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Xu T, Wang Q, Wang Q, Sun L. Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 38973469 DOI: 10.1039/d4ay00651h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Proteoforms are all forms of protein molecules from the same gene because of variations at the DNA, RNA, and protein levels, e.g., alternative splicing and post-translational modifications (PTMs). Delineation of proteins in a proteoform-specific manner is crucial for understanding their biological functions. Mass spectrometry (MS)-intensive top-down proteomics (TDP) is promising for comprehensively characterizing intact proteoforms in complex biological systems. It has achieved substantial progress in technological development, including sample preparation, proteoform separations, MS instrumentation, and bioinformatics tools. In a single TDP study, thousands of proteoforms can be identified and quantified from a cell lysate. It has also been applied to various biomedical research to better our understanding of protein function in regulating cellular processes and to discover novel proteoform biomarkers of diseases for early diagnosis and therapeutic development. This review covers the most recent technological development and biomedical applications of MS-intensive TDP.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
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2
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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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3
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Stiving AQ, Foreman DJ, VanAernum ZL, Durr E, Wang S, Vlasak J, Galli J, Kafader JO, Tsukidate T, Li X, Schuessler HA, Richardson DD. Dissecting the Heterogeneous Glycan Profiles of Recombinant Coronavirus Spike Proteins with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:62-73. [PMID: 38032172 DOI: 10.1021/jasms.3c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Surface-embedded glycoproteins, such as the spike protein trimers of coronaviruses MERS, SARS-CoV, and SARS-CoV-2, play a key role in viral function and are the target antigen for many vaccines. However, their significant glycan heterogeneity poses an analytical challenge. Here, we utilized individual ion mass spectrometry (I2MS), a multiplexed charge detection measurement with similarities to charge detection mass spectrometry (CDMS), in which a commercially available Orbitrap analyzer is used to directly produce mass profiles of these heterogeneous coronavirus spike protein trimers under native-like conditions. Analysis by I2MS shows that glycosylation contributes to the molecular mass of each protein trimer more significantly than expected by bottom-up techniques, highlighting the importance of obtaining complementary intact mass information when characterizing glycosylation of such heterogeneous proteins. Enzymatic dissection to remove sialic acid or N-linked glycans demonstrates that I2MS can be used to better understand the glycan profile from a native viewpoint. Deglycosylation of N-glycans followed by I2MS analysis indicates that the SARS-CoV-2 spike protein trimer contains glycans that are more difficult to remove than its MERS and SARS-CoV counterparts, and these differences are correlated with solvent accessibility. I2MS technology enables characterization of protein mass and intact glycan profile and is orthogonal to traditional mass analysis methods such as size exclusion chromatography-multiangle light scattering (SEC-MALS) and field flow fractionation-multiangle light scattering (FFF-MALS). An added advantage of I2MS is low sample use, requiring 100-fold less than other methodologies. This work highlights how I2MS technology can enable efficient development of vaccines and therapeutics for pharmaceutical development.
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Affiliation(s)
- Alyssa Q Stiving
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - David J Foreman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary L VanAernum
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eberhard Durr
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shiyi Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Josef Vlasak
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer Galli
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Taku Tsukidate
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Hillary A Schuessler
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Douglas D Richardson
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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4
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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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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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Gonzales MF, Piya DK, Koehler B, Zhang K, Yu Z, Zeng L, Gill JJ. New Insights into the Structure and Assembly of Bacteriophage P1. Viruses 2022; 14:v14040678. [PMID: 35458408 PMCID: PMC9024508 DOI: 10.3390/v14040678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophage P1 is the premier transducing phage of E. coli. Despite its prominence in advancing E. coli genetics, modern molecular techniques have not been applied to thoroughly understand P1 structure. Here, we report the proteome of the P1 virion as determined by liquid chromatography tandem mass-spectrometry. Additionally, a library of single-gene knockouts identified the following five previously unknown essential genes: pmgA, pmgB, pmgC, pmgG, and pmgR. In addition, proteolytic processing of the major capsid protein is a known feature of P1 morphogenesis, and we identified the processing site by N-terminal sequencing to be between E120 and S121, producing a 448-residue, 49.3 kDa mature peptide. Furthermore, the P1 defense against restriction (Dar) system consists of six known proteins that are incorporated into the virion during morphogenesis. The largest of these, DarB, is a 250 kDa protein that is believed to translocate into the cell during infection. DarB deletions indicated the presence of an N-terminal packaging signal, and the N-terminal 30 residues of DarB are shown to be sufficient for directing a heterologous reporter protein to the capsid. Taken together, the data expand on essential structural P1 proteins as well as introduces P1 as a nanomachine for cellular delivery.
