1
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Villafuerte-Vega RC, Li HW, Bergman AE, Slaney TR, Chennamsetty N, Chen G, Tao L, Ruotolo BT. Ion Mobility-Mass Spectrometry and Collision-Induced Unfolding Rapidly Characterize the Structural Polydispersity and Stability of an Fc-Fusion Protein. Anal Chem 2024; 96:10003-10012. [PMID: 38853531 DOI: 10.1021/acs.analchem.4c01408] [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: 06/11/2024]
Abstract
Fc-fusion proteins are an emerging class of protein therapeutics that combine the properties of biological ligands with the unique properties of the fragment crystallizable (Fc) domain of an immunoglobulin G (IgG). Due to their diverse higher-order structures (HOSs), Fc-fusion proteins remain challenging characterization targets within biopharmaceutical pipelines. While high-resolution biophysical tools are available for HOS characterization, they frequently demand extended time frames and substantial quantities of purified samples, rendering them impractical for swiftly screening candidate molecules. Herein, we describe the development of ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) workflows that aim to fill this technology gap, where we focus on probing the HOS of a model Fc-Interleukin-10 (Fc-IL-10) fusion protein engineered using flexible glycine-serine linkers. We evaluate the ability of these techniques to probe the flexibility of Fc-IL-10 in the absence of bulk solvent relative to other proteins of similar size, as well as localize structural changes of low charge state Fc-IL-10 ions to specific Fc and IL-10 unfolding events during CIU. We subsequently apply these tools to probe the local effects of glycine-serine linkers on the HOS and stability of IL-10 homodimer, which is the biologically active form of IL-10. Our data reveals that Fc-IL-10 produces significantly more structural transitions during CIU and broader IM profiles when compared to a wide range of model proteins, indicative of its exceptional structural dynamism. Furthermore, we use a combination of enzymatic approaches to annotate these intricate CIU data and localize specific transitions to the unfolding of domains within Fc-IL-10. Finally, we detect a strong positive, quadratic relationship between average linker mass and fusion protein stability, suggesting a cooperative influence between glycine-serine linkers and overall fusion protein stability. This is the first reported study on the use of IM-MS and CIU to characterize HOS of Fc-fusion proteins, illustrating the practical applicability of this approach.
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Affiliation(s)
| | - Henry W Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Addison E Bergman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas R Slaney
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Naresh Chennamsetty
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Guodong Chen
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Li Tao
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Donnelly RB, Pingali SV, Heroux L, Brinson RG, Wagner NJ, Liu Y. Hydrogen-Deuterium Exchange Dynamics of NISTmAb Measured by Small Angle Neutron Scattering. Mol Pharm 2023; 20:6358-6367. [PMID: 37961914 DOI: 10.1021/acs.molpharmaceut.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Understanding protein dynamics and conformational stability holds great significance in biopharmaceutical research. Hydrogen-deuterium exchange (HDX) is a quantitative methodology used to examine these fundamental properties of proteins. HDX involves measuring the exchange of solvent-accessible hydrogens with deuterium, which yields valuable insights into conformational fluctuations and conformational stability. While mass spectrometry is commonly used to measure HDX on the peptide level, we explore a different approach using small-angle neutron scattering (SANS). In this work, SANS is demonstrated as a complementary and noninvasive HDX method (HDX-SANS). By assessing subtle changes in the tertiary and quaternary structure during the exchange process in deuterated buffer, along with the influence of added electrolytes on protein stability, SANS is validated as a complementary HDX technique. The HDX of a model therapeutic antibody, NISTmAb, an IgG1κ, is monitored by HDX-SANS over many hours using several different formulations, including salts from the Hofmeister series of anions, such as sodium perchlorate, sodium thiocyanate, and sodium sulfate. The impact of these formulation conditions on the thermal stability of NISTmAb is probed by differential scanning calorimetry. The more destabilizing salts led to heightened conformational dynamics in mAb solutions even at temperatures significantly below the denaturation point. HDX-SANS is demonstrated as a sensitive and noninvasive technique for quantifying HDX kinetics directly in mAb solution, providing novel information about mAb conformational fluctuations. Therefore, HDX-SANS holds promise as a potential tool for assessing protein stability in formulation.
