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Oates RN, Lieu LB, Srzentić K, Damoc E, Fornelli L. Characterization of a Monoclonal Antibody by Native and Denaturing Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2197-2208. [PMID: 39105725 DOI: 10.1021/jasms.4c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methods─namely, higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociation─in their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points toward disulfide bonds as the primary reason behind the largely overlapping dissociation patterns.
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Affiliation(s)
- Ryan N Oates
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Linda B Lieu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | - Eugen Damoc
- Thermo Fisher Scientific, Bremen, DE-HB 28199, Germany
| | - Luca Fornelli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
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2
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Borotto NB. The path forward for protein footprinting, covalent labeling, and mass spectrometry-based protein conformational analyses. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5064. [PMID: 38873895 PMCID: PMC11210343 DOI: 10.1002/jms.5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Mass spectrometry-based approaches to assess protein conformation have become widely utilized due to their sensitivity, low sample requirements, and broad applicability to proteins regardless of size and environment. Their wide applicability and sensitivity also make these techniques suitable for the analysis of complex mixtures of proteins, and thus, they have been applied at the cell and even the simple organism levels. These works are impressive, but they predominately employ "bottom-up" workflows and require proteolytic digestion prior to analysis. Once digested, it is not possible to distinguish the proteoform from which any single peptide is derived and therefore, one cannot associate distal-in primary structure-concurrent post-translational modifications (PTMs) or covalent labels, as they would be found on separate peptides. Thus, analyses via bottom-up proteomics report the average PTM status and higher-order structure (HOS) of all existing proteoforms. Second, these works predominately employ promiscuous reagents to probe protein HOS. While this does lead to improved conformational resolution, the formation of many products can divide the signal associated with low-copy number proteins below signal-to-noise thresholds and complicate the bioinformatic analysis of these already challenging systems. In this perspective, I further detail these limitations and discuss the positives and negatives of top-down proteomics as an alternative.
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3
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Hjernø K, Højrup P. Interpretation of Tandem Mass Spectrometry (MS-MS) Spectra for Peptide Analysis. Methods Mol Biol 2024; 2821:91-110. [PMID: 38997483 DOI: 10.1007/978-1-0716-3914-6_8] [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: 07/14/2024]
Abstract
The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines, we will demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus will be on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides.
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Affiliation(s)
- Karin Hjernø
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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4
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Sun R, Qian MG, Zhang X. T and B cell epitope analysis for the immunogenicity evaluation and mitigation of antibody-based therapeutics. MAbs 2024; 16:2324836. [PMID: 38512798 PMCID: PMC10962608 DOI: 10.1080/19420862.2024.2324836] [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] [Received: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The surge in the clinical use of therapeutic antibodies has reshaped the landscape of pharmaceutical therapy for many diseases, including rare and challenging conditions. However, the administration of exogenous biologics could potentially trigger unwanted immune responses such as generation of anti-drug antibodies (ADAs). Real-world experiences have illuminated the clear correlation between the ADA occurrence and unsatisfactory therapeutic outcomes as well as immune-related adverse events. By retrospectively examining research involving immunogenicity analysis, we noticed the growing emphasis on elucidating the immunogenic epitope profiles of antibody-based therapeutics aiming for mechanistic understanding the immunogenicity generation and, ideally, mitigating the risks. As such, we have comprehensively summarized here the progress in both experimental and computational methodologies for the characterization of T and B cell epitopes of therapeutics. Furthermore, the successful practice of epitope-driven deimmunization of biotherapeutics is exceptionally highlighted in this article.
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Affiliation(s)
- Ruoxuan Sun
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Mark G. Qian
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Xiaobin Zhang
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
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5
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Lin Y, Moyle AB, Beaumont VA, Liu LL, Polleck S, Liu H, Shi H, Rouse JC, Kim HY, Zhang Y, Gross ML. Characterization of Higher Order Structural Changes of a Thermally Stressed Monoclonal Antibody via Mass Spectrometry Footprinting and Other Biophysical Approaches. Anal Chem 2023; 95:16840-16849. [PMID: 37933954 PMCID: PMC10909587 DOI: 10.1021/acs.analchem.3c02422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Characterizing changes in the higher order structure (HOS) of monoclonal antibodies upon stressed conditions is critical to gaining a better understanding of the product and process. One single biophysical approach may not be best suited to assess HOS comprehensively; thus, the synergy from multiple, complementary approaches improves characterization accuracy and resolution. In this study, we employed two mass spectrometry (MS )-based footprinting techniques, namely, fast photochemical oxidation of proteins (FPOP)-MS and hydrogen-deuterium exchange (HDX)-MS, supported by dynamic light scattering (DLS), differential scanning calorimetry (DSC), circular dichroism (CD), and nuclear magnetic resonance (NMR) to study changes to the HOS of a mAb upon thermal stress. The biophysical techniques report a nuanced characterization of the HOS in which CD detects no changes to the secondary or tertiary structure, yet DLS measurements show an increase in the hydrodynamic radius. DSC indicates that the stability decreases, and chemical or conformational changes accumulate with incubation time according to NMR. Furthermore, whereas HDX-MS does not indicate HOS changes, FPOP-MS footprinting reveals conformational changes at residue resolution for some amino acids. The local phenomena observed with FPOP-MS indicate that several residues show various patterns of degradation during thermal stress: no change, an increase in solvent exposure, and a biphasic response to solvent exposure. All evidences show that FPOP-MS efficiently resolves subtle structural changes and novel degradation pathways upon thermal stress treatment at residue-level resolution.
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Affiliation(s)
- Yanchun Lin
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Austin B Moyle
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Victor A Beaumont
- Pharmaceutical Sciences Small Molecules, Analytical Research and Development, Pfizer, Inc., Sandwich CT13 9FF, U.K
| | - Lucy L Liu
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Sharon Polleck
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Haijun Liu
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
| | - Heliang Shi
- Global Product Development, Rare Disease Statistics, Pfizer, Inc., New York, New York 10017, United States
| | - Jason C Rouse
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Hai-Young Kim
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Ying Zhang
- Biotherapeutics Pharmaceutical Sciences, Analytical Research and Development, Pfizer, Inc., Andover, Massachusetts 01810, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri 63105, United States
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6
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Kumar S, Savane TS, Rathore AS. Multiattribute Monitoring of Aggregates and Charge Variants of Monoclonal Antibody through Native 2D-SEC-MS-WCX-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37327380 DOI: 10.1021/jasms.2c00325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Monitoring of critical quality attributes such as size and charge-related heterogeneities is essential for biopharmaceutical manufacturers. Size-exclusion chromatography (SEC) is the preferred analytical technique for the quantification of aggregates and fragments in the product, whereas weak-cation exchange chromatography (WCX) is widely used for the characterization of charge variants of biotherapeutic products, in particular monoclonal antibodies (mAbs). Multiattribute monitoring offers the ability to monitor these attributes in a single run flow using two-dimensional liquid chromatography (2D-LC). Typically, in this approach, only the second-dimension samples are directly analyzed through mass spectrometry, as the first dimension has limitations concerning direct coupling with mass spectrometry. In the present study, a novel 2D-SEC-MS/WCX-MS workflow has been proposed, in which chromatography of both dimensions (D1 and D2) was directly coupled with mass spectrometry, through which size-related and charge-related variants of monoclonal antibody mAb A were analyzed simultaneously in their native form. In comparison to stand-alone SEC and WCX methods, this method enables simultaneous analysis of size and charge variants in a single workflow without manual intervention, allowing analysis of low abundant variants. Further, this method has 75% less sample requirement and a shorter analysis time (25 min vs 90 min) when size and charge variants were analyzed individually. The proposed native 2D-LC-MS workflow was used to analyze a stressed sample of mAb A, in which D1 analysis revealed the presence of aggregates (8-20%), which were primarily dimers, whereas D2 analysis showed an increment in acidic variants (9-21%).