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Affiliation(s)
- Miguel F. Gonzales
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Interdisciplinary Program in Genetics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| | - Denish K. Piya
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Brian Koehler
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Kailun Zhang
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Zihao Yu
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Lanying Zeng
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Interdisciplinary Program in Genetics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA
- Correspondence: ; Tel.: +1-979-458-6368
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7
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Barnes LF, Draper BE, Jarrold MF. Analysis of Recombinant Adenovirus Vectors by Ion Trap Charge Detection Mass Spectrometry: Accurate Molecular Weight Measurements beyond 150 MDa. Anal Chem 2022; 94:1543-1551. [PMID: 35023731 DOI: 10.1021/acs.analchem.1c02439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenovirus is one of the largest nonenveloped, double-stranded DNA viruses. It is widely used as a gene therapy vector and has recently received a lot of attention as a novel vaccine platform for SARS-CoV-2. Human adenovirus 5 (HAdV5) contains over 2500 protein molecules and has a 36 kbp genome. Adenovirus is well beyond the range of conventional mass spectrometry, and it was unclear how well such a large complex could be desolvated. Here, we report molecular weight (MW) distributions measured for HAdV5 and for 11 recombinant AdV vectors with genomes of varying lengths. The MW distributions were recorded using ion trap charge detection mass spectrometry (CDMS), a single-particle technique where m/z and charge are measured for individual ions. The results show that ions as large as 150 MDa can be effectively desolvated and accurate MW distributions obtained. The MW distribution for HAdV5 contains a narrow peak at 156.1 MDa, assigned to the infectious virus. A smaller peak at 129.6 MDa is attributed to incomplete particles that have not packaged a genome. The ions in the 129.6 MDa peak have a much lower average charge than those in the peak at 156.1 MDa. This is attributed to the empty particles missing some or all of the fibers that decorate the surface of the virion. The MW measured for the mature virus (156.1 MDa) is much larger than that predicted from sequence masses and copy numbers of the constituents (142.5 MDa). Measurements performed for recombinant AdV as a function of genome length show that for every 1 MDa increase in the genome MW, the MW of the mature virus increases by around 2.3 MDa. The additional 1.3 MDa is attributed to core proteins that are copackaged with the DNA. This observation suggests that the discrepancy between the measured and expected MWs for mature HAdV5 is due to an underestimate in the copy numbers of the core proteins.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, Inc., 3750 E Bluebird Lane, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Miller LM, Bond KM, Draper BE, Jarrold MF. Characterization of Classical Vaccines by Charge Detection Mass Spectrometry. Anal Chem 2021; 93:11965-11972. [PMID: 34435777 DOI: 10.1021/acs.analchem.1c01893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vaccines induce immunity by presenting disease antigens through several platforms ranging from individual protein subunits to whole viruses. Due to the large difference in antigen size, the analytical techniques employed for vaccine characterization are often platform-specific. A single, robust analytical technique capable of widespread, cross-platform use would be of great benefit and allow for comparisons across manufacturing processes. One method that spans the antigen mass range is charge detection mass spectrometry (CDMS). CDMS is a single-ion approach where the mass-to-charge ratio (m/z) and charge are measured simultaneously, allowing accurate mass distributions to be measured for heterogeneous analytes over a broad size range. In this work, CDMS was used to characterize the antigens from three classical multivalent vaccines, inactivated poliomyelitis vaccine (IPOL), RotaTeq, and Gardasil-9, directly from commercial samples. For each vaccine, the antigen purity was inspected, and in the whole virus vaccines, empty virus particles were detected. For IPOL, information on the extent of formaldehyde cross-linking was obtained. RotaTeq shows a narrow peak at 61.06 MDa. This is at a slightly lower mass than expected for the double-layer particle, suggesting that around 10 pentonal trimers are missing. For Gardasil-9, buffer exchange of the vaccine resulted in very broad mass distributions. However, removal of the virus-like particles from the aluminum adjuvant using a displacement reaction generated a spectrum with narrow peaks.
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Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Kevin M Bond
- Chemistry Department, Indiana University, 800 E Kirkwood Ave., Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, 3750 E Bluebird Lane, 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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9
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Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins. Viruses 2021; 13:v13081504. [PMID: 34452369 PMCID: PMC8402733 DOI: 10.3390/v13081504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Tailed double-stranded DNA bacteriophages inject some proteins with their dsDNA during infection. Phage P22 injects about 12, 12, and 30 molecules of the proteins encoded by genes 7, 16 and 20, respectively. After their ejection from the virion, they assemble into a trans-periplasmic conduit through which the DNA passes to enter the cytoplasm. The location of these proteins in the virion before injection is not well understood, although we recently showed they reside near the portal protein barrel in DNA-filled heads. In this report we show that when these proteins are missing from the virion, a longer than normal DNA molecule is encapsidated by the P22 headful DNA packaging machinery. Thus, the ejection proteins occupy positions within the virion that can be occupied by packaged DNA when they are absent.
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10
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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: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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11
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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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12
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Pathak P, Sarycheva A, Baird MA, Shvartsburg AA. Delineation of Isomers by the 13C Shifts in Ion Mobility Spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:340-345. [PMID: 33201698 DOI: 10.1021/jasms.0c00350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry (MS) and isotopes were intertwined for a century, with stable isotopes central to many MS identification and quantification protocols. In contrast, the analytical separations including ion mobility spectrometry (IMS) largely ignored isotopes, partly because of insufficient resolution. We recently delineated various halogenated aniline isomers by structurally specific splitting in FAIMS spectra. While this capability hinges on the 13C shifts, all preceding studies leveraged 37Cl or 81Br to enhance the differentiation. However, such abundant heavy isotopes are absent from typical organic compounds. With single I isotope, iodinated organics generate similar isotopic envelopes dominated by the 13C atoms. Here, we distinguish the three monoiodoaniline isomers based on the shifts solely for one or two 13C atoms. The differentiation may be somewhat improved using multipoint peak position descriptions for more reproducible shifts. The interisomer order of shifts differs from those for chlorinated or brominated analogues, showcasing the specificity of approach. We also investigated the mass scaling of isotopic shifts, encountering divergent trends for different structural families.
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Affiliation(s)
- Pratima Pathak
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Anastasia Sarycheva
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Matthew A Baird
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
| | - Alexandre A Shvartsburg
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260, United States
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13
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Todd AR, Barnes LF, Young K, Zlotnick A, Jarrold MF. Higher Resolution Charge Detection Mass Spectrometry. Anal Chem 2020; 92:11357-11364. [PMID: 32806905 PMCID: PMC8587657 DOI: 10.1021/acs.analchem.0c02133] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Charge detection mass spectrometry is a single particle technique where the masses of individual ions are determined from simultaneous measurements of each ion's m/z ratio and charge. The ions pass through a conducting cylinder, and the charge induced on the cylinder is detected. The cylinder is usually placed inside an electrostatic linear ion trap so that the ions oscillate back and forth through the cylinder. The resulting time domain signal is analyzed by fast Fourier transformation; the oscillation frequency yields the m/z, and the charge is determined from the magnitudes. The mass resolving power depends on the uncertainties in both quantities. In previous work, the mass resolving power was modest, around 30-40. In this work we report around an order of magnitude improvement. The improvement was achieved by coupling high-accuracy charge measurements (obtained with dynamic calibration) with higher resolution m/z measurements. The performance was benchmarked by monitoring the assembly of the hepatitis B virus (HBV) capsid. The HBV capsid assembly reaction can result in a heterogeneous mixture of intermediates extending from the capsid protein dimer to the icosahedral T = 4 capsid with 120 dimers. Intermediates of all possible sizes were resolved, as well as some overgrown species. Despite the improved mass resolving power, the measured peak widths are still dominated by instrumental resolution. Heterogeneity makes only a small contribution. Resonances were observed in some of the m/z spectra. They result from ions with different masses and charges having similar m/z values. Analogous resonances are expected whenever the sample is a heterogeneous mixture assembled from a common building block.
