory experiments. Experimental results in all cases agreed with the simulations. Using a charge detector with multiple, 12.7 mm-long cylindrical electrodes, experimental velocities across and between electrodes agreed within 0.25% relative standard deviation (RSD) when this method was used to correct for effective electrode lengths, corresponding to an uncertainty in the effective electrode length of only 40 μm. For a detector with multiple electrodes and varied electrode spacing, experiments showed that the peak amplitude and shape vary with the geometry and with the particle path through the detector, whereas all peak areas agreed to within 2.3% RSD. For a charge detector made of two printed circuit boards, the velocities agreed within 0.44% RSD using the calculated effective electrode length.
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Affiliation(s)
- Elaura L Gustafson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Halle V Murray
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Tabitha Caldwell
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Daniel E Austin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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18
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Antoine R. Weighing synthetic polymers of ultra-high molar mass and polymeric nanomaterials: What can we learn from charge detection mass spectrometry? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 2:e8539. [PMID: 31353622 DOI: 10.1002/rcm.8539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Advances in soft ionization techniques for mass spectrometry (MS) of polymeric materials make it possible to determine the masses of intact molecular ions exceeding megadaltons. Interfacing MS with separation and fragmentation methods has additionally led to impressive advances in the ability to structurally characterize polymers. Even if the gap to the megadalton range has been bridged by MS for polymers standards, the MS-based analysis for more complex polymeric materials is still challenging. Charge detection mass spectrometry (CDMS) is a single-molecule method where the mass and the charge of each ion are directly determined from individual measurements. The entire molecular mass distribution of a polymer sample can be thus accurately measured. Described in this perspective paper is how molecular weight distribution as well as charge distribution can provide new insights into the structural and compositional studies of synthetic polymers and polymeric nanomaterials in the megadalton to gigadalton range of molecular weight. The recent multidimensional CDMS studies involving couplings with separation and dissociation techniques will be presented. And, finally, an outlook for the future avenues of the CDMS technique in the field of synthetic polymers of ultra-high molar mass and polymeric nanomaterials will be provided.
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Affiliation(s)
- Rodolphe Antoine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR 5306, F-69622, Lyon, France
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19
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Park SG, Anderson GA, Bruce JE. Parallel Detection of Fundamental and Sixth Harmonic Signals Using an ICR Cell with Dipole and Sixth Harmonic Detectors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:719-726. [PMID: 31967815 PMCID: PMC7970440 DOI: 10.1021/jasms.9b00144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a powerful instrument for high-resolution analysis of biomolecules. However, relatively long signal acquisition periods are needed to achieve mass spectra with high resolution. The use of multiple detector electrodes for detection of harmonic frequencies has been introduced as one approach to increase scan rate for a given resolving power or to obtain increased resolving power for a given detection period. The achieved resolving power and scan rate increase linearly with the order of detected harmonic signals. In recent years, ICR cell geometries have been investigated to increase the order of the harmonic frequencies and enhance harmonic signal intensities. In this study, we demonstrated PCB-based ICR cell designs with dipole and sixth harmonic detectors for parallel detection of fundamental and harmonic (6f) signals. The sixth harmonic signals from the sixth harmonic detector showed an expected 6 times higher resolving power with (M + 3H)3+ charge state insulin ions as compared with that from fundamental signals from the dipole detector. Moreover, the insulin isotopic peaks with sixth harmonic frequency signals acquired with the sixth harmonic detector were resolved for a 40 ms data acquisition period but unresolved with the same duration dipole detector signals, corresponding to a 6-fold improvement in achievable spectral acquisition rates for a given resolving power.