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Affiliation(s)
- Sunil Kumar
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Tushar Sharad Savane
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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7
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Haque HME, Mantis NJ, Weis DD. High-Throughput Epitope Mapping by Hydrogen Exchange-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:123-127. [PMID: 36449379 DOI: 10.1021/jasms.2c00255] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In this paper, we introduce a screening protocol for epitope mapping by hydrogen exchange mass spectrometry (HX-MS) that has higher throughput than a traditional HX-MS epitope mapping. In the screening protocol, three HX labeling times (20, 1000, and 86400 s) are each measured without replicates. The experimental protocol is anchored on a single epitope mapping experiment conducted using the traditional complete protocol (five HX times measured in triplicate) that is used to define HX times and define significance limits. Previously, we reported traditional epitope mapping results on the Borrelia burgdorferi outer surface protein A (OspA) antigen that are in excellent agreement with the X-ray crystallography results. Here, we show that the screening protocol and complete HX-MS identify identical epitopes of OspA but that the screening protocol has a 5-fold higher throughput.
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Affiliation(s)
- H M Emranul Haque
- Department of Chemistry, University of Kansas, Lawrence, Kansas66045, United States
| | - Nicholas J Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York12208, United States
| | - David D Weis
- Department of Chemistry, University of Kansas, Lawrence, Kansas66045, United States
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8
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Recent progress in drying technologies for improving the stability and delivery efficiency of biopharmaceuticals. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2023; 53:35-57. [PMID: 36568503 PMCID: PMC9768793 DOI: 10.1007/s40005-022-00610-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Background Most biopharmaceuticals are developed in liquid dosage forms that are less stable than solid forms. To ensure the stability of biopharmaceuticals, it is critical to use an effective drying technique in the presence of an appropriate stabilizing excipient. Various drying techniques are available for this purpose, such as freeze drying or lyophilization, spray drying, spray freeze-drying, supercritical fluid drying, particle replication in nonwetting templates, and fluidized bed drying. Area covered In this review, we discuss drying technologies and their applications in the production of stable solid-state biopharmaceuticals, providing examples of commercially available products or clinical trial formulations. Alongside this, we also review how different analytical methods may be utilized in the evaluation of aerosol performance and powder characteristics of dried protein powders. Finally, we assess the protein integrity in terms of conformational and physicochemical stability and biological activity. Expert opinion With the aim of treating either infectious respiratory diseases or systemic disorders, inhaled biopharmaceuticals reduce both therapeutic dose and cost of therapy. Drying methods in the presence of optimized protein/stabilizer combinations, produce solid dosage forms of proteins with greater stability. A suitable drying method was chosen, and the process parameters were optimized based on the route of protein administration. With the ongoing trend of addressing deficiencies in biopharmaceutical production, developing new methods to replace conventional drying methods, and investigating novel excipients for more efficient stabilizing effects, these products have the potential to dominate the pharmaceutical industry in the future.
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9
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Madren S, Yi L. Microchip electrophoresis separation coupled to mass spectrometry (MCE-MS) for the rapid monitoring of multiple quality attributes of monoclonal antibodies. Electrophoresis 2022; 43:2453-2465. [PMID: 36027045 DOI: 10.1002/elps.202200129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) are highly heterogeneous as a result of posttranslational modifications (PTMs) during bioprocessing and storage. The modifications that impact mAb product quality are regarded as critical quality attributes and require monitoring. The conventional LC-mass spectrometer (MS) method used for product quality monitoring may require protein A purification prior to analysis. In this paper, we present a high-throughput microchip electrophoresis (<4 min) in-line with MS (MCE-MS) that enables baseline separation and characterization of Fc, Fd', and light chain (LC) domains of IdeS-treated mAb sample directly from bioreactor. The NISTmAb was used to optimize the MCE separation and to assess its capability of multiple attribute monitoring. The MCE-MS can uniquely separate and characterize deamidated species at domain level compared to LC-MS method. Two case studies were followed to demonstrate the method capability of monitoring product quality of mAb samples from stability studies or directly from bioreactors.
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Affiliation(s)
- Seth Madren
- Analytical Development Department, Biogen, Research Triangle Park, Durham, North Carolina, USA
| | - Linda Yi
- Analytical Development Department, Biogen, Research Triangle Park, Durham, North Carolina, USA
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10
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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11
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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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12
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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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13
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Legrand P, Dembele O, Alamil H, Lamoureux C, Mignet N, Houzé P, Gahoual R. Structural identification and absolute quantification of monoclonal antibodies in suspected counterfeits using capillary electrophoresis and liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 2022; 414:2699-2712. [PMID: 35099584 PMCID: PMC8802745 DOI: 10.1007/s00216-022-03913-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/09/2022] [Accepted: 01/18/2022] [Indexed: 11/29/2022]
Abstract
Monoclonal antibodies (mAbs) represent a major category of biopharmaceutical products which due to their success as therapeutics have recently experienced the emergence of mAbs originating from different types of trafficking. We report the development of an analytical strategy which enables the structural identification of mAbs in addition to comprehensive characterization and quantification in samples in potentially counterfeit samples. The strategy is based on the concomitant use of capillary zone electrophoresis analysis (CZE-UV), size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS) and liquid chromatography hyphenated to tandem mass spectrometry (LC-MS/MS). This analytical strategy was applied to the investigation of different samples having unknown origins seized by the authorities, and potentially incorporating an IgG 4 or an IgG 1. The results achieved from the different techniques demonstrated to provide orthogonal and complementary information regarding the nature and the structure of the different mAbs. Therefore, they allowed to conclude unequivocally on the identification of the mAbs in the potentially counterfeit samples. Finally, a LC-MS/MS quantification method was developed which specificity was to incorporate a different mAbs labeled with stable isotopes as internal standard. The LC-MS/MS quantification method was validated and thus demonstrated the possibility to use common peptides with the considered IgG in order to achieve limit of quantification as low as 41.4 nM. The quantification method was used to estimate the concentration in the investigated samples using a single type of internal standard and experimental conditions, even in the case of mAbs with no stable isotope labeled homologues available.
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Affiliation(s)
- Pauline Legrand
- Faculté de Sciences Pharmaceutiques et Biologiques, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm U1022, Université de Paris, Paris, France.,Département Recherche Et Développement Pharmaceutique, Agence Générale Des Equipements Et Produits de Santé (AGEPS), Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Oumar Dembele
- Faculté de Sciences Pharmaceutiques et Biologiques, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm U1022, Université de Paris, Paris, France
| | - Héléna Alamil
- Faculté de Sciences Pharmaceutiques et Biologiques, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm U1022, Université de Paris, Paris, France
| | - Catherine Lamoureux
- Service Commun de Laboratoire DGCCRF-DGCCI (SCL), Laboratoire de Paris, Massy, France
| | - Nathalie Mignet
- Faculté de Sciences Pharmaceutiques et Biologiques, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm U1022, Université de Paris, Paris, France
| | - Pascal Houzé
- Faculté de Sciences Pharmaceutiques et Biologiques, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm U1022, Université de Paris, Paris, France.,Laboratoire de Toxicologie Biologique, Hôpital Lariboisière, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Rabah Gahoual
- Faculté de Sciences Pharmaceutiques et Biologiques, Unité de Technologies Chimiques et Biologiques pour la Santé (UTCBS), CNRS UMR8258, Inserm U1022, Université de Paris, Paris, France. .,Unité de Technologies Biologiques Et Chimiques Pour La Santé (UTCBS), Faculté de Pharmacie, Université Paris Descartes, 4, avenue de l'observatoire, 75270, Cedex 06, Paris, France.