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14
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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: 10] [Impact Index Per Article: 2.5] [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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15
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Sansa M, Defoort M, Brenac A, Hermouet M, Banniard L, Fafin A, Gely M, Masselon C, Favero I, Jourdan G, Hentz S. Optomechanical mass spectrometry. Nat Commun 2020; 11:3781. [PMID: 32728047 PMCID: PMC7391691 DOI: 10.1038/s41467-020-17592-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022] Open
Abstract
Nanomechanical mass spectrometry has proven to be well suited for the analysis of high mass species such as viruses. Still, the use of one-dimensional devices such as vibrating beams forces a trade-off between analysis time and mass resolution. Complex readout schemes are also required to simultaneously monitor multiple resonance modes, which degrades resolution. These issues restrict nanomechanical MS to specific species. We demonstrate here single-particle mass spectrometry with nano-optomechanical resonators fabricated with a Very Large Scale Integration process. The unique motion sensitivity of optomechanics allows designs that are impervious to particle position, stiffness or shape, opening the way to the analysis of large aspect ratio biological objects of great significance such as viruses with a tail or fibrils. Compared to top-down beam resonators with electrical read-out and state-of-the-art mass resolution, we show a three-fold improvement in capture area with no resolution degradation, despite the use of a single resonance mode. The use of one dimensional devices in nanomechanical mass spectrometry leads to a trade-off between analysis time and resolution. Here, the authors report single-particle mass spectrometry using integrated optomechanical resonators, impervious to particle position, stiffness or shape.
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Affiliation(s)
- Marc Sansa
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Martial Defoort
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France.,Université Grenoble Alpes, CNRS, Grenoble INP, TIMA, 38000, Grenoble, France
| | - Ariel Brenac
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG-Spintec, 38000, Grenoble, France
| | - Maxime Hermouet
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Louise Banniard
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Alexandre Fafin
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Marc Gely
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Christophe Masselon
- CEA, IRIG, Biologie à Grande Echelle, F-38054, Grenoble, France.,Inserm, Unité 1038, F-38054, Grenoble, France
| | - Ivan Favero
- Matériaux et Phénomènes Quantiques, CNRS UMR 7162, Université de Paris, 75013, Paris, France
| | | | - Sébastien Hentz
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France.
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16
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Todd AR, Jarrold MF. Dynamic Calibration Enables High-Accuracy Charge Measurements on Individual Ions for Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1241-1248. [PMID: 32353231 DOI: 10.1021/jasms.0c00081] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. For high-accuracy charge measurements, the detection cylinder is embedded in an electrostatic linear ion trap (ELIT), and the ions oscillate back and forth through the cylinder so that multiple measurements are made. To assign the charge state with a low error rate, the charge of each ion must be determined with an uncertainty (root-mean-square deviation) of around 0.2 elementary charges. We show here that high-accuracy charge measurements can be achieved for large ions by dynamic calibration of the charge measurement using an internal standard. The internal standard is generated by irradiating the detection cylinder, by means of a small antenna, with a radiofrequency signal. Using this approach, we have obtained a relative charge uncertainty of around 5 × 10-4, allowing charge-state resolution to be achieved for single ions with up to 500 charges. In another application of this approach, the detection cylinder is irradiated with a signal that counteracts the transients generated when the potentials on the ELIT end-caps are switched to trapping mode. Using this approach, the dead time after switching (during which the signal cannot be analyzed) has been reduced by more than an order of magnitude. With charge-state resolution for ions with up to 500 charges, we were able to calibrate the charges precisely. The results show that the response of the charge-sensitive amplifier with dynamic calibration is linear to within a small fraction of an elementary charge.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405 United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405 United States
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17
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Russier-Antoine I, Fakhouri H, Basu S, Bertorelle F, Dugourd P, Brevet PF, Velayudhan P, Thomas S, Kalarikkal N, Antoine R. Second harmonic scattering from mass characterized 2D graphene oxide sheets. Chem Commun (Camb) 2020; 56:3859-3862. [PMID: 32134076 DOI: 10.1039/d0cc00111b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this communication, we report the second harmonic scattering from mass characterized 2D graphene oxide sheets dispersed in an aqueous suspension, in the femtosecond regime at 800 nm laser excitation. Charge-detection mass-spectrometry, performing at the single sheet level, allows for an exhaustive molar mass distribution and thus concentration for these 2D nanomaterials samples. The orientation-averaged hyperpolarizability value is (1.36 ± 0.15) × 10-25 esu as determined by the concentration-dependent harmonic scattering signal. In addition, the multi-photon excited fluorescence spectrum is characterized by a broad band in the visible range between 350 and 700 nm centered at about 500 nm.
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Affiliation(s)
- Isabelle Russier-Antoine
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, F-69100 Villeurbanne, France.
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18
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Kafader JO, Durbin KR, Melani RD, Des Soye BJ, Schachner LF, Senko MW, Compton PD, Kelleher NL. Individual Ion Mass Spectrometry Enhances the Sensitivity and Sequence Coverage of Top-Down Mass Spectrometry. J Proteome Res 2020; 19:1346-1350. [PMID: 32032494 PMCID: PMC7060802 DOI: 10.1021/acs.jproteome.9b00797] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Charge detection mass spectrometry (CDMS) is mainly utilized to determine the mass of intact molecules. Previous applications of CDMS have determined the mass-to-charge ratio and the charge of large polymers, DNA molecules, and native protein complexes, from which corresponding mass values could be assigned. Recent advances have demonstrated that CDMS using an Orbitrap mass analyzer yields the reliable assignment of integer charge states that enables individual ion mass spectrometry (I2MS) and spectral output directly into the mass domain. Here I2MS analysis was extended to isotopically resolved fragment ions from intact proteoforms for the first time. With a radically different bias for ion readout, I2MS identified low-abundance fragment ions containing many hundreds of residues that were undetectable by standard Orbitrap measurements, leading to a doubling in the sequence coverage of triosephosphate isomerase. Thus MS/MS with the detection of individual ions (MS/I2MS) provides a far greater ability to detect high mass fragment ions and exhibits strong complementarity to traditional spectral readout in this, its first application to top-down mass spectrometry.
