1
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Chen Q, Dai R, Yao X, Chaihu L, Tong W, Huang Y, Wang G. Improving Accuracy in Mass Spectrometry-Based Mass Determination of Intact Heterogeneous Protein Utilizing the Universal Benefits of Charge Reduction and Alternative Gas-Phase Reactions. Anal Chem 2022; 94:13869-13878. [PMID: 36170625 DOI: 10.1021/acs.analchem.2c02586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In mass analysis of proteins, mass spectrometry directly measures the mass to charge ratios of ionized proteins and promises higher accuracy than that of indirect approaches measuring other physicochemical properties, provided that the charge states of detected ions are determined. Accurate mass determination of heterogeneously glycosylated proteins is often hindered by unreliable charge determination due to the insufficient resolution of signals from different charge states and inconsistency among mass profiles of ions in individual charge states. Limited charge reduction of a subpopulation of proteoforms using electron transfer/capture reactions (ETnoD/ETnoD) solves this problem by narrowing the mass distribution of examined proteoforms and preserving the mass profile of the precursor charge state in the reduced charge states. However, the limited availability of ETnoD/ETnoD function in commercial instruments limits the application of this approach. Here, utilizing a range of charge-dependent and accuracy-affecting spectral features revealed by a systematic evaluation at levels of both the ensemble and subpopulation of proteoforms based on theoretical models and experiments, we developed a limited charge reduction workflow that enables using collision-induced dissociation and higher energy collisional dissociation, two widely available reactions, as alternatives to ETnoD/ETnoD while providing adequate accuracy. Alternatively, substituting proton transfer charge reduction for ETnoD/ETnoD provides higher accuracy of mass determination. Performing mass selection in a window-sliding manner improves the accuracy and allows profiling of the whole proteoform distribution. The proposed workflow may facilitate the development of universal characterization strategies for more complex and heterogeneous protein systems.
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Affiliation(s)
- Qingrong Chen
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Rongrong Dai
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaopeng Yao
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Lingxiao Chaihu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Wenjun Tong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yanyi Huang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
| | - Guanbo Wang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
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2
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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3
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Abstract
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Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 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 for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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4
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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5
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Pukala T. Importance of collision cross section measurements by ion mobility mass spectrometry in structural biology. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:72-82. [PMID: 30265417 DOI: 10.1002/rcm.8294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The field of ion mobility mass spectrometry (IM-MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM-MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures.
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Affiliation(s)
- Tara Pukala
- Discipline of Chemistry, University of Adelaide, North Terrace, Adelaide, South Australia, 5005
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6
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Patil AA, Chou SW, Chang PY, Lee CW, Cheng CY, Chu ML, Peng WP. High Mass Ion Detection with Charge Detector Coupled to Rectilinear Ion Trap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1066-1078. [PMID: 27966174 DOI: 10.1007/s13361-016-1548-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Conventional linear ion trap mass analyzers (LIT-MS) provide high ion capacity and show their MS n ability; however, the detection of high mass ions is still challenging because LIT-MS with secondary electron detectors (SED) cannot detect high mass ions. To detect high mass ions, we coupled a charge detector (CD) to a rectilinear ion trap mass spectrometer (RIT-MS). Immunoglobulin G ions (m/z ~150,000) are measured successfully with controlled ion kinetic energy. In addition, when mass-to-charge (m/z) ratios of singly charged ions exceed 10 kTh, the detection efficiency of CD is found to be greater than that of SED. The CD can be coupled to LIT-MS to extend the detection mass range and provide the potential to perform MS n of high mass ions inside the ion trap. Graphical Abstract ᅟ.
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Affiliation(s)
- Avinash A Patil
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Szu-Wei Chou
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
- AcroMass technologies Inc., Hukou, Hsinchu, Taiwan, 30352, Republic of China
| | - Pei-Yu Chang
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Chen-Wei Lee
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Chun-Yen Cheng
- AcroMass technologies Inc., Hukou, Hsinchu, Taiwan, 30352, Republic of China
| | - Ming-Lee Chu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China.