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Schick AJ, Lundin V, Low J, Peng K, Vandlen R, Wecksler AT. Epitope mapping of anti-drug antibodies to a clinical candidate bispecific antibody. MAbs 2022; 14:2028337. [PMID: 35072596 PMCID: PMC8794239 DOI: 10.1080/19420862.2022.2028337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Anti-drug antibodies (ADA) can limit the efficacy and safety of therapeutic antibodies. However, determining the exact nature of ADA interactions with the target drug via epitope mapping is challenging due to the polyclonal nature of the IgG response. Here, we demonstrate successful proof-of-concept for the application of hydroxyl radical footprinting (HRF)-mass spectrometry for epitope mapping of ADAs obtained from goats that were administered a knob-into-hole bispecific antibody (BsAb1). Subsequently, we performed epitope mapping of ADAs obtained from cynomolgus (cyno) monkeys that were administered BsAb1 as we described in a recently published paper. Herein, we provide the first data to demonstrate the feasibility of using HRF for ADA epitope mapping, and show that both goat and cyno-derived ADAs specifically target the complementary-determining regions in both arms of BsAb1, suggesting that the ADA epitopes on BsAb1 may be species-independent.
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Affiliation(s)
- Arthur J Schick
- Protein Analytical Chemistry, Genentech Inc, South San Francisco, California, USA
| | - Victor Lundin
- Protein Analytical Chemistry, Genentech Inc, South San Francisco, California, USA
| | - Justin Low
- BioAnalytical Sciences, Genentech Inc, South San Francisco, California, USA
| | - Kun Peng
- BioAnalytical Sciences, Genentech Inc, South San Francisco, California, USA
| | - Richard Vandlen
- Protein Chemistry, Genentech Inc. South San Francisco, California, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech Inc, South San Francisco, California, USA
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15
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Yang W, Ivanov DG, Kaltashov IA. Extending the capabilities of intact-mass analyses to monoclonal immunoglobulins of the E-isotype (IgE). MAbs 2022; 14:2103906. [PMID: 35895856 PMCID: PMC9336480 DOI: 10.1080/19420862.2022.2103906] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mass spectrometry (MS) has become an indispensable tool in structural characterization and quality control of monoclonal antibodies (mAbs). Intact-mass analysis is a particularly attractive option that provides a powerful and cost-effective means to not only confirm the structural integrity of the protein, but also probe its interactions with therapeutic targets. To a certain extent, this success can be attributed to relatively modest glycosylation levels exhibited by IgG molecules, which limits their structural heterogeneity and enables straightforward mass measurements at the intact molecule level. The recent surge of interest in expanding the repertoire of mAbs to include other classes of immunoglobulins places a premium on efforts to adapt the IgG-tailored experimental strategies to other classes of antibodies, but their dramatically higher levels of glycosylation may create insurmountable obstacles. The monoclonal murine IgE antibody explored in this work provides a challenging model system, as its glycosylation level exceeds that of conventional IgG mAbs by a factor of nine. The commercial sample, which included various IgE fragments, yields a poorly resolved ionic signal in intact-mass measurements, from which little useful information can be extracted. However, coupling MS measurements with the limited charge reduction of select polycationic species in the gas phase gives rise to well-defined charge ladders, from which both ionic masses and charges can be readily determined. The measurements reveal significant variation of the extent of glycosylation within intact IgE molecules, as well as the presence of low-molecular weight impurities in the commercial IgE sample. Furthermore, incubation of the monoclonal IgE with its antigen (ovalbumin) gives rise to the formation of complexes with varying stoichiometries, which can also be uniquely identified using a combination of native MS, limited charge reduction in the gas phase and data fitting procedures. This work demonstrates that following appropriate modifications, intact-mass analysis measurements can be successfully applied to mAbs beyond the IgG isotype, providing a wealth of information not only on the mass distribution of the intact IgE molecules, but also their large-scale conformational integrity, the integrity of their covalent structure, and their interactions with antigens.
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Affiliation(s)
- Wenhua Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.,College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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16
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Greisch JF, den Boer MA, Lai SH, Gallagher K, Bondt A, Commandeur J, Heck AJR. Extending Native Top-Down Electron Capture Dissociation to MDa Immunoglobulin Complexes Provides Useful Sequence Tags Covering Their Critical Variable Complementarity-Determining Regions. Anal Chem 2021; 93:16068-16075. [PMID: 34813704 PMCID: PMC8655740 DOI: 10.1021/acs.analchem.1c03740] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Native top-down mass
spectrometry (MS) is gaining traction for
the analysis and sequencing of intact proteins and protein assemblies,
giving access to their mass and composition, as well as sequence information
useful for identification. Herein, we extend and apply native top-down
MS, using electron capture dissociation, to two submillion Da IgM-
and IgG-based oligomeric immunoglobulins. Despite structural similarities,
these two systems are quite different. The ∼895 kDa noncovalent
IgG hexamer consists of six IgG subunits hexamerizing in solution
due to three specifically engineered mutations in the Fc region, whereas
the ∼935 kDa IgM oligomer results from the covalent assembly
of one joining (J) chain and 5 IgM subunits into an asymmetric “pentamer”
stabilized by interchain disulfide bridges. Notwithstanding their
size, structural differences, and complexity, we observe that their
top-down electron capture dissociation spectra are quite similar and
straightforward to interpret, specifically providing informative sequence
tags covering the highly variable CDR3s and FR4s of the Ig subunits
they contain. Moreover, we show that the electron capture dissociation
fragmentation spectra of immunoglobulin oligomers are essentially
identical to those obtained for their respective monomers. Demonstrated
for recombinantly produced systems, the approach described here opens
up new prospects for the characterization and identification of IgMs
circulating in plasma, which is important since IgMs play a critical
role in the early immune response to pathogens such as viruses and
bacteria.
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Affiliation(s)
- Jean-Francois Greisch
- 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
| | - Maurits A den Boer
- 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
| | - Szu-Hsueh Lai
- 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
| | - Kelly Gallagher
- 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 Bondt
- 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
| | - Jan Commandeur
- MSVision, Televisieweg 40, 1322 AM Almere, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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17
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Ban D, Rice CT, McCoy MA. Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments. MAbs 2021; 13:1978132. [PMID: 34612804 PMCID: PMC8496538 DOI: 10.1080/19420862.2021.1978132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Biotherapeutics are an important class of molecules for the treatment of a wide range of diseases. They include low molecular weight peptides, highly engineered protein scaffolds and monoclonal antibodies. During their discovery and development, assessments of the biophysical attributes is critical to understanding the solution behavior of therapeutic proteins and for de-risking liabilities. Thus, methods that can quantify, characterize, and provide a basis to inform risks and drive the selection of more optimal antibody and alternative scaffolds are needed. Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides a means to probe antibody and antibody-like molecules in solution, at atomic resolution, under any formulated conditions. Here, all samples were profiled at natural abundance requiring no isotope enrichment. We present a numerical approach that quantitates two-dimensional methyl spectra. The approach was tested with a reference dataset that contained different types of antibody and antibody-like molecules. This dataset was processed through a procedure we call a Random Sampling of NMR Peaks for Covariance Analysis. This analysis revealed that the first two components were well correlated with the hydrodynamic radius of the molecules included in the reference set. Higher-order principal components were also linked to dynamic features between different tethered antibody-like molecules and contributed to decisions around candidate selection. The reference set provides a basis to characterize molecules with unknown solution behavior and is sensitive to the behavior of a molecule formulated under different conditions. The approach is independent of protein design, scaffold, formulation and provides a facile method to quantify solution behavior.