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Affiliation(s)
- Jared O. Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R. Durbin
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Benjamin J. Des Soye
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Luis F. Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Michael W. Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Philip D. Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, the Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
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19
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Brown BA, Zeng X, Todd AR, Barnes LF, Winstone JMA, Trinidad JC, Novotny MV, Jarrold MF, Clemmer DE. Charge Detection Mass Spectrometry Measurements of Exosomes and other Extracellular Particles Enriched from Bovine Milk. Anal Chem 2020; 92:3285-3292. [PMID: 31989813 PMCID: PMC7236431 DOI: 10.1021/acs.analchem.9b05173] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The masses of particles in a bovine milk extracellular vesicle (EV) preparation enriched for exosomes were directly determined for the first time by charge detection mass spectrometry (CDMS). In CDMS, both the mass-to-charge ratio (m/z) and z are determined simultaneously for individual particles, enabling mass determinations for particles that are far beyond the mass limit (∼1.0 MDa) of conventional mass spectrometry (MS). Particle masses and charges span a wide range from m ∼ 2 to ∼90 MDa and z ∼ 50 to ∼1300 e (elementary charges) and are highly dependent upon the conditions used to extract and isolate the EVs. EV particles span a continuum of masses, reflecting the highly heterogeneous nature of these samples. However, evidence for unique populations of particles is obtained from correlation of the charges and masses. An analysis that uses a two-dimensional Gaussian model, provides evidence for six families of particles, four of which having masses in the range expected for exosomes. Complementary proteomics measurements and electron microscopy (EM) imaging are used to further characterize the EVs and confirm that these samples have been enriched in exosomes. The ability to characterize such extremely heterogeneous mixtures of large particles with rapid, sensitive, and high-resolution MS techniques is critical to ongoing analytical efforts to separate and purify exosomes and exosome subpopulations. Direct measurement of each particle's mass and charge is a new means of characterizing the physical and chemical properties of exosomes and other EVs.
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Affiliation(s)
- Brooke A Brown
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Xuyao Zeng
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Aaron R Todd
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Lauren F Barnes
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Jonathan M A Winstone
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Jonathan C Trinidad
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Milos V Novotny
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - Martin F Jarrold
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana 47505 , United States
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20
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Todd AR, Alexander AW, Jarrold MF. Implementation of a Charge-Sensitive Amplifier without a Feedback Resistor for Charge Detection Mass Spectrometry Reduces Noise and Enables Detection of Individual Ions Carrying a Single Charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:146-154. [PMID: 32881508 DOI: 10.1021/jasms.9b00010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. Electrical noise limits the accuracy of the charge measurement and the smallest charge that can be detected. Thermal noise in the feedback resistor is a major source of electrical noise. We describe the implementation of a charge-sensitive amplifier without a feedback resistor. The design has significantly reduced 1/f noise facilitating the detection of high m/z ions and substantially reducing the measurement time required to achieve almost perfect charge accuracy. With the new design we have been able to detect individual ions carrying a single charge. This is an important milestone in the development of CDMS.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew W Alexander
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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21
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Fernández-García J, Compton S, Wick D, Fernandez de la Mora J. Virus Size Analysis by Gas-Phase Mobility Measurements: Resolution Limits. Anal Chem 2019; 91:12962-12970. [PMID: 31509389 DOI: 10.1021/acs.analchem.9b03023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Electrospraying (ES) dissolved viral particles, followed by charge reduction and size analysis with a differential mobility analyzer (DMA), offers a flexible size-analysis tool for small particles in solution. The technique relies on pioneering work by Kaufman and colleagues, commercialized by TSI, and often referred to as GEMMA. However, viral studies with TSI's GEMMA have suffered from limited resolving power, possibly because of imperfections in either the instrument (DMA or charge reduction) or the sample solution preparation. Here, we explore the limits of the resolution achievable by GEMMA, taking advantage of (i) cleaner charge reduction methods and (ii) DMAs of higher resolving power. Analysis of the literature provides indications that mobility peak widths (fwhm) of 2% or less may be achieved by combining careful sample preparation with improved instrumentation. Working with purified PP7 bacteriophage particles small enough to be classifiable by existing high-resolution DMAs, we confirm that fairly narrow viral mobility peaks may be obtained (relative full width at half-maximum fwhm <5%). Comparison of spectra of a given apian virus sample obtained with TSI's GEMMA and our improved instrumentation confirms that one critical limitation is the DMA. This is further verified by narrow peaks from murine parvovirus, norovirus, and encephalomyelitis virus samples, obtained in our improved GEMMA with little sample preparation, directly from infected cell cultures. Classification of purified large (60 nm) coliphage PR772 particles leads to broad peaks, due to both viral degradation and limited intrinsic resolution of the DMAs used to cover the range of such large particles. We conclude that improved DMAs suitable for high-resolution analysis of particles larger than 30 nm need to be developed to determine the intrinsic mobility width of viral particles.
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Affiliation(s)
- J Fernández-García
- Yale University , Department of Mechanical Engineering , New Haven , Connecticut 06520 , United States
| | - S Compton
- Yale University , School of Medicine , New Haven , Connecticut 06520 , United States
| | - D Wick
- BVS, Inc. , Stevensville , Montana 59870 , United States
| | - J Fernandez de la Mora
- Yale University , Department of Mechanical Engineering , New Haven , Connecticut 06520 , United States
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22
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Todd AR, Jarrold MF. Dramatic Improvement in Sensitivity with Pulsed Mode Charge Detection Mass Spectrometry. Anal Chem 2019; 91:14002-14008. [PMID: 31589418 DOI: 10.1021/acs.analchem.9b03586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Charge detection mass spectrometry (CDMS) is emerging as a valuable tool to determine mass distributions for heterogeneous and high-mass samples. It is a single-particle technique where masses are determined for individual ions from simultaneous measurements of their mass-to-charge ratio (m/z) and charge. Ions are trapped in an electrostatic linear ion trap (ELIT) and oscillate back and forth through a detection cylinder. The trap is open and able to trap ions for a small fraction of the total measurement time so most of the ions (>99.8%) in a continuous ion beam are lost. Here, we implement an ion storage scheme where ions are accumulated and stored in a hexapole and then injected into the ELIT at the right time for them to be trapped. This pulsed mode of operation increases the sensitivity of CDMS by more than 2 orders of magnitude, which allows much lower titer samples to be analyzed. A limit of detection of 3.3 × 108 particles/mL was obtained for hepatitis B virus T = 4 capsids with a 1.3 μL sample. The hexapole where the ions are accumulated and stored is a significant distance from the ion trap so ions are dispersed in time by their m/z values as they travel between the hexapole and the ELIT. By varying the delay time between ion release and trapping, different windows of m/z values can be trapped.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