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Affiliation(s)
- Róisín B Donnelly
- Department of Biomedical Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Luke Heroux
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland 20850, United States
| | - Norman J Wagner
- Department of Biomedical Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Yun Liu
- Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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3
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Deslignière E, Ollivier S, Beck A, Ropartz D, Rogniaux H, Cianférani S. Benefits and Limitations of High-Resolution Cyclic IM-MS for Conformational Characterization of Native Therapeutic Monoclonal Antibodies. Anal Chem 2023; 95:4162-4171. [PMID: 36780376 DOI: 10.1021/acs.analchem.2c05265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Monoclonal antibodies (mAbs) currently represent the main class of therapeutic proteins. mAbs approved by regulatory agencies are selected from IgG1, IgG2, and IgG4 subclasses, which possess different interchain disulfide connectivities. Ion mobility coupled to native mass spectrometry (IM-MS) has emerged as a valuable approach to tackle the challenging characterization of mAbs' higher order structures. However, due to the limited resolution of first-generation IM-MS instruments, subtle conformational differences on large proteins have long been hard to capture. Recent technological developments have aimed at increasing available IM resolving powers and acquisition mode capabilities, namely, through the release of high-resolution IM-MS (HR-IM-MS) instruments, like cyclic IM-MS (cIM-MS). Here, we outline the advantages and drawbacks of cIM-MS for better conformational characterization of intact mAbs (∼150 kDa) in native conditions compared to first-generation instruments. We first assessed the extent to which multipass cIM-MS experiments could improve the separation of mAbs' conformers. These initial results evidenced some limitations of HR-IM-MS for large native biomolecules which possess rich conformational landscapes that remain challenging to decipher even with higher IM resolving powers. Conversely, for collision-induced unfolding (CIU) approaches, higher resolution proved to be particularly useful (i) to reveal new unfolding states and (ii) to enhance the separation of coexisting activated states, thus allowing one to apprehend gas-phase CIU behaviors of mAbs directly at the intact level. Altogether, this study offers a first panoramic overview of the capabilities of cIM-MS for therapeutic mAbs, paving the way for more widespread HR-IM-MS/CIU characterization of mAb-derived formats.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
| | - Simon Ollivier
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Alain Beck
- IRPF Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois 74160, France
| | - David Ropartz
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Hélène Rogniaux
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
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4
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Sipe SN, Sanders JD, Reinecke T, Clowers BH, Brodbelt JS. Separation and Collision Cross Section Measurements of Protein Complexes Afforded by a Modular Drift Tube Coupled to an Orbitrap Mass Spectrometer. Anal Chem 2022; 94:9434-9441. [PMID: 35736993 PMCID: PMC9302900 DOI: 10.1021/acs.analchem.2c01653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
New developments in analytical technologies and biophysical methods have advanced the characterization of increasingly complex biomolecular assemblies using native mass spectrometry (MS). Ion mobility methods, in particular, have enabled a new dimension of structural information and analysis of proteins, allowing separation of conformations and providing size and shape insights based on collision cross sections (CCSs). Based on the concepts of absorption-mode Fourier transform (aFT) multiplexing ion mobility spectrometry (IMS), here, a modular drift tube design proves capable of separating native-like proteins up to 148 kDa with resolution up to 45. Coupled with high-resolution Orbitrap MS, binding of small ligands and cofactors can be resolved in the mass domain and correlated to changes in structural heterogeneity observed in the ion-neutral CCS distributions. We also demonstrate the ability to rapidly determine accurate CCSs for proteins with 1-min aFT-IMS-MS sweeps without the need for calibrants or correction factors.