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Affiliation(s)
- David Ban
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Cory T Rice
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Mark A McCoy
- Department of Computational and Structural Chemistry, Merck & Co., Inc, Kenilworth, NJ, USA
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18
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Sundaria N, Upadhyay A, Prasad A, Prajapati VK, Poluri KM, Mishra A. Neurodegeneration & imperfect ageing: Technological limitations and challenges? Mech Ageing Dev 2021; 200:111574. [PMID: 34562507 DOI: 10.1016/j.mad.2021.111574] [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] [Received: 05/30/2021] [Revised: 08/29/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022]
Abstract
Cellular homeostasis is regulated by the protein quality control (PQC) machinery, comprising multiple chaperones and enzymes. Studies suggest that the loss of the PQC mechanisms in neurons may lead to the formation of abnormal inclusions that may lead to neurological disorders and defective aging. The questions could be raised how protein aggregate formation precisely engenders multifactorial molecular pathomechanism in neuronal cells and affects different brain regions? Such questions await thorough investigation that may help us understand how aberrant proteinaceous bodies lead to neurodegeneration and imperfect aging. However, these studies face multiple technological challenges in utilizing available tools for detailed characterizations of the protein aggregates or amyloids and developing new techniques to understand the biology and pathology of proteopathies. The lack of detection and analysis methods has decelerated the pace of the research in amyloid biology. Here, we address the significance of aggregation and inclusion formation, followed by exploring the evolutionary contribution of these structures. We also provide a detailed overview of current state-of-the-art techniques and advances in studying amyloids in the diseased brain. A comprehensive understanding of the structural, pathological, and clinical characteristics of different types of aggregates (inclusions, fibrils, plaques, etc.) will aid in developing future therapies.
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Affiliation(s)
- Naveen Sundaria
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH‑8 Bandarsindri, Ajmer, Rajasthan, 305817, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India.
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19
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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20
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Zhang Z, Hug C, Tao Y, Bitsch F, Yang Y. Solving Complex Biologics Truncation Problems by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1928-1935. [PMID: 33395284 DOI: 10.1021/jasms.0c00343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With increasing protein therapeutics being designed as non-mAb (non-monoclonal antibody) modalities, additional efforts and resources are required to develop and characterize such therapeutic proteins. Truncation is an emerging issue for manufacturing of non-mAb drug substances and requires sophisticated methods to investigate. In this paper, we describe two cases with complex truncation problems where traditional methods such as intact mass spectrometry led to inclusive or wrong identifications. Therefore, we developed an online top-down LC-MS (liquid chromatography-mass spectrometry) based workflow to study truncated drug substances, and we successfully identified the clipping locations. Compared to other orthogonal methods, this method provides a unique capability of solving protein clipping problems. The successful identification of truncated species and the high compatibility to routine intact MS make it a very valuable tool for resolving truncation problems during protein production in the pharmaceutical industry.
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Affiliation(s)
- Zhe Zhang
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Christian Hug
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Klybeckstrasse 141, CH-4057, Basel, Switzerland
| | - Yuanqi Tao
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Francis Bitsch
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Klybeckstrasse 141, CH-4057, Basel, Switzerland
| | - Yang Yang
- NIBR Biologics Center, Novartis Institutes for BioMedical Research, Klybeckstrasse 141, CH-4057, Basel, Switzerland
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21
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Bobst CE, Sperry J, Friese OV, Kaltashov IA. Simultaneous Evaluation of a Vaccine Component Microheterogeneity and Conformational Integrity Using Native Mass Spectrometry and Limited Charge Reduction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1631-1637. [PMID: 34006091 PMCID: PMC8514165 DOI: 10.1021/jasms.1c00091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Analytical characterization of extensively modified proteins (such as haptenated carrier proteins in synthetic vaccines) remains a challenging task due to the high degree of structural heterogeneity. Native mass spectrometry (MS) combined with limited charge reduction allows these obstacles to be overcome and enables meaningful characterization of a heavily haptenated carrier protein CRM197 (inactivated diphtheria toxin conjugated with nicotine), a major component of a smoking cessation vaccine. The extensive conjugation results in a near-continuum distribution of ionic signal in electrospray ionization (ESI) mass spectra of haptenated CRM197 even after size-exclusion chromatographic fractionation. However, supplementing the ESI MS measurements with limited charge reduction of ionic populations selected within narrow m/z windows gives rise to well-resolved charge ladders, from which both masses and charge states of the ionic species can be readily deduced. Application of this technique to a research-grade material of CRM197/H7 conjugate not only reveals its marginal conformational stability (manifested by the appearance of high charge-density ions in ESI MS) but also establishes a role of the extent of haptenation as a major factor driving the loss of the higher order structure integrity. The unique information provided by native MS used in combination with limited charge reduction provides a strong argument for this technique to become a standard/required tool in the analytical arsenal in the field of biotechnology and biopharmaceutical analysis, where protein conjugates are becoming increasingly common.
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Affiliation(s)
- Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003
| | - Justin Sperry
- BioTherapeutics Pharmaceutical Sciences, Pfizer, St. Louis, MO 63017
| | - Olga V. Friese
- BioTherapeutics Pharmaceutical Sciences, Pfizer, St. Louis, MO 63017
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003
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22
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Filep C, Szigeti M, Farsang R, Haberger M, Reusch D, Guttman A. Multilevel capillary gel electrophoresis characterization of new antibody modalities. Anal Chim Acta 2021; 1166:338492. [PMID: 34023000 DOI: 10.1016/j.aca.2021.338492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 01/06/2023]
Abstract
Capillary gel electrophoresis-based methods were applied to comprehensively characterize two development phase new modality monoclonal antibodies including a glycoengineered and a bispecific test compound. The samples were subjected to multilevel characterization at the intact (both by SDS-SGE and cIEF) as well as the reduced protein and the released N-glycan levels. SDS capillary gel electrophoresis analysis showed excellent separation of the light and heavy chains of both samples. The bispecific antibody required a special temperature gradient denaturation process and a longer capillary to resolve its two light chain fragments. Separation of PNGase F digested antibodies revealed migration time shifts, suggesting the presence of N-linked glycosylation on the corresponding subunits. For efficient glycan removal, the highly glycosylated glycoengineered monoclonal antibody was trypsin digested prior to the endoglycosidase treatment. The released glycans were profiled by capillary gel electrophoresis after APTS labeling and their oligosaccharide structures were identified by exoglycosidase based carbohydrate sequencing. Finally, capillary isoelectric focusing shed light on the charge heterogeneity of the test compounds, providing important complementary information. A flowchart was established for workflow optimization.
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Affiliation(s)
- Csenge Filep
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary.
| | - Marton Szigeti
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary; Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
| | - Robert Farsang
- Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
| | - Markus Haberger
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany.
| | - Dietmar Reusch
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany.
| | - Andras Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, Doctoral School of Molecular Medicine, University of Debrecen, 98 Nagyerdei Krt, H-4032, Debrecen, Hungary; Translational Glycomics Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, H-8200, Veszprem, Hungary.