| | - Martin F Jarrold
- Chemistry Department , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405 , United States
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23
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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24
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Weiss VU, Pogan R, Zoratto S, Bond KM, Boulanger P, Jarrold MF, Lyktey N, Pahl D, Puffler N, Schelhaas M, Selivanovitch E, Uetrecht C, Allmaier G. Virus-like particle size and molecular weight/mass determination applying gas-phase electrophoresis (native nES GEMMA). Anal Bioanal Chem 2019; 411:5951-5962. [PMID: 31280479 PMCID: PMC6706367 DOI: 10.1007/s00216-019-01998-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/29/2019] [Accepted: 06/24/2019] [Indexed: 02/04/2023]
Abstract
(Bio-)nanoparticle analysis employing a nano-electrospray gas-phase electrophoretic mobility molecular analyzer (native nES GEMMA) also known as nES differential mobility analyzer (nES DMA) is based on surface-dry analyte separation at ambient pressure. Based on electrophoretic principles, single-charged nanoparticles are separated according to their electrophoretic mobility diameter (EMD) corresponding to the particle size for spherical analytes. Subsequently, it is possible to correlate the (bio-)nanoparticle EMDs to their molecular weight (MW) yielding a corresponding fitted curve for an investigated analyte class. Based on such a correlation, (bio-)nanoparticle MW determination via its EMD within one analyte class is possible. Turning our attention to icosahedral, non-enveloped virus-like particles (VLPs), proteinaceous shells, we set up an EMD/MW correlation. We employed native electrospray ionization mass spectrometry (native ESI MS) to obtain MW values of investigated analytes, where possible, after extensive purification. We experienced difficulties in native ESI MS with time-of-flight (ToF) detection to determine MW due to sample inherent characteristics, which was not the case for charge detection (CDMS). nES GEMMA exceeds CDMS in speed of analysis and is likewise less dependent on sample purity and homogeneity. Hence, gas-phase electrophoresis yields calculated MW values in good approximation even when charge resolution was not obtained in native ESI ToF MS. Therefore, both methods-native nES GEMMA-based MW determination via an analyte class inherent EMD/MW correlation and native ESI MS-in the end relate (bio-)nanoparticle MW values. However, they differ significantly in, e.g., ease of instrument operation, sample and analyte handling, or costs of instrumentation. Graphical abstract ![]()
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Affiliation(s)
- Victor U Weiss
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria.
| | - Ronja Pogan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Samuele Zoratto
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Kevin M Bond
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Pascale Boulanger
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Nicholas Lyktey
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Dominik Pahl
- Institute of Cellular Virology, WWU Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Nicole Puffler
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Mario Schelhaas
- Institute of Cellular Virology, WWU Münster, Von-Esmarch-Str. 56, 48149, Münster, Germany
| | - Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Günter Allmaier
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
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25
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Dunbar CA, Rayaprolu V, Wang JCY, Brown CJ, Leishman E, Jones-Burrage S, Trinidad JC, Bradshaw HB, Clemmer DE, Mukhopadhyay S, Jarrold MF. Dissecting the Components of Sindbis Virus from Arthropod and Vertebrate Hosts: Implications for Infectivity Differences. ACS Infect Dis 2019; 5:892-902. [PMID: 30986033 DOI: 10.1021/acsinfecdis.8b00356] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Sindbis virus (SINV) is an enveloped, single-stranded RNA virus, which is transmitted via mosquitos to a wide range of vertebrate hosts. SINV produced by vertebrate, baby hamster kidney (BHK) cells is more than an order of magnitude less infectious than SINV produced from mosquito (C6/36) cells. The cause of this difference is poorly understood. In this study, charge detection mass spectrometry was used to determine the masses of intact SINV particles isolated from BHK and C6/36 cells. The measured masses are substantially different: 52.88 MDa for BHK derived SINV and 50.69 MDa for C6/36 derived. Further analysis using several mass spectrometry-based methods and biophysical approaches indicates that BHK derived SINV has a substantially higher mass than C6/36 derived because in the lipid bilayer, there is a higher portion of lipids containing long chain fatty acids. The difference in lipid composition could influence the organization of the lipid bilayer. As a result, multiple stages of the viral lifecycle may be affected including assembly and budding, particle stability during transmission, and fusion events, all of which could contribute to the differences in infectivity.
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Affiliation(s)
- Carmen A. Dunbar
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Vamseedhar Rayaprolu
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Joseph C.-Y. Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall, 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
| | - Christopher J. Brown
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Emma Leishman
- Department of Psychological and Brain Sciences, Indiana University, 1101 East Tenth Street, Bloomington, Indiana 47405, United States
| | - Sara Jones-Burrage
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Heather B. Bradshaw
- Department of Psychological and Brain Sciences, Indiana University, 1101 East Tenth Street, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Suchetana Mukhopadhyay
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, Indiana 47405, United States
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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26
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Draper BE, Jarrold MF. Real-Time Analysis and Signal Optimization for Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:898-904. [PMID: 30993638 DOI: 10.1007/s13361-019-02172-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/23/2019] [Accepted: 02/23/2019] [Indexed: 06/09/2023]
Abstract
Charge detection mass spectrometry (CDMS) is an important tool for measuring mass distributions for high mass samples and heterogeneous mixtures. In CDMS, single ions are trapped and their m/z and charge are measured simultaneously. As a single particle technique, the average signal must be optimized to maximize the number of single ion trapping events. If the average signal is too small, most of the trapping events will be empty, and if the average signal is too large, most of the trapping events will contain multiple ions. In recent embodiments, the time domain signal from the trapped ion is analyzed by fast Fourier transforms. The analysis time is much longer that the data collection time which precludes real-time optimization of the experimental conditions. In this paper, we describe the implementation of CDMS with real-time analysis. Processing the data in real time allows the average signal intensities to be dynamically optimized to maximize the number of single ion trapping events. Real-time analysis also allows the experimental settings to be optimized in a timely manner to target specific mass regimes to maximize the useful information content of the measurements. Graphical Abstract .
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Affiliation(s)
- Benjamin E Draper
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA.