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Affiliation(s)
- Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Gordon A Anderson
- GAA Custom Engineering, LLC, Benton City, Washington 99320, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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20
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Harper CC, Williams ER. Enhanced Multiplexing in Fourier Transform Charge Detection Mass Spectrometry by Decoupling Ion Frequency from Mass to Charge Ratio. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2637-2645. [PMID: 31720975 DOI: 10.1007/s13361-019-02330-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Weighing single ions with charge detection mass spectrometry (CDMS) makes it possible to obtain the masses of molecules of essentially unlimited size even in highly heterogeneous samples, but producing a mass histogram that is representative of all of the components in a mixture requires substantial measurement time. Multiple ions can be trapped to reduce analysis time but ion signals can overlap. To determine the maximum gains in analysis speed possible with current instrumentation with multiple ion trapping, simulations calculating the frequency and overlap rate of ions with different mass, charge, and energy ranges were performed. For an analyte with a broad mass distribution, such as long chain polyethylene glycol (PEG, 8 MDa), gains in analysis speed of up to 160 times that of prior CDMS experiments are possible. For signals from homogeneous samples, ions with the same m/z have frequencies that overlap and interfere, reducing the effectiveness of multiplexing in experiments where ions have the same energy per charge. We show that by maximizing the decoupling of ion m/z from frequency using a broad range of ion energies, the rate of signal overlap is significantly reduced making it possible to trap more ions. Under optimum decoupling conditions, a measurement speed nearly 50 times greater than that of prior CDMS experiments is possible for RuBisCO (517 kDa). The reduction in overlap due to decoupling also results in more accurate quantitation in samples that contain multiple analytes with different concentrations.
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Affiliation(s)
- Conner C Harper
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
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21
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Elliott AG, Harper CC, Lin HW, Williams ER. Effects of Individual Ion Energies on Charge Measurements in Fourier Transform Charge Detection Mass Spectrometry (FT-CDMS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:946-955. [PMID: 30430436 DOI: 10.1007/s13361-018-2094-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 06/09/2023]
Abstract
A method to correct for the effect of ion energy on charge measurements of individual ions trapped and weighed with charge detection mass spectrometry (CDMS) is demonstrated. Ions with different energies induce different signal patterns inside an electrostatic ion trap. The sum of the amplitudes of the fundamental and second harmonic frequencies in the Fourier transform of the induced signal, which has been used to obtain the ion charge, depends on both ion energy and charge. The amplitudes of the fundamental frequencies of ions increase over time as ions lose energy by collisions with background gas and solvent loss from larger ions. Model ion signals are simulated with the same time-domain amplitude at different energies and frequencies and the resulting fundamental frequency amplitudes are used to normalize real ion signals for energy and frequency effects. The fundamental frequency amplitude decreases dramatically below 20 kHz and increases by ~ 17% from the highest energy to lowest energy that is stable with a given trap potential at all frequencies. Normalizing the fundamental frequency amplitude with the modeled amplitudes removes the systematic changes in the charge measurement of polyethylene glycol (PEG) and other ions and makes it possible to signal average the amplitude over long times, which reduces the charge uncertainty to 0.04% for a PEG ion for a 500-ms measurement. This method improves charge measurement accuracy and uncertainty, which are important for high-accuracy mass measurement with CDMS. Graphical abstract ᅟ.
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Affiliation(s)
- Andrew G Elliott
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Conner C Harper
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Haw-Wei Lin
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
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22
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Harper CC, Elliott AG, Oltrogge LM, Savage DF, Williams ER. Multiplexed Charge Detection Mass Spectrometry for High-Throughput Single Ion Analysis of Large Molecules. Anal Chem 2019; 91:7458-7465. [PMID: 31082222 DOI: 10.1021/acs.analchem.9b01669] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Applications of charge detection mass spectrometry (CDMS) for measuring the masses of large molecules, macromolecular complexes, and synthetic polymers that are too large or heterogeneous for conventional mass spectrometry measurements are made possible by weighing individual ions in order to avoid interferences between ions. Here, a new multiplexing method that makes it possible to measure the masses of many ions simultaneously in CDMS is demonstrated. Ions with a broad range of kinetic energies are trapped. The energy of each ion is obtained from the ratio of the intensity of the fundamental to the second harmonic frequencies of the periodic trapping motion making it possible to measure both the m/ z and charge of each ion. Because ions with the exact same m/ z but with different energies appear at different frequencies, the probability of ion-ion interference is significantly reduced. We show that the measured mass of a protein complex consisting of 16 protomers, RuBisCO (517 kDa), is not affected by the number of trapped ions with up to 21 ions trapped simultaneously in these experiments. Ion-ion interactions do not affect the ion trapping lifetime up to 1 s, and there is no influence of the number of ions on the measured charge-state distribution of bovine serum albumin (66.5 kDa), indicating that ion-ion interactions do not adversely affect any of these measurements. Over an order of magnitude gain in measurement speed over single ion analysis is demonstrated, and significant additional gains are expected with this multi-ion measurement method.
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