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23
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Xu X, Hu Q, Liu D, Qiu H, Shameem M, Li N. Characterization of Proteinaceous Particles in Monoclonal Antibody Drug Products Using Mass Spectrometry. J Pharm Sci 2021; 110:3403-3409. [PMID: 34139261 DOI: 10.1016/j.xphs.2021.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/28/2022]
Abstract
In recent years, monoclonal antibodies (mAb) have become one of the most important classes of therapeutic proteins. Among many of the quality attributes monitored and controlled throughout therapeutic antibody development, particulate matter is one of the critical quality attributes (CQAs) for drug products. Visible and subvisible particulates in drug products may pose safety and immunogenicity risks to patients and therefore are tightly controlled and regulated. Characterization of the particle composition in drug products is essential to understand the origin of particulates and their mechanism of formation. In this study, we developed a liquid chromatography-mass spectrometry (LC-MS) based method and integrated it into the typical particulate characterization workflow to identify and quantify the composition of proteinaceous particles isolated from a therapeutic mAb drug product. The LC-MS workflow provides a useful tool to study particle formation and monitor the protein composition of particulates during therapeutic mAb development.
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Affiliation(s)
- Xiaobin Xu
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
| | - Qingyan Hu
- Formulation Development, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Dingjiang Liu
- Formulation Development, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Haibo Qiu
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
| | - Mohammed Shameem
- Formulation Development, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
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24
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Sun Y, Izadi S, Callahan M, Deperalta G, Wecksler AT. Antibody-receptor interactions mediate antibody-dependent cellular cytotoxicity. J Biol Chem 2021; 297:100826. [PMID: 34044019 PMCID: PMC8214220 DOI: 10.1016/j.jbc.2021.100826] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/04/2021] [Accepted: 05/21/2021] [Indexed: 12/20/2022] Open
Abstract
Binding of antibodies to their receptors is a core component of the innate immune system. Understanding the precise interactions between antibodies and their Fc receptors has led to the engineering of novel mAb biotherapeutics with tailored biological activities. One of the most significant findings is that afucosylated monoclonal antibodies demonstrate increased affinity toward the receptor FcγRIIIa, with a commensurate increase in antibody-dependent cellular cytotoxicity. Crystal structure analysis has led to the hypothesis that afucosylation in the Fc region results in reduced steric hindrance between antibody–receptor intermolecular glycan interactions, enhancing receptor affinity; however, solution-phase data have yet to corroborate this hypothesis. In addition, recent work has shown that the fragment antigen-binding (Fab) region may directly interact with Fc receptors; however, the biological consequences of these interactions remain unclear. By probing differences in solvent accessibility between native and afucosylated immunoglobulin G1 (IgG1) using hydroxyl radical footprinting–MS, we provide the first solution-phase evidence that an IgG1 bearing an afucosylated Fc region appears to require fewer conformational changes for FcγRIIIa binding. In addition, we performed extensive molecular dynamics (MD) simulations to understand the molecular mechanism behind the effects of afucosylation. The combination of these techniques provides molecular insight into the steric hindrance from the core Fc fucose in IgG1 and corroborates previously proposed Fab–receptor interactions. Furthermore, MD-guided rational mutagenesis enabled us to demonstrate that Fab–receptor interactions directly contribute to the modulation of antibody-dependent cellular cytotoxicity activity. This work demonstrates that in addition to Fc–polypeptide and glycan-mediated interactions, the Fab provides a third component that influences IgG–Fc receptor biology.
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Affiliation(s)
- Yue Sun
- Protein Analytical Chemistry Department, Genentech Inc, South San Francisco, California, USA
| | - Saeed Izadi
- Pharmaceutical Development Department, Genentech Inc, South San Francisco, California, USA
| | - Matthew Callahan
- Protein Analytical Chemistry Department, Genentech Inc, South San Francisco, California, USA
| | - Galahad Deperalta
- Protein Analytical Chemistry Department, Genentech Inc, South San Francisco, California, USA
| | - Aaron T Wecksler
- Protein Analytical Chemistry Department, Genentech Inc, South San Francisco, California, USA.
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25
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Römer J, Stolz A, Kiessig S, Moritz B, Neusüß C. Online top-down mass spectrometric identification of CE(SDS)-separated antibody fragments by two-dimensional capillary electrophoresis. J Pharm Biomed Anal 2021; 201:114089. [PMID: 33940498 DOI: 10.1016/j.jpba.2021.114089] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/01/2021] [Accepted: 04/19/2021] [Indexed: 12/26/2022]
Abstract
Size heterogeneity analysis by capillary sieving electrophoresis utilizing sodium dodecyl sulfate (CE(SDS)) with optical detection is a major method applied for release and stability testing of monoclonal antibodies (mAbs) in biopharmaceutical applications. Identification of mAb-fragments and impurities observed with CE(SDS) is of outstanding importance for the assessment of critical quality attributes and development of the analytical control system. Mass spectrometric (MS) detection is a powerful tool for protein identification and characterization. Unfortunately, CE(SDS) is incompatible with online MS-hyphenation due to strong ionization suppression of SDS and other separation buffer components. Here, we present a comprehensive platform for full characterization of individual CE(SDS)-separated peaks by CE(SDS)-capillary zone electrophoresis-top-down-MS. The peak of interest is transferred from the first to the second dimension via an 8-port valve to remove MS-incompatible components. Full characterization of mAb byproducts is performed by intact mass determination and fragmentation by electron transfer dissociation, higher-energy collisional dissociation, and ultraviolet photodissociation. This enables online determination of intact mass as well as sequence verification of individual CE(SDS)-separated peaks simultaneously. A more substantiated characterization of unknown CE(SDS) peaks by exact localization of modifications without prior digestion is facilitated. High sensitivity is demonstrated by successful mass and sequence verification of low abundant, unknown CE(SDS) peaks from two stressed mAb samples. Good fragmentation coverages are obtained by MS2, enabling unequivocal identification of these mAb-fragments. Also, the differentiation of reduced/non-reduced intra-protein disulfide bonds is demonstrated. In summary, a reliable and unambiguous online MS2 identification of unknown compounds of low-abundant individual CE(SDS) peaks is enabled.
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Affiliation(s)
- Jennifer Römer
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany; Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Regensburg, Germany
| | - Alexander Stolz
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany; Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University, Jena, Germany
| | - Steffen Kiessig
- F. Hoffmann-La Roche Ltd, Grenzacherstraße 124, 4070, Basel, Switzerland
| | - Bernd Moritz
- F. Hoffmann-La Roche Ltd, Grenzacherstraße 124, 4070, Basel, Switzerland
| | - Christian Neusüß
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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26
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Sun H, Ma L, Wang L, Xiao P, Li H, Zhou M, Song D. Research advances in hydrogen-deuterium exchange mass spectrometry for protein epitope mapping. Anal Bioanal Chem 2021; 413:2345-2359. [PMID: 33404742 DOI: 10.1007/s00216-020-03091-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/01/2022]
Abstract
With the development of biomedical technology, epitope mapping of proteins has become critical for developing and evaluating new protein drugs. The application of hydrogen-deuterium exchange for protein epitope mapping holds great potential. Although several reviews addressed the hydrogen-deuterium exchange, to date, only a few systematic reviews have focused on epitope mapping using this technology. Here, we introduce the basic principles, development history, and review research progress in hydrogen-deuterium exchange epitope mapping technology and discuss its advantages. We summarize the main hurdles in applying hydrogen-deuterium exchange epitope mapping technology, combined with relevant examples to provide specific solutions. We describe the epitope mapping of virus assemblies, disease-associated proteins, and polyclonal antibodies as examples of pattern introduction. Finally, we discuss the outlook of hydrogen-deuterium exchange epitope mapping technology. This review will help researchers studying protein epitopes to gain a more comprehensive understanding of this technology.