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Affiliation(s)
- Sarah N. Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D. Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Tobias Reinecke
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H. Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Vallejo DD, Jeon CK, Parson KF, Herderschee HR, Eschweiler JD, Filoti DI, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals the Structures and Stabilities of Biotherapeutic Antibody Aggregates. Anal Chem 2022; 94:6745-6753. [PMID: 35475624 DOI: 10.1021/acs.analchem.2c00160] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Stability is a key critical quality attribute monitored throughout the development of monoclonal antibody (mAb) therapeutics. Minor changes in their higher order structure (HOS) caused by stress or environment may alter mAb aggregation, immunogenicity, and efficacy. In addition, the structures of the resulting mAb aggregates are largely unknown, as are their dependencies on conditions under which they are created. In this report, we investigate the HOS of mAb monomers and dimers under a variety of forced degradation conditions with ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) technologies. We evaluate two model IgG1 antibodies that differ significantly only in their complementarity-determinant regions: IgG1α and IgG1β. Our data covering both heat- and pH-based forced degradation conditions, aquired on two different IM-MS platforms, show that these mAbs undergo global HOS changes at both monomer and dimer levels upon degradation, but shifts in collision cross section (CCS) differ under pH or heat degradation conditions. In addition, the level of CCS change detected is different between IgG1α and IgG1β, suggesting that differences in the CDR drive differential responses to degradation that influence the antibody HOS. Dramatically different CIU fingerprints are obtained for IgG1α and IgG1β monomers and dimers for both degradation conditions. Finally, we constructed a series of computational models of mAb dimers for comparison with experimental CCS values and found evidence for a compact, overlapped dimer structure under native and heat degradation conditions, possibly adopting an inverted or nonoverlapped quaternary structure when produced through pH degredation. We conclude by discussing the potential impact of our findings on ongoing biotherapeutic discovery and development efforts.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chae Kyung Jeon
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hayley R Herderschee
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Dana I Filoti
- AbbVie, North Chicago, Illinois 60064, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Vallejo DD, Ramírez CR, Parson KF, Han Y, Gadkari VG, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 PMCID: PMC9197173 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D. Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F. Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun G. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Fouque KJD, Garabedian A, Leng F, Tse-Dinh YC, Ridgeway ME, Park MA, Fernandez-Lima F. Trapped Ion Mobility Spectrometry of Native Macromolecular Assemblies. Anal Chem 2021; 93:2933-2941. [PMID: 33492949 PMCID: PMC8327357 DOI: 10.1021/acs.analchem.0c04556] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structural elucidation of native macromolecular assemblies has been a subject of considerable interest in native mass spectrometry (MS), and more recently in tandem with ion mobility spectrometry (IMS-MS), for a better understanding of their biochemical and biophysical functions. In the present work, we describe a new generation trapped ion mobility spectrometer (TIMS), with extended mobility range (K0 = 0.185-1.84 cm2·V-1·s-1), capable of trapping high-molecular-weight (MW) macromolecular assemblies. This compact 4 cm long TIMS analyzer utilizes a convex electrode, quadrupolar geometry with increased pseudopotential penetration in the radial dimension, extending the mobility trapping to high-MW species under native state (i.e., lower charge states). The TIMS capabilities to perform variable scan rate (Sr) mobility measurements over short time (100-500 ms), high-mobility resolution, and ion-neutral collision cross-section (CCSN2) measurements are presented. The trapping capabilities of the convex electrode TIMS geometry and ease of operation over a wide gas flow, rf range, and electric field trapping range are illustrated for the first time using a comprehensive list of standards varying from CsI clusters (n = 6-73), Tuning Mix oligomers (n = 1-5), common proteins (e.g., ubiquitin, cytochrome C, lysozyme, concanavalin (n = 1-4), carbonic anhydrase, β clamp (n = 1-4), topoisomerase IB, bovine serum albumin (n = 1-3), topoisomerase IA, alcohol dehydrogenase), IgG antibody (e.g., avastin), protein-DNA complexes, and macromolecular assemblies (e.g., GroEL and RNA polymerase (n = 1-2)) covering a wide mass (up to m/z 19 000) and CCS range (up to 22 000 Å2 with <0.6% relative standard deviation (RSD)).