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27
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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: 49] [Impact Index Per Article: 9.8] [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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28
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Dominguez-Medina S, Fostner S, Defoort M, Sansa M, Stark AK, Halim MA, Vernhes E, Gely M, Jourdan G, Alava T, Boulanger P, Masselon C, Hentz S. Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators. Science 2019; 362:918-922. [PMID: 30467165 DOI: 10.1126/science.aat6457] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/20/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022]
Abstract
Measurement of the mass of particles in the mega- to gigadalton range is challenging with conventional mass spectrometry. Although this mass range appears optimal for nanomechanical resonators, nanomechanical mass spectrometers often suffer from prohibitive sample loss, extended analysis time, or inadequate resolution. We report on a system architecture combining nebulization of the analytes from solution, their efficient transfer and focusing without relying on electromagnetic fields, and the mass measurements of individual particles using nanomechanical resonator arrays. This system determined the mass distribution of ~30-megadalton polystyrene nanoparticles with high detection efficiency and effectively performed molecular mass measurements of empty or DNA-filled bacteriophage T5 capsids with masses up to 105 megadaltons using less than 1 picomole of sample and with an instrument resolution above 100.
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Affiliation(s)
- Sergio Dominguez-Medina
- Université Grenoble Alpes, F-38000 Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, F-38054 Grenoble, France.,Inserm, Unité 1038, F-38054 Grenoble, France
| | - Shawn Fostner
- Université Grenoble Alpes, CEA, LETI, 38000 Grenoble, France
| | - Martial Defoort
- Université Grenoble Alpes, CEA, LETI, 38000 Grenoble, France
| | - Marc Sansa
- Université Grenoble Alpes, CEA, LETI, 38000 Grenoble, France
| | - Ann-Kathrin Stark
- Université Grenoble Alpes, F-38000 Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, F-38054 Grenoble, France.,Inserm, Unité 1038, F-38054 Grenoble, France
| | - Mohammad Abdul Halim
- Université Grenoble Alpes, F-38000 Grenoble, France.,CEA, BIG, Biologie à Grande Echelle, F-38054 Grenoble, France.,Inserm, Unité 1038, F-38054 Grenoble, France
| | - Emeline Vernhes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif sur Yvette cedex, France
| | - Marc Gely
- Université Grenoble Alpes, CEA, LETI, 38000 Grenoble, France
| | | | - Thomas Alava
- Université Grenoble Alpes, CEA, LETI, 38000 Grenoble, France
| | - Pascale Boulanger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif sur Yvette cedex, France
| | - Christophe Masselon
- Université Grenoble Alpes, F-38000 Grenoble, France. .,CEA, BIG, Biologie à Grande Echelle, F-38054 Grenoble, France.,Inserm, Unité 1038, F-38054 Grenoble, France
| | - Sébastien Hentz
- Université Grenoble Alpes, CEA, LETI, 38000 Grenoble, France.
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29
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Kondylis P, Schlicksup CJ, Zlotnick A, Jacobson SC. Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids. Anal Chem 2019; 91:622-636. [PMID: 30383361 PMCID: PMC6472978 DOI: 10.1021/acs.analchem.8b04824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Panagiotis Kondylis
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Christopher J. Schlicksup
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
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30
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Dunbar CA, Callaway HM, Parrish CR, Jarrold MF. Probing Antibody Binding to Canine Parvovirus with Charge Detection Mass Spectrometry. J Am Chem Soc 2018; 140:15701-15711. [PMID: 30398860 DOI: 10.1021/jacs.8b08050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There are many techniques for monitoring and measuring the interactions between proteins and ligands. Most of these techniques are ensemble methods that can provide association constants and in some cases stoichiometry. Here we use charge detection mass spectrometry (CDMS), a single particle technique, to probe the interactions of antigen binding fragments (Fabs) from a series of antibodies with the canine parvovirus (CPV) capsid. In addition to providing the average number of bound Fabs as a function of Fab concentration (i.e., the binding curve), CDMS measurements provide information about the distribution of bound Fabs. We show that the distribution of bound ligands is much better at distinguishing between different binding models than the binding curve. The binding of Fab E to CPV is a textbook example. A maximum of 60 Fabs bind and the results are consistent with a model where all sites have the same binding affinity. However, for Fabs B, F, and 14, the distributions can only be fit by a model where there are distinct virus subpopulations with different binding affinities. This behavior can be distinguished from a situation where all CPV particles are identical, and each particle has the same distribution of sites with different binding affinities. The different responses to viral heterogeneity can be traced to the Fab binding sites. A comparison of Fab binding to new and aged CPV capsids reveals that a post-translational modification at the binding site for Fab E (M569) probably reduces the binding affinity.
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Affiliation(s)
- Carmen A Dunbar
- Department of Chemistry , Indiana University , 800 E. Kirkwood Ave. , Bloomington , Indiana 47405 , United States
| | - Heather M Callaway
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , New York 14850 , United States
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine , Cornell University , Ithaca , New York 14850 , United States
| | - Martin F Jarrold
- Department of Chemistry , Indiana University , 800 E. Kirkwood Ave. , Bloomington , Indiana 47405 , United States
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31
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Draper BE, Anthony SN, Jarrold MF. The FUNPET-a New Hybrid Ion Funnel-Ion Carpet Atmospheric Pressure Interface for the Simultaneous Transmission of a Broad Mass Range. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2160-2172. [PMID: 30112619 DOI: 10.1007/s13361-018-2038-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
An atmospheric pressure interface transports ions from ambient pressure to the low-pressure environment of a mass spectrometer. A capillary coupled to an ion funnel is widely used. However, conventional ion funnels do little to negate the large amount of energy picked up by high-mass ions from the gas flow through the capillary. There has been little work done on the effects of gas flow on ion transmission, and the previous studies have all been limited to low-mass, low-charge ions. In this work, we account for the effects of gas flow, diffusion, and electric fields (static and oscillating) on ion trajectories and use simulations to design a new hybrid ion funnel-ion carpet (FUNPET) interface that transmits a broad mass range with a single set of instrument conditions. The design incorporates a virtual jet disruptor where pressure buildup and counter flow dissipate the supersonic jet that results from gas flow into the interface. This, and the small exit aperture that can be used with the FUNPET, reduces the gas flow into the next stage of differential pumping. The virtual jet disruptor thermalizes ions with a broad range of masses (1 kDa to 1 GDa), and once thermalized, they are transmitted into next region of the mass spectrometer with low excess kinetic energy. The FUNPET interface is easy to fabricate from flexible printed circuit board and a support frame made by 3D printing. The performance of the interface was evaluated using charge detection mass spectrometry. Graphical Abstract ᅟ.
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Affiliation(s)
- Benjamin E Draper
- Chemistry Department, Indiana University, Bloomington, IN, 47405, USA
| | - Staci N Anthony
- Chemistry Department, Indiana University, Bloomington, IN, 47405, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, IN, 47405, USA.