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7
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Lu J, Trnka MJ, Roh SH, Robinson PJJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2141-51. [PMID: 26323614 PMCID: PMC5067139 DOI: 10.1007/s13361-015-1235-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 05/11/2023]
Abstract
Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.
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Affiliation(s)
- Jonathan Lu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Princeton University, Princeton, NJ, 08544, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
| | - Soung-Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Philip J J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Carrie Shiau
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, 94158, USA
| | - Danica Galonic Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
| | - Shenheng Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA.
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94143, USA.
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8
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Quantifying the stabilizing effects of protein-ligand interactions in the gas phase. Nat Commun 2015; 6:8551. [PMID: 26440106 PMCID: PMC4600733 DOI: 10.1038/ncomms9551] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/02/2015] [Indexed: 01/14/2023] Open
Abstract
The effects of protein–ligand interactions on protein stability are typically monitored by a number of established solution-phase assays. Few translate readily to membrane proteins. We have developed an ion-mobility mass spectrometry approach, which discerns ligand binding to both soluble and membrane proteins directly via both changes in mass and ion mobility, and assesses the effects of these interactions on protein stability through measuring resistance to unfolding. Protein unfolding is induced through collisional activation, which causes changes in protein structure and consequently gas-phase mobility. This enables detailed characterization of the ligand-binding effects on the protein with unprecedented sensitivity. Here we describe the method and software required to extract from ion mobility data the parameters that enable a quantitative analysis of individual binding events. This methodology holds great promise for investigating biologically significant interactions between membrane proteins and both drugs and lipids that are recalcitrant to characterization by other means. Relatively few techniques can quantitatively measure the effect of ligands on membrane protein stability. Here the authors demonstrate the use of ion-mobility mass spectrometry to accurately measure and quantify ligand-induced protein stabilization in the gas phase.
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9
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Lermyte F, Williams JP, Brown JM, Martin EM, Sobott F. Extensive Charge Reduction and Dissociation of Intact Protein Complexes Following Electron Transfer on a Quadrupole-Ion Mobility-Time-of-Flight MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1068-76. [PMID: 25862188 DOI: 10.1007/s13361-015-1124-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/25/2015] [Accepted: 03/01/2015] [Indexed: 05/23/2023]
Abstract
Non-dissociative charge reduction, typically considered to be an unwanted side reaction in electron transfer dissociation (ETD) experiments, can be enhanced significantly in order to reduce the charge state of intact protein complexes to as low as 1+ on a commercially available Q-IM-TOF instrument. This allows for the detection of large complexes beyond 100,000 m/z, while at the same time generating top-down ETD fragments, which provide sequence information from surface-exposed parts of the folded structure. Optimization of the supplemental activation has proven to be crucial in these experiments and the charge-reduced species are most likely the product of both proton transfer (PTR) and non-dissociative electron transfer (ETnoD) reactions that occur prior to the ion mobility cell. Applications of this approach range from deconvolution of complex spectra to the manipulation of charge states of gas-phase ions.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
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10
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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11
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Boeri Erba E. Investigating macromolecular complexes using top-down mass spectrometry. Proteomics 2014; 14:1259-70. [PMID: 24723549 DOI: 10.1002/pmic.201300333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 12/25/2022]
Abstract