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Affiliation(s)
- Haofeng Sun
- National Institute of Metrology, Beijing, 100029, China
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lingyun Ma
- National Institute of Metrology, Beijing, 100029, China
| | - Leyu Wang
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peng Xiao
- National Institute of Metrology, Beijing, 100029, China
| | - Hongmei Li
- National Institute of Metrology, Beijing, 100029, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China.
| | - Dewei Song
- National Institute of Metrology, Beijing, 100029, China.
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27
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Camperi J, Goyon A, Guillarme D, Zhang K, Stella C. Multi-dimensional LC-MS: the next generation characterization of antibody-based therapeutics by unified online bottom-up, middle-up and intact approaches. Analyst 2021; 146:747-769. [DOI: 10.1039/d0an01963a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review presents an overview of current analytical trends in antibody characterization by multidimensional LC-MS approaches.
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Affiliation(s)
- Julien Camperi
- Department of Protein Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Alexandre Goyon
- Department of Small Molecule Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Davy Guillarme
- School of Pharmaceutical Sciences
- University of Geneva
- 1206 Geneva
- Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO)
| | - Kelly Zhang
- Department of Small Molecule Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
| | - Cinzia Stella
- Department of Protein Analytical Chemistry
- Genentech Inc
- South San Francisco
- USA
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28
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Habazin S, Štambuk J, Šimunović J, Keser T, Razdorov G, Novokmet M. Mass Spectrometry-Based Methods for Immunoglobulin G N-Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:73-135. [PMID: 34687008 DOI: 10.1007/978-3-030-76912-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. Boost in immunoglobulin G (IgG) glycan and glycopeptide profiling demands for both applied biomedical and research applications has brought many new advances in the field in terms of technical innovations, sample preparation, improved throughput, and confidence in glycan structural characterization. This chapter summarizes mass spectrometry basics, focusing on IgG and monoclonal antibody N-glycosylation analysis on several complexity levels. Different approaches, including antibody enrichment, glycan release, labeling, and glycopeptide preparation and purification, are covered and illustrated with recent breakthroughs and examples from the literature omitting excessive theoretical frameworks. Finally, selected highly popular methodologies in IgG glycoanalytics such as liquid chromatography-mass spectrometry and matrix-assisted laser desorption ionization are discussed more thoroughly yet in simple terms making this text a practical starting point either for the beginner in the field or an experienced clinician trying to make sense out of the IgG glycomic or glycoproteomic dataset.
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Affiliation(s)
- Siniša Habazin
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Jerko Štambuk
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | - Mislav Novokmet
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia.
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29
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Glycoproteomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:413-434. [PMID: 33205259 DOI: 10.1007/10_2020_144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Glycosylation is a key factor determining the pharmacological properties of biotherapeutics, including their stability, solubility, bioavailability, pharmacokinetics, and immunogenicity. As such, comprehensive information about glycosylation of biotherapeutics is critical to demonstrate similarity. Regulatory agencies also require extensive documentation of the comprehensive analyses of glycosylation-related critical quality attributes (CQAs) during the development, manufacturing, and release of biosimilars. Mass spectrometry has catalysed tremendous advancements in the characterisation of glycosylation CQAs of biotherapeutics. Here we provide a perspective overview on the MS-based technologies relevant for biotherapeutic product characterisation with an emphasis on the recent developments that allow determination of glycosylation features such as site of glycosylation, sialic acid linkage, glycan structure, and content.
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30
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Gstöttner C, Nicolardi S, Haberger M, Reusch D, Wuhrer M, Domínguez-Vega E. Intact and subunit-specific analysis of bispecific antibodies by sheathless CE-MS. Anal Chim Acta 2020; 1134:18-27. [DOI: 10.1016/j.aca.2020.07.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/18/2020] [Accepted: 07/27/2020] [Indexed: 01/15/2023]
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31
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Lodge JM, Schauer KL, Brademan DR, Riley NM, Shishkova E, Westphall MS, Coon JJ. Top-Down Characterization of an Intact Monoclonal Antibody Using Activated Ion Electron Transfer Dissociation. Anal Chem 2020; 92:10246-10251. [PMID: 32608969 DOI: 10.1021/acs.analchem.0c00705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Monoclonal antibodies (mAbs) are important therapeutic glycoproteins, but their large size and structural complexity make them difficult to rapidly characterize. Top-down mass spectrometry (MS) has the potential to overcome challenges of other common approaches by minimizing sample preparation and preserving endogenous modifications. However, comprehensive mAb characterization requires generation of many, well-resolved fragments and remains challenging. While ETD retains modifications and cleaves disulfide bonds-making it attractive for mAb characterization-it can be less effective for precursors having high m/z values. Activated ion electron transfer dissociation (AI-ETD) uses concurrent infrared photoactivation to promote product ion generation and has proven effective in increasing sequence coverage of intact proteins. Here, we present the first application of AI-ETD to mAb sequencing. For the standard NIST mAb, we observe a high degree of complementarity between fragments generated using standard ETD with a short reaction time and AI-ETD with a long reaction time. Most importantly, AI-ETD reveals disulfide-bound regions that have been intractable, thus far, for sequencing with top-down MS. We conclude AI-ETD has the potential to rapidly and comprehensively analyze intact mAbs.
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32
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Limpikirati PK, Zhao B, Pan X, Eyles SJ, Vachet RW. Covalent Labeling/Mass Spectrometry of Monoclonal Antibodies with Diethylpyrocarbonate: Reaction Kinetics for Ensuring Protein Structural Integrity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1223-1232. [PMID: 32310649 PMCID: PMC7370534 DOI: 10.1021/jasms.0c00067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Diethylpyrocarbonate (DEPC)-based covalent labeling together with mass spectrometry is a promising tool for the higher-order structural analysis of antibody therapeutics. Reliable information about antibody higher-order structure can be obtained, though, only when the protein's structural integrity is preserved during labeling. In this work, we have evaluated the applicability of DEPC reaction kinetics for ensuring the structural integrity of monoclonal antibodies (mAbs) during labeling. By monitoring the modification extent of selected proteolytic fragments as a function of DEPC concentration, we find that a common DEPC concentration can be used for different monoclonal antibodies in formulated samples without perturbing their higher-order structure. Under these labeling conditions, we find that the antibodies can accommodate up to four DEPC modifications without being structurally perturbed, indicating that multidomain proteins can withstand more than one label, which contrasts to previously studied single-domain proteins. This more extensive labeling provides a more sensitive measure of structure, making DEPC-based covalent labeling-mass spectrometry suitable for the higher-order structural analyses of mAbs.
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Affiliation(s)
- Patanachai K. Limpikirati
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bo Zhao
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Xiao Pan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Corresponding author, Phone: (413) 545-2733 (R.W.V.)