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32
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Hogan JA, Jarrold MF. Optimized Electrostatic Linear Ion Trap for Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2086-2095. [PMID: 29987663 DOI: 10.1007/s13361-018-2007-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
In charge detection mass spectrometry (CDMS), ions are passed through a detection tube and the m/z ratio and charge are determined for each ion. The uncertainty in the charge and m/z determinations can be dramatically reduced by embedding the detection tube in an electrostatic linear ion trap (ELIT) so that ions oscillate back and forth through the detection tube. The resulting time domain signal can be analyzed by fast Fourier transforms (FFTs). The ion's m/z is proportional to the square of the oscillation frequency, and its charge is derived from the FFT magnitude. The ion oscillation frequency is dependent on the physical dimensions of the trap as well as the ion energy. A new ELIT has been designed for CDMS using the central particle method. In the new design, the kinetic energy dependence of the ion oscillation frequency is reduced by an order of magnitude. An order of magnitude reduction in energy dependence should have led to an order of magnitude reduction in the uncertainty of the m/z determination. In practice, a factor of four improvements was achieved. This discrepancy is probably mainly due to the trajectory dependence of the ion oscillation frequency. The new ELIT design uses a duty cycle of 50%. We show that a 50% duty cycle produces the lowest uncertainty in the charge determination. This is due to the absence of even-numbered harmonics in the FFT, which in turn leads to an increase in the magnitude of the peak at the fundamental frequency. Graphical Abstract ᅟ.
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Affiliation(s)
- Joanna A Hogan
- Chemistry Department, Indiana University, Bloomington, IN, 47405, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, IN, 47405, USA.
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33
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Elliott AG, Harper CC, Lin HW, Williams ER. Mass, mobility and MS n measurements of single ions using charge detection mass spectrometry. Analyst 2018. [PMID: 28636005 DOI: 10.1039/c7an00618g] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Charge detection mass spectrometry is used to measure the mass, charge, MSn and mobility of an individual ion produced by electrospray ionization of a 8 MDa polyethylene glycol sample. The charge detection mass spectrometer is an electrostatic ion trap that uses cone electrodes and a single tube detector and can detect ions for up to the full trapping time of 4.0 s. The time-domain signal induced on the detector tube by a single multiply charged ion can be complex owing to sequential fragmentation of the original precursor ion as well as increasing oscillation frequencies of the single ion owing to collisions with background gas that reduce the kinetic energy of the ion inside the trap. Simulations show that the ratio of the time for the ion to turn around inside the cone region of the trap to the time for the ion to travel through the detector tube is constant with m/z and increases with the ion energy per charge. By measuring this ratio, the kinetic energy of an ion can be obtained with good precision (∼1%) and this method to measure ion kinetic energies eliminates the necessity of ion energy selection prior to trapping for high precision mass measurement of large molecules in complex mixtures. This method also makes it possible to measure the masses of each sequential fragment ion formed from the original precursor ion. MS7 of a single multiply charged PEG molecule is demonstrated, and from these ion energy measurements and effects of collisions on the ion motion inside the trap, information about the ion mobility of the precursor ion and its fragments is obtained.
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Affiliation(s)
- Andrew G Elliott
- 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.
| | - Haw-Wei Lin
- 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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34
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Halim MA, Clavier C, Dagany X, Kerleroux M, Dugourd P, Dunbar RC, Antoine R. Infrared laser dissociation of single megadalton polymer ions in a gated electrostatic ion trap: the added value of statistical analysis of individual events. Phys Chem Chem Phys 2018; 20:11959-11966. [PMID: 29670983 DOI: 10.1039/c8cp00404h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report the unimolecular dissociation mechanism of megadalton SO3-containing poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) polymer cations and anions with the aid of infrared multiphoton dissociation coupled to charge detection ion trap mass spectrometry. A gated electrostatic ion trap ("Benner trap") is used to store and detect single gaseous polymer ions generated by positive and negative polarity in an electrospray ionization source. The trapped ions are then fragmented due to the sequential absorption of multiple infrared photons produced from a continuous-wave CO2 laser. Several fragmentation pathways having distinct signatures are observed. Highly charged parent ions characteristically adopt a distinctive "stair-case" pattern (assigned to the "fission" process) whereas low charge species take on a "funnel like" shape (assigned to the "evaporation" process). Also, the log-log plot of the dissociation rate constants as a function of laser intensity between PAMPS positive and negative ions is significantly different.
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Affiliation(s)
- Mohammad A Halim
- Institut Lumière Matière, UMR 5306, Université Claude Bernard Lyon 1, CNRS, F-69622 Lyon, France.
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35
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Pansieri J, Halim MA, Vendrely C, Dumoulin M, Legrand F, Sallanon MM, Chierici S, Denti S, Dagany X, Dugourd P, Marquette C, Antoine R, Forge V. Mass and charge distributions of amyloid fibers involved in neurodegenerative diseases: mapping heterogeneity and polymorphism. Chem Sci 2018; 9:2791-2796. [PMID: 29732065 PMCID: PMC5914292 DOI: 10.1039/c7sc04542e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/02/2018] [Indexed: 12/22/2022] Open
Abstract
Heterogeneity and polymorphism are generic features of amyloid fibers with some important effects on the related disease development. We report here the characterization, by charge detection mass spectrometry, of amyloid fibers made of three polypeptides involved in neurodegenerative diseases: Aβ1-42 peptide, tau and α-synuclein. Beside the mass of individual fibers, this technique enables to characterize the heterogeneity and the polymorphism of the population. In the case of Aβ1-42 peptide and tau protein, several coexisting species could be distinguished and characterized. In the case of α-synuclein, we show how the polymorphism affects the mass and charge distributions.
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Affiliation(s)
- Jonathan Pansieri
- Univ. Grenoble Alpes , CNRS , CEA , BIG/CBM/AFFOND , F-38000 Grenoble , France .
| | - Mohammad A Halim
- Institut Lumière Matière , UMR 5306 , Université Claude Bernard Lyon 1 , CNRS , F-69622 Lyon , France .
| | - Charlotte Vendrely
- ERRMECe , I-MAT FD4122 , Université de Cergy-Pontoise , F-95302 Cergy-Pontoise Cedex , France
| | - Mireille Dumoulin
- Enzymology and Protein Folding , Centre for Protein Engineering , InBIOS , University of Liège , 4000 Liège 1 , Belgium
| | - François Legrand
- Enzymology and Protein Folding , Centre for Protein Engineering , InBIOS , University of Liège , 4000 Liège 1 , Belgium
- Centre de Recherches des Instituts Groupés , Haute Ecole Libre Mosane , Mont Saint-Martin, 41 , 4000 Liège , Belgium
| | - Marcelle Moulin Sallanon
- Radiopharmaceutique Biocliniques (INSERM U1039) , Faculté de Médecine de Grenoble , F-38700 La Tronche , France
| | - Sabine Chierici
- Département de Chimie Moléculaire , Univ. Grenoble Alpes , CNRS , UMR 5250 , F-38000 Grenoble , France
| | - Simona Denti
- Radiopharmaceutique Biocliniques (INSERM U1039) , Faculté de Médecine de Grenoble , F-38700 La Tronche , France
| | - Xavier Dagany
- Institut Lumière Matière , UMR 5306 , Université Claude Bernard Lyon 1 , CNRS , F-69622 Lyon , France .
| | - Philippe Dugourd
- Institut Lumière Matière , UMR 5306 , Université Claude Bernard Lyon 1 , CNRS , F-69622 Lyon , France .
| | - Christel Marquette
- Univ. Grenoble Alpes , CNRS , CEA , BIG/CBM/AFFOND , F-38000 Grenoble , France .
| | - Rodolphe Antoine
- Institut Lumière Matière , UMR 5306 , Université Claude Bernard Lyon 1 , CNRS , F-69622 Lyon , France .
| | - Vincent Forge
- Univ. Grenoble Alpes , CNRS , CEA , BIG/CBM/AFFOND , F-38000 Grenoble , France .
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36
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Abstract
Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.
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37
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Root K, Frey R, Hilvert D, Zenobi R. High‐Mass
MALDI
‐
MS
Analysis for the Investigation of Protein Encapsulation within an Engineered Capsid Forming Protein. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences ETH Zurich CH‐8093 Zurich Switzerland
| | - Raphael Frey
- Department of Chemistry and Applied Biosciences ETH Zurich CH‐8093 Zurich Switzerland
| | - Donald Hilvert
- Department of Chemistry and Applied Biosciences ETH Zurich CH‐8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich CH‐8093 Zurich Switzerland
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38
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From molecular chaperones to membrane motors: through the lens of a mass spectrometrist. Biochem Soc Trans 2017; 45:251-260. [PMID: 28202679 PMCID: PMC5310722 DOI: 10.1042/bst20160395] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 12/25/2022]
Abstract
Twenty-five years ago, we obtained our first mass spectra of molecular chaperones in complex with protein ligands and entered a new field of gas-phase structural biology. It is perhaps now time to pause and reflect, and to ask how many of our initial structure predictions and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made. Moreover, in the light of powerful new electron microscopy methods, what role is there now for MS? In considering these questions, I will give my personal view on progress and problems as well as my predictions for future directions.
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39
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Elliott AG, Harper CC, Lin HW, Susa AC, Xia Z, Williams ER. Simultaneous Measurements of Mass and Collisional Cross-Section of Single Ions with Charge Detection Mass Spectrometry. Anal Chem 2017. [PMID: 28621517 DOI: 10.1021/acs.analchem.7b01675] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The masses and mobilities of single multiply charged ions of cytochrome c, ubiquitin, myoglobin, and bovine serum albumin formed by electrospray ionization are measured using charge detection mass spectrometry (CDMS). Single ions are trapped and repeatedly measured as they oscillate inside an electrostatic ion trap with cone electrodes for up to the maximum trapping time set at 500 ms. The histograms of the many single ion oscillation frequencies have resolved peaks that correspond to the different charge states of each protein. The m/z of each ion is determined from the initial oscillation frequency histogram, and the evolution of the ion energy with time is obtained from the changing frequency. A short-time Fourier transform of the time-domain data indicates that the increase in ion frequency occurs gradually with time with occasional sudden jumps in frequency. The frequency jumps are similar for each protein and may be caused by collision-induced changes in the ion trajectory. The rate of the gradual frequency shift increases with protein mass and charge state. This gradual frequency change is due to ion energy loss from collisions with the background gas. The total energy lost by an ion is determined from the latter frequency shifts normalized to a 500 ms lifetime, and these values increase nearly linearly with measured collisional cross-sections for these protein ions. These results show that the mass and collisional cross-section of single multiply charged ions can be obtained from these CDMS measurements by using proteins with known collisional cross-sections for calibration.
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Affiliation(s)
- Andrew G Elliott
- 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
| | - Haw-Wei Lin
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
| | - Anna C Susa
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
| | - Zijie Xia
- 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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40
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Susa AC, Xia Z, Williams ER. Native Mass Spectrometry from Common Buffers with Salts That Mimic the Extracellular Environment. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Anna C. Susa
- Department of Chemistry; University of California, Berkeley, California; B42 Hildebrand Hall Berkeley CA 94720 USA
| | - Zijie Xia
- Department of Chemistry; University of California, Berkeley, California; B42 Hildebrand Hall Berkeley CA 94720 USA
| | - Evan R. Williams
- Department of Chemistry; University of California, Berkeley, California; B42 Hildebrand Hall Berkeley CA 94720 USA
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41
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Susa AC, Xia Z, Williams ER. Native Mass Spectrometry from Common Buffers with Salts That Mimic the Extracellular Environment. Angew Chem Int Ed Engl 2017; 56:7912-7915. [DOI: 10.1002/anie.201702330] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Anna C. Susa
- Department of Chemistry; University of California, Berkeley, California; B42 Hildebrand Hall Berkeley CA 94720 USA
| | - Zijie Xia
- Department of Chemistry; University of California, Berkeley, California; B42 Hildebrand Hall Berkeley CA 94720 USA
| | - Evan R. Williams
- Department of Chemistry; University of California, Berkeley, California; B42 Hildebrand Hall Berkeley CA 94720 USA
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42
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Keifer DZ, Pierson EE, Jarrold MF. Charge detection mass spectrometry: weighing heavier things. Analyst 2017; 142:1654-1671. [DOI: 10.1039/c7an00277g] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Charge detection mass spectrometry (CDMS) is a single molecule method where the mass of each ion is directly determined from individual measurements of its mass-to-charge ratio and charge.
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Affiliation(s)
| | - Elizabeth E. Pierson
- Department of Analytical Sciences
- Pharmaceutical Sciences and Clinical Supplies
- Merck Research Laboratories
- Merck & Co
- Inc
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