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
| | | | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, MA 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, United States
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8
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Larriba-Andaluz C, Prell JS. Fundamentals of ion mobility in the free molecular regime. Interlacing the past, present and future of ion mobility calculations. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1826708] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Carlos Larriba-Andaluz
- Department of Mechanical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - James S. Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
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9
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Campuzano IDG, Nshanian M, Spahr C, Lantz C, Netirojjanakul C, Li H, Wongkongkathep P, Wolff JJ, Loo JA. High Mass Analysis with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: From Inorganic Salt Clusters to Antibody Conjugates and Beyond. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1155-1162. [PMID: 32196330 PMCID: PMC7261417 DOI: 10.1021/jasms.0c00030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Analysis of proteins and complexes under native mass spectrometric (MS) and solution conditions was typically performed using time-of-flight (ToF) analyzers, due to their routine high m/z transmission and detection capabilities. However, over recent years, the ability of Orbitrap-based mass spectrometers to transmit and detect a range of high molecular weight species is well documented. Herein, we describe how a 15 Tesla Fourier transform ion cyclotron resonance mass spectrometer (15 T FT-ICR MS) is more than capable of analyzing a wide range of ions in the high m/z scale (>5000), in both positive and negative instrument polarities, ranging from the inorganic cesium iodide salt clusters; a humanized IgG1k monoclonal antibody (mAb; 148.2 kDa); an IgG1-mertansine drug conjugate (148.5 kDa, drug-to-antibody ratio; DAR 2.26); an IgG1-siRNA conjugate (159.1 kDa; ribonucleic acid to antibody ratio; RAR 1); the membrane protein aquaporin-Z (97.2 kDa) liberated from a C8E4 detergent micelle; the empty MSP1D1-nanodisc (142.5 kDa) and the tetradecameric chaperone protein complex GroEL (806.2 kDa; GroEL dimer at 1.6 MDa). We also investigate different regions of the FT-ICR MS that impact ion transmission and desolvation. Finally, we demonstrate how the transmission of these species and resultant spectra are highly consistent with those previously generated on both quadrupole-ToF (Q-ToF) and Orbitrap instrumentation. This report serves as an impactful example of how FT-ICR mass analyzers are competitive to Q-ToFs and Orbitraps for high mass detection at high m/z.
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Affiliation(s)
| | - Michael Nshanian
- Department of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Christopher Spahr
- Amgen Research, Amgen Inc, Thousand Oaks, California 91320, United States
| | - Carter Lantz
- Department of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | | | - Huilin Li
- Department of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Jeremy J. Wolff
- Bruker Daltonics Inc, Billerica, Massachusetts 01821, United States
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
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10
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Historical, current and future developments of travelling wave ion mobility mass spectrometry: A personal perspective. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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11
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Campuzano IDG, Robinson JH, Hui JO, Shi SDH, Netirojjanakul C, Nshanian M, Egea PF, Lippens JL, Bagal D, Loo JA, Bern M. Native and Denaturing MS Protein Deconvolution for Biopharma: Monoclonal Antibodies and Antibody-Drug Conjugates to Polydisperse Membrane Proteins and Beyond. Anal Chem 2019; 91:9472-9480. [PMID: 31194911 PMCID: PMC6703902 DOI: 10.1021/acs.analchem.9b00062] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a ubiquitously used analytical method applied across multiple departments in biopharma, ranging from early research discovery to process development. Accurate, efficient, and consistent protein MS spectral deconvolution across multiple instrument and detector platforms (time-of-flight, Orbitrap, Fourier-transform ion cyclotron resonance) is essential. When proteins are ionized during the ESI process, a distribution of consecutive multiply charged ions are observed on the m/z scale, either positive [M + nH]n+ or negative [M - nH]n- depending on the ionization polarity. The manual calculation of the neutral molecular weight (MW) of single proteins measured by ESI-MS is simple; however, algorithmic deconvolution is required for more complex protein mixtures to derive accurate MWs. Multiple deconvolution algorithms have evolved over the past two decades, all of which have their advantages and disadvantages, in terms of speed, user-input parameters (or ideally lack thereof), and whether they perform optimally on proteins analyzed under denatured or native-MS and solution conditions. Herein, we describe the utility of a parsimonious deconvolution algorithm (explaining the observed spectra with a minimum number of masses) to process a wide range of highly diverse biopharma relevant and research grade proteins and complexes (PEG-GCSF; an IgG1k; IgG1- and IgG2-biotin covalent conjugates; the membrane protein complex AqpZ; a highly polydisperse empty MSP1D1 nanodisc and the tetradecameric chaperone protein complex GroEL) analyzed under native-MS, denaturing LC-MS, and positive and negative modes of ionization, using multiple instruments and therefore multiple data formats. The implementation of a comb filter and peak sharpening option is also demonstrated to be highly effective for deconvolution of highly polydisperse and enhanced separation of a low level lysine glycation post-translational modification (+162.1 Da), partially processed heavy chain lysine residues (+128.1 Da), and loss of N-acetylglucosamine (GlcNAc; -203.1 Da).
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Affiliation(s)
- Iain D. G. Campuzano
- Amgen Discovery Research, Discovery Attribute Sciences, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - John H. Robinson
- Amgen Discovery Research, Discovery Attribute Sciences, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - John O. Hui
- Amgen Discovery Research, Discovery Attribute Sciences, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Stone D.-H. Shi
- Amgen Discovery Research, Discovery Attribute Sciences, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Chawita Netirojjanakul
- Amgen Discovery Research, Hybrid Modality Engineering, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Michael Nshanian
- University of California-Los Angeles, Dept. Chemistry and Biochemistry, Los Angeles, CA, 90095, USA
| | - Pascal F. Egea
- University of California-Los Angeles, Dept. Biological Chemistry, Los Angeles, CA, USA
| | - Jennifer L. Lippens
- Amgen Discovery Research, Discovery Attribute Sciences, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Dhanashri Bagal
- Amgen Discovery Research, Discovery Attribute Sciences, Veterans Ways, South San Francisco, CA, 94080, USA
| | - Joseph A. Loo
- Amgen Discovery Research, Hybrid Modality Engineering, One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
- University of California-Los Angeles, Dept. Biological Chemistry, Los Angeles, CA, USA
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12
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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: 19] [Impact Index Per Article: 3.8] [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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13
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Vallejo DD, Polasky DA, Kurulugama RT, Eschweiler JD, Fjeldsted JC, Ruotolo BT. A Modified Drift Tube Ion Mobility-Mass Spectrometer for Charge-Multiplexed Collision-Induced Unfolding. Anal Chem 2019; 91:8137-8146. [PMID: 31194508 DOI: 10.1021/acs.analchem.9b00427] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Collision-induced unfolding (CIU) of protein ions and their noncovalent complexes offers relatively rapid access to a rich portfolio of biophysical information, without the need to tag or purify proteins prior to analysis. Such assays have been characterized extensively for a range of therapeutic proteins, proving exquisitely sensitive to alterations in protein sequence, structure, and post-translational modification state. Despite advantages over traditional probes of protein stability, improving the throughput and information content of gas-phase protein unfolding assays remains a challenge for current instrument platforms. In this report, we describe modifications to an Agilent 6560 drift tube ion mobility-mass spectrometer in order to perform robust, simultaneous CIU across all precursor ions detected. This approach dramatically increases the speed associated with typical CIU assays, which typically involve mass selection of narrow m/ z regions prior to collisional activation, and thus their development requires a comprehensive assessment of charge-stripping reactions that can unintentionally pollute CIU data with chemical noise when more than one precursor ion is allowed to undergo simultaneous activation. By studying the unfolding and dissociation of intact antibody ions, a key analyte class associated with biotherapeutics, we reveal a predictive relationship between the precursor charge state, the amount of buffer components bound to the ions of interest, and the amount of charge stripping detected. We then utilize our knowledge of antibody charge stripping to rapidly capture CIU data for a range of antibody subclasses and subtypes across all charge states simultaneously, demonstrating a strong charge state dependence on the information content of CIU. Finally, we demonstrate that CIU data collection times can be further reduced by scanning fewer voltage steps, enabling us to optimize the throughput of our improved CIU methods and confidently differentiate antibody variant ions using ∼20% of the data typically collected during CIU. Taken together, our results characterize a new instrument platform for biotherapeutic stability measurements with dramatically improved throughput and information content.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Daniel A Polasky