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33
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Analytical challenges and advancements in bioanalysis of therapeutic proteins. Bioanalysis 2020; 12:207-209. [DOI: 10.4155/bio-2020-0006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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34
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Shi RL, Xiao G, Dillon TM, Ricci MS, Bondarenko PV. Characterization of therapeutic proteins by cation exchange chromatography-mass spectrometry and top-down analysis. MAbs 2020; 12:1739825. [PMID: 32292112 PMCID: PMC7188404 DOI: 10.1080/19420862.2020.1739825] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 01/10/2023] Open
Abstract
Recently, cation exchange chromatography (CEX) using aqueous volatile buffers was directly coupled with mass spectrometry (MS) and applied for intact analysis of therapeutic proteins and antibodies. In our study, chemical modifications responsible for charge variants were identified by CEX-UV-MS for a monoclonal antibody (mAb), a bispecific antibody, and an Fc-fusion protein. We also report post-CEX column addition of organic solvent and acid followed by mixing at elevated temperatures, which unfolded proteins, increased ion intensity (sensitivity) and facilitated top-down analysis. mAb stressed by hydrogen peroxide oxidation was used as a model system, which produced additional CEX peaks. The on-line CEX-UV-MS top-down analysis produced gas-phase fragments containing one or two methionine residues. Oxidation of some methionine residues contributed to earlier (acidic), some to later (basic) eluting peaks, while oxidation of other residues did not change CEX elution. The abundance of the oxidized and non-oxidized fragment ions also allowed estimation of the oxidation percentage of different methionine residues in stressed mAb. CEX-UV-MS measurement revealed a new intact antibody proteoform at 5% that eluted as a basic peak and included paired modifications: high-mannose glycosylation and remaining C-terminal lysine residue (M5/M5 + K). This finding was confirmed by peptide mapping and on-column disulfide reduction coupled with reversed-phase liquid chromatography - top-down MS analysis of the collected basic peak. Overall, our results demonstrate the utility of the on-line method in providing site-specific structural information of charge modifications without fraction collection and laborious peptide mapping.
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Affiliation(s)
- Rachel Liuqing Shi
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Gang Xiao
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Thomas M. Dillon
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Margaret S. Ricci
- Attribute Sciences, Process Development, Amgen Inc., Thousand Oaks, CA, USA
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35
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Machiesky L, Côté O, Kirkegaard LH, Mefferd SC, Larkin C. A rapid lateral flow immunoassay for identity testing of biotherapeutics. J Immunol Methods 2019; 474:112666. [DOI: 10.1016/j.jim.2019.112666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022]
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36
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Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions. Amino Acids 2019; 51:1409-1431. [DOI: 10.1007/s00726-019-02787-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/07/2019] [Indexed: 12/12/2022]
Abstract
AbstractPeptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.
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37
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Reader PP, Olkhov RV, Reeksting S, Lubben A, Hyde CJ, Shaw AM. A rapid and quantitative technique for assessing IgG monomeric purity, calibrated with the NISTmAb reference material. Anal Bioanal Chem 2019; 411:6487-6496. [PMID: 31375854 PMCID: PMC6718376 DOI: 10.1007/s00216-019-02029-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/19/2019] [Accepted: 07/10/2019] [Indexed: 11/28/2022]
Abstract
The fraction of intact monomer in a sample (moles/moles), the monomeric purity, is measured as a quality control in therapeutic monoclonal antibodies but is often unknown in research samples and remains a major source of variation in quantitative antibody-based techniques such as immunoassay development. Here, we describe a novel multiplex technique for estimating the monomeric purity and antigen affinity of research grade antibody samples. Light scattering was used to simultaneously observe the mass of antibody binding to biosensor surfaces functionalised with antigen (revealing Fab binding kinetics) or protein A/G (PAG). Initial estimates of monomeric purity in 7 antibody samples including a therapeutic infliximab biosimilar were estimated by observing a mass deficit on the PAG surface compared to the NISTmAb standard of high monomeric purity. Monomeric purity estimates were improved in a second step by observing the mass of antigen binding to the mass of antibody on the PAG surface. The NISTmAb and infliximab biosimilar displayed tightly controlled stoichiometries for antigen binding of 1.31 ± 0.57 and 1.71 ± 0.16 (95% confidence interval)—within the theoretical limit of 1–2 antigens per antibody depending on avidity. The other antibodies in the panel displayed antigen binding stoichiometries in the range 0.06–1.15, attributed to lower monomeric purity. The monomeric purity estimates were verified by electrospray ionization mass spectrometry (ESI), the gold standard technique for structural characterization of antibodies. ESI data indicated that the NISTmAb and infliximab biosimilar samples had monomeric purity values of 93.5% and 94.7%, respectively, whilst the research grade samples were significantly lower (54–89%). Our results demonstrate rapid quality control testing for monomeric purity of antibody samples (< 15 min) which could improve the reproducibility of antibody-based experiments.
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Affiliation(s)
- Peter P Reader
- University of Exeter Medical School, Heavitree Road, Exeter, EX1 2LU, UK.,College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Rouslan V Olkhov
- College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Shaun Reeksting
- Chemical Characterisation and Analysis Facility, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Anneke Lubben
- Chemical Characterisation and Analysis Facility, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Christopher J Hyde
- University of Exeter Medical School, Heavitree Road, Exeter, EX1 2LU, UK
| | - Andrew M Shaw
- College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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38
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Schachner LF, Ives AN, McGee JP, Melani RD, Kafader JO, Compton PD, Patrie SM, Kelleher NL. Standard Proteoforms and Their Complexes for Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1190-1198. [PMID: 30963455 PMCID: PMC6592724 DOI: 10.1007/s13361-019-02191-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 05/09/2023]
Abstract
Native mass spectrometry (nMS) is a technique growing at the interface of analytical chemistry, structural biology, and proteomics that enables the detection and partial characterization of non-covalent protein assemblies. Currently, the standardization and dissemination of nMS is hampered by technical challenges associated with instrument operation, benchmarking, and optimization over time. Here, we provide a standard operating procedure for acquiring high-quality native mass spectra of 30-300 kDa proteins using an Orbitrap mass spectrometer. By describing reproducible sample preparation, loading, ionization, and nMS analysis, we forward two proteoforms and three complexes as possible standards to advance training and longitudinal assessment of instrument performance. Spectral data for five standards can guide assessment of instrument parameters, data production, and data analysis. By introducing this set of standards and protocols, we aim to help normalize native mass spectrometry practices across labs and provide benchmarks for reproducibility and high-quality data production in the years ahead. Graphical abstract.
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Affiliation(s)
- Luis F Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Ashley N Ives
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Steven M Patrie
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA.