MS has emerged as an important tool to investigate noncovalent interactions between proteins and various ligands (e.g. other proteins, small molecules, or drugs). In particular, ESI under so-called "native conditions" (a.k.a. "native MS") has considerably expanded the scope of such investigations. For instance, ESI quadrupole time of flight (Q-TOF) instruments have been used to probe the precise stoichiometry of protein assemblies, the interactions between subunits and the position of subunits within the complex (i.e. defining core and peripheral subunits). This review highlights several illustrative native Q-TOF-based investigations and recent seminal contributions of top-down MS (i.e. Fourier transform (FT) MS) to the characterization of noncovalent complexes. Combined top-down and native MS, recently demonstrated in "high-mass modified" orbitrap mass spectrometers, and further improvements needed for the enhanced investigation of biologically significant noncovalent interactions by MS will be discussed.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institute of Structural Biology (Institut de Biologie Structurale), Centre National de la Recherche Scientifique (CNRS), University of Grenoble Alpes (Université de Grenoble Alpes), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), DSV, Grenoble, France
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12
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Snijder J, Heck AJR. Analytical approaches for size and mass analysis of large protein assemblies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:43-64. [PMID: 25014341 DOI: 10.1146/annurev-anchem-071213-020015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Analysis of the size and mass of nanoparticles, whether they are natural biomacromolecular or synthetic supramolecular assemblies, is an important step in the characterization of such molecular species. In recent years, electrospray ionization (ESI) has emerged as a technology through which particles with masses up to 100 MDa can be ionized and transferred into the gas phase, preparing them for accurate mass analysis. Here we review currently used methodologies, with a clear focus on native mass spectrometry (MS). Additional complementary methodologies are also covered, including ion-mobility analysis, nanomechanical mass sensors, and charge-detection MS. The literature discussed clearly demonstrates the great potential of ESI-based methodologies for the size and mass analysis of nanoparticles, including very large naturally occurring protein assemblies. The analytical approaches discussed are powerful tools in not only structural biology, but also nanotechnology.
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Affiliation(s)
- Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands; ,
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13
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Peng WP, Chou SW, Patil AA. Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques. Analyst 2014; 139:3507-23. [DOI: 10.1039/c3an02329j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mass spectrometric techniques can measure the masses and fragments of large biomolecules and bioparticles.
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Affiliation(s)
- Wen-Ping Peng
- Department of Physics
- National Dong Hwa University
- Hualien, Republic of China
| | - Szu-Wei Chou
- Department of Physics
- National Dong Hwa University
- Hualien, Republic of China
| | - Avinash A. Patil
- Department of Physics
- National Dong Hwa University
- Hualien, Republic of China
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14
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Tseng YH, Uetrecht C, Yang SC, Barendregt A, Heck AJR, Peng WP. Game-Theory-Based Search Engine to Automate the Mass Assignment in Complex Native Electrospray Mass Spectra. Anal Chem 2013; 85:11275-83. [DOI: 10.1021/ac401940e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yao-Hsin Tseng
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Charlotte Uetrecht
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Sample
Environment Group, European XFEL GmbH, Notkestraße 85, 22607 Hamburg, Germany
| | - Shih-Chieh Yang
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Arjan Barendregt
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Wen-Ping Peng
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
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15
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Sivalingam GN, Yan J, Sahota H, Thalassinos K. Amphitrite: A program for processing travelling wave ion mobility mass spectrometry data. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 345-347:54-62. [PMID: 25844045 PMCID: PMC4375678 DOI: 10.1016/j.ijms.2012.09.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/04/2012] [Accepted: 09/13/2012] [Indexed: 05/11/2023]
Abstract
Since the introduction of travelling wave (T-Wave)-based ion mobility in 2007 a large number of research laboratories have embraced the technique, particularly those working in the field of structural biology. The development of software to process the data generated from this technique, however, has been limited. We present a novel software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest. A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.
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Affiliation(s)
- Ganesh N. Sivalingam
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Jun Yan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Corresponding author. Tel.: +44 20 7679 2197; fax: +44 20 7679 7193.
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16
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Snijder J, Rose RJ, Veesler D, Johnson JE, Heck AJ. Studying 18 MDa virus assemblies with native mass spectrometry. Angew Chem Int Ed Engl 2013; 52:4020-3. [PMID: 23450509 PMCID: PMC3949431 DOI: 10.1002/anie.201210197] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Rebecca J. Rose
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - David Veesler
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John E. Johnson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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17
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Snijder J, Rose RJ, Veesler D, Johnson JE, Heck AJR. Untersuchung von 18 MDa großen Viruspartikeln mit nativer Massenspektrometrie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Abzalimov RR, Bobst CE, Salinas PA, Savickas P, Thomas JJ, Kaltashov IA. Studies of pH-Dependent Self-Association of a Recombinant Form of Arylsulfatase A with Electrospray Ionization Mass Spectrometry and Size-Exclusion Chromatography. Anal Chem 2013; 85:1591-6. [DOI: 10.1021/ac302829k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Rinat R. Abzalimov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts,
United States
| | - Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts,
United States
| | - Paul A. Salinas
- Pharmaceutical
and Analytical
Development, Shire Human Genetic Therapies, Lexington, Massachusetts, United States
| | - Philip Savickas
- Pharmaceutical
and Analytical
Development, Shire Human Genetic Therapies, Lexington, Massachusetts, United States
| | - John J. Thomas
- Pharmaceutical
and Analytical
Development, Shire Human Genetic Therapies, Lexington, Massachusetts, United States
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts,
United States
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19
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Thompson NJ, Rosati S, Rose RJ, Heck AJR. The impact of mass spectrometry on the study of intact antibodies: from post-translational modifications to structural analysis. Chem Commun (Camb) 2012. [PMID: 23183499 DOI: 10.1039/c2cc36755f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Monoclonal antibodies (mAbs) are important therapeutics, targeting a variety of diseases ranging from cancers to neurodegenerative disorders. In developmental stages and prior to clinical use, these molecules require thorough structural characterisation, but their large size and heterogeneity present challenges for most analytical techniques. Over the past 20 years, mass spectrometry (MS) has transformed from a tool for small molecule analysis to a technique that can be used to study large intact proteins and non-covalent protein complexes. Here, we review several MS-based techniques that have emerged for the analysis of intact mAbs and discuss the prospects of using these technologies for the analysis of biopharmaceuticals.
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Affiliation(s)
- Natalie J Thompson
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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20
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Zhong Y, Hyung SJ, Ruotolo BT. Ion mobility-mass spectrometry for structural proteomics. Expert Rev Proteomics 2012; 9:47-58. [PMID: 22292823 DOI: 10.1586/epr.11.75] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility-mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility-mass spectrometry data with more classical (e.g., 'bottom-up') proteomics approaches for the rapid structural characterization of protein networks.
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Affiliation(s)
- Yueyang Zhong
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
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21
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Morgner N, Robinson CV. Massign: an assignment strategy for maximizing information from the mass spectra of heterogeneous protein assemblies. Anal Chem 2012; 84:2939-48. [PMID: 22409725 DOI: 10.1021/ac300056a] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has evolved into a powerful adjunct for structural biology, helping to unravel the quaternary structure of protein complexes. Increasing interest has led to the study of ever larger multicomponent systems. Investigating these large complexes with ESI has meant that progressively more complicated mass spectra have been recorded. Correct assignment of these spectra is essential to maximize the information content available. Here we present a new assignment strategy and a supporting software package that allows the investigation of large heterogeneous systems, previously beyond the scope of full spectral assignment due to their complexity. The strategy involves two parts. The first includes a peak fitting routine to determine charge state distributions and consequently the masses of the various subcomplexes. The second module distinguishes between solution and gas phase products depending on their mass to charge ratio and assigns these charge states to different subunit combinations. These fitting and assignment routines contain many internal checks for consistency and reveal mass shifts, dependent upon desolvation conditions and small molecule binding. Using a rotary ATPase as a working example, we show how this assignment strategy is capable of determining the stoichiometry and interactions of the 8 different subunits within this 29-subunit assembly.
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Affiliation(s)
- Nina Morgner
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
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