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | | | - Joseph D Eschweiler
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States.,AbbVie , North Chicago , Illinois 60064 , United States
| | - John C Fjeldsted
- Agilent Technologies , Santa Clara , California 95051 , United States
| | - Brandon T Ruotolo
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
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14
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Chen X, Raab SA, Poe T, Clemmer DE, Larriba-Andaluz C. Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:905-918. [PMID: 30993642 DOI: 10.1007/s13361-019-02184-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The strong synergy arising from coupling two orthogonal analytical techniques such as ion mobility and mass spectrometry can be used to separate complex mixtures and determine structural information of analytes in the gas phase. A tandem study is performed using two systems with different gases and pressures to ascertain gas-phase conformations of homopolymer ions. Aside from spherical and stretched configurations, intermediate configurations formed by a multiply charged globule and a "bead-on-a-string" appendix are confirmed for polyethylene-glycol (PEG), polycaprolactone (PCL), and polydimethylsiloxane (PDMS). These intermediate configurations are shown to be ubiquitous for all charge states and masses present. For each charge state, configurations evolve in two distinctive patterns: an inverse evolution which occurs as an elementary charge attached to the polymer leaves the larger globule and incorporates itself into the appendage, and a forward evolution which reduces the globule without relinquishing a charge while leaving the appendix relatively constant. Forward evolutions are confirmed to form self-similar family shapes that transcend charge states for all polymers. Identical structural changes occur at the same mass over charge regardless of the system, gas or pressure strongly suggesting that conformations are only contingent on number of charges and chain length, and start arranging once the ion is at least partially ejected from the droplet, supporting a charge extrusion mechanism. Configurational changes are smoother for PDMS which is attributed to the larger steric hindrance caused by protruding pendant groups. This study has implications in the study of the configurational space of more complex homopolymers and heteropolymers. Graphical Abstract.
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Affiliation(s)
- Xi Chen
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA
- Department of Mechanical Engineering, Purdue Universiy, West Lafayette, IN, 47907, USA
| | - Shannon A Raab
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Timothy Poe
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Carlos Larriba-Andaluz
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA.
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15
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Polasky DA, Dixit SM, Fantin SM, Ruotolo BT. CIUSuite 2: Next-Generation Software for the Analysis of Gas-Phase Protein Unfolding Data. Anal Chem 2019; 91:3147-3155. [DOI: 10.1021/acs.analchem.8b05762] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah M. Fantin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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16
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Schiel JE, Turner A. The NISTmAb Reference Material 8671 lifecycle management and quality plan. Anal Bioanal Chem 2018; 410:2067-2078. [PMID: 29430600 PMCID: PMC5830479 DOI: 10.1007/s00216-017-0844-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/07/2017] [Accepted: 12/19/2017] [Indexed: 12/26/2022]
Abstract
Comprehensive analysis of monoclonal antibody therapeutics involves an ever expanding cadre of technologies. Lifecycle-appropriate application of current and emerging techniques requires rigorous testing followed by discussion between industry and regulators in a pre-competitive space, an effort that may be facilitated by a widely available test metric. Biopharmaceutical quality materials, however, are often difficult to access and/or are protected by intellectual property rights. The NISTmAb, humanized IgG1κ Reference Material 8671 (RM 8671), has been established with the intent of filling that void. The NISTmAb embodies the quality and characteristics of a typical biopharmaceutical product, is widely available to the biopharmaceutical community, and is an open innovation tool for development and dissemination of results. The NISTmAb lifecyle management plan described herein provides a hierarchical strategy for maintenance of quality over time through rigorous method qualification detailed in additional submissions in the current publication series. The NISTmAb RM 8671 is a representative monoclonal antibody material and provides a means to continually evaluate current best practices, promote innovative approaches, and inform regulatory paradigms as technology advances. Graphical abstract The NISTmAb Reference Material (RM) 8671 is intended to be an industry standard monoclonal antibody for pre-competitive harmonization of best practices and designing next generation characterization technologies for identity, quality, and stability testing.
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Affiliation(s)
- John E Schiel
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, MD, 20850, USA.
| | - Abigail Turner
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, MD, 20850, USA
- Medimmune, LLC, 55 Watkins Mill Rd, Gaithersburg, MD, 20878, USA
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17
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Dixit SM, Polasky DA, Ruotolo BT. Collision induced unfolding of isolated proteins in the gas phase: past, present, and future. Curr Opin Chem Biol 2018; 42:93-100. [PMID: 29207278 PMCID: PMC5828980 DOI: 10.1016/j.cbpa.2017.11.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/14/2017] [Accepted: 11/19/2017] [Indexed: 01/30/2023]
Abstract
Rapidly characterizing the three-dimensional structures of proteins and the multimeric machines they form remains one of the great challenges facing modern biological and medical sciences. Ion mobility-mass spectrometry based techniques are playing an expanding role in characterizing these functional complexes, especially in drug discovery and development workflows. Despite this expansion, ion mobility-mass spectrometry faces many challenges, especially in the context of detecting small differences in protein tertiary structure that bear functional consequences. Collision induced unfolding is an ion mobility-mass spectrometry method that enables the rapid differentiation of subtly-different protein isoforms based on their unfolding patterns and stabilities. In this review, we summarize the modern implementation of such gas-phase unfolding experiments and provide an overview of recent developments in both methods and applications.
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Affiliation(s)
- Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, United States
| | - Daniel A Polasky
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, United States.
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18
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Ion mobility in the pharmaceutical industry: an established biophysical technique or still niche? Curr Opin Chem Biol 2018; 42:147-159. [DOI: 10.1016/j.cbpa.2017.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
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19
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Campuzano IDG, Netirojjanakul C, Nshanian M, Lippens JL, Kilgour DPA, Van Orden S, Loo JA. Native-MS Analysis of Monoclonal Antibody Conjugates by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2017; 90:745-751. [DOI: 10.1021/acs.analchem.7b03021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Michael Nshanian
- Department
of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California−Los Angeles, Los Angeles, California 90095, United States
| | | | - David P. A. Kilgour
- Department
of Chemistry and Forensics, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
| | - Steve Van Orden
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Joseph A. Loo
- Department
of Chemistry and Biochemistry, and Department of Biological Chemistry, University of California−Los Angeles, Los Angeles, California 90095, United States
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20
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Devine PWA, Fisher HC, Calabrese AN, Whelan F, Higazi DR, Potts JR, Lowe DC, Radford SE, Ashcroft AE. Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1855-1862. [PMID: 28484973 PMCID: PMC5556138 DOI: 10.1007/s13361-017-1689-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.
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Affiliation(s)
- Paul W A Devine
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Henry C Fisher
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fiona Whelan
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Daniel R Higazi
- Ipsen Ltd. UK, Wrexham Industrial Estate, 9 Ash Road North, Wrexham, LL13 9UF, UK
| | | | - David C Lowe
- MedImmune, Sir Aaron Klug Building, Granta Science Park, Cambridge, CB21 6GH, UK
| | - Sheena E Radford
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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