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39
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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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40
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Morsa D, Baiwir D, La Rocca R, Zimmerman TA, Hanozin E, Grifnée E, Longuespée R, Meuwis MA, Smargiasso N, Pauw ED, Mazzucchelli G. Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics? J Proteome Res 2019; 18:2501-2513. [DOI: 10.1021/acs.jproteome.9b00044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Morsa
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Tyler A. Zimmerman
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Rémi Longuespée
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Marie-Alice Meuwis
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU, Liege 4000, Belgium
- Laboratory of Translational Gastroenterology, GIGA, Liege 4000, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
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41
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Shi L, Gross ML. Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry. Protein Pept Lett 2019; 26:27-34. [PMID: 30484399 DOI: 10.2174/0929866526666181128124554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 09/27/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Determination of the composition and some structural features of macromolecules can be achieved by using structural proteomics approaches coupled with mass spectrometry (MS). One approach is hydroxyl radical protein footprinting whereby amino-acid side chains are modified with reactive reagents to modify irreversibly a protein side chain. The outcomes, when deciphered with mass-spectrometry-based proteomics, can increase our knowledge of structure, assembly, and conformational dynamics of macromolecules in solution. Generating the hydroxyl radicals by laser irradiation, Hambly and Gross developed the approach of Fast Photochemical Oxidation of Proteins (FPOP), which labels proteins on the sub millisecond time scale and provides, with MS analysis, deeper understanding of protein structure and protein-ligand and protein- protein interactions. This review highlights the fundamentals of FPOP and provides descriptions of hydroxyl-radical and other radical and carbene generation, of the hydroxyl labeling of proteins, and of determination of protein modification sites. We also summarize some recent applications of FPOP coupled with MS in protein footprinting. CONCLUSION We survey results that show the capability of FPOP for qualitatively measuring protein solvent accessibility on the residue level. To make these approaches more valuable, we describe recent method developments that increase FPOP's quantitative capacity and increase the spatial protein sequence coverage. To improve FPOP further, several new labeling reagents including carbenes and other radicals have been developed. These growing improvements will allow oxidative- footprinting methods coupled with MS to play an increasingly significant role in determining the structure and dynamics of macromolecules and their assemblies.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
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Beck A, D’Atri V, Ehkirch A, Fekete S, Hernandez-Alba O, Gahoual R, Leize-Wagner E, François Y, Guillarme D, Cianférani S. Cutting-edge multi-level analytical and structural characterization of antibody-drug conjugates: present and future. Expert Rev Proteomics 2019; 16:337-362. [DOI: 10.1080/14789450.2019.1578215] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alain Beck
- Biologics CMC and Developability, IRPF - Centre d’Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Valentina D’Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Geneva, Switzerland
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
| | - Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Geneva, Switzerland
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
| | - Rabah Gahoual
- Unité de Technologies Biologiques et Chimiques pour la Santé (UTCBS), Paris 5-CNRS UMR8258 Inserm U1022, Faculté de Pharmacie, Université Paris Descartes, Paris, France
| | - Emmanuel Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140, Université de Strasbourg, CNRS, Strasbourg, France
| | - Yannis François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- Biologics CMC and Developability, IRPF - Centre d’Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
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Shi L, Liu T, Gross ML, Huang Y. Recognition of Human IgG1 by Fcγ Receptors: Structural Insights from Hydrogen-Deuterium Exchange and Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry. Biochemistry 2019; 58:1074-1080. [PMID: 30666863 DOI: 10.1021/acs.biochem.8b01048] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antibody-dependent cell-mediated cytotoxicity (ADCC) is an effector function of immunoglobulins (IgGs) involved in the killing of target cells by a cytotoxic effector cell. Recognition of IgG by Fc receptors expressed on natural killer cells, mostly FcγIII receptors (FcγRIII), underpins the ADCC mechanism, thus motivating investigations of these interactions. In this paper, we describe the combination of hydrogen-deuterium exchange and fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry to study the interactions of the human IgG1/FcγRIII complex. Using these orthogonal approaches, we identified critical peptide regions and residues involved in the recognition of IgG1 by FcγRIII. The footprinting results are consistent with the previously published crystal structure of the IgG1 Fc/FcγRIII complex. Additionally, our FPOP results reveal the conformational changes in the Fab domain upon binding of the Fc domain to FcγRIII. These data demonstrate the value of footprinting as part of a comprehensive toolbox for identifying the changes in the higher-order structure of therapeutic antibodies in solution.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry , Washington University in St. Louis , Campus Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Tun Liu
- Bioproduct Research and Development, Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | - Michael L Gross
- Department of Chemistry , Washington University in St. Louis , Campus Box 1134, One Brookings Drive , St. Louis , Missouri 63130 , United States
| | - Yining Huang
- Bioproduct Research and Development, Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
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Guerra A, von Stosch M, Glassey J. Toward biotherapeutic product real-time quality monitoring. Crit Rev Biotechnol 2019; 39:289-305. [DOI: 10.1080/07388551.2018.1524362] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- André Guerra
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Moritz von Stosch
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jarka Glassey
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne, United Kingdom
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van der Burgt YEM, Kilgour DPA, Tsybin YO, Srzentić K, Fornelli L, Beck A, Wuhrer M, Nicolardi S. Structural Analysis of Monoclonal Antibodies by Ultrahigh Resolution MALDI In-Source Decay FT-ICR Mass Spectrometry. Anal Chem 2019; 91:2079-2085. [PMID: 30571088 PMCID: PMC6365908 DOI: 10.1021/acs.analchem.8b04515] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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The
emergence of complex protein therapeutics in general and monoclonal
antibodies (mAbs) in particular have stimulated analytical chemists
to develop new methods and strategies for their structural characterization.
Mass spectrometry plays a key role in providing information on the
primary amino acid sequence, post-translational modifications, and
other structure characteristics that must be monitored during the
manufacturing process and subsequent quality control assessment. In
this study, we present a novel method that allows structural characterization
of mAbs based on MALDI in-source decay (ISD) fragmentation, coupled
with Fourier transform ion cyclotron resonance (FT-ICR) MS. The method
benefits from higher resolution of absorption mode FT mass spectra,
compared to magnitude mode, which enables simultaneous identification
of ISD fragments from both the heavy and light chains with a higher
confidence in a wide mass range up to m/z 13 500. This method was applied to two standard mAbs, namely
NIST mAb and trastuzumab, in preparation for method application in
an interlaboratory study on mAbs structural analysis coordinated by
the Consortium for Top-Down Proteomics. Extensive sequence coverage
was obtained from the middle-down analysis (IdeS- and GingisKHAN-digested
mAbs) that complemented the top-down analysis of intact mAbs. In addition,
MALDI FT-ICR MS of IdeS-digested mAbs allowed isotopic-level profiling
of proteoforms with regard to heavy chain N-glycosylation.
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Affiliation(s)
- Yuri E M van der Burgt
- Center for Proteomics and Metabolomics , Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC , Leiden , The Netherlands
| | - David P A Kilgour
- Department of Chemistry , Nottingham Trent University , Nottingham , NG11 0JN , U.K
| | - Yury O Tsybin
- Spectroswiss , EPFL Innovation Park , 1015 Lausanne , Switzerland
| | - Kristina Srzentić
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 N. Sheridan Road , Evanston , Illinois 60208 , United States
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence , Northwestern University , 2145 N. Sheridan Road , Evanston , Illinois 60208 , United States
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre , 74160 St. Julien-en-Genevois , France
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics , Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC , Leiden , The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics , Leiden University Medical Center (LUMC) , PO Box 9600, 2300 RC , Leiden , The Netherlands
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Intact Mass Spectrometry Analysis of Immuno-Isolated Human Therapeutic Antibodies from Serum. Methods Mol Biol 2019; 2024:153-166. [PMID: 31364048 DOI: 10.1007/978-1-4939-9597-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antibody-based therapeutics have emerged as novel class of biopharmaceuticals over the last couple of decades with the advancements made in production and downstream processing technologies. The structural diversity of therapeutic antibodies has also evolved with the development of bispecific (and multispecific) antibodies and antibody-drug conjugates. With increased structural complexities and multi-modularity, there is a need to demonstrate that the entire structure is stable in vivo and arriving at its target site in an intact form. Proving that antibodies reach their target site unscathed is a challenging but essential step for showing effective delivery as well as showing whether failure in efficacy (if any) was related to its in vivo instability. This chapter describes a method for highly specific immuno-isolation followed by intact mass spectrometry of human Fc-containing antibody from serum of rats dosed with the antibody. The method provides an opportunity for evaluating antibody stability in the physiological environment by providing accurate validation of its molecular mass in vivo, as well as the potential to identify breakdown products.
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Rafalik M, Spodzieja M, Kołodziejczyk A, Rodziewicz-Motowidło S, Szymańska A, Grubb A, Czaplewska P. The identification of discontinuous epitope in the human cystatin C – Monoclonal antibody HCC3 complex. J Proteomics 2019; 191:58-67. [DOI: 10.1016/j.jprot.2018.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/26/2018] [Accepted: 04/14/2018] [Indexed: 11/15/2022]
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48
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Jin Y, Lin Z, Xu Q, Fu C, Zhang Z, Zhang Q, Pritts WA, Ge Y. Comprehensive characterization of monoclonal antibody by Fourier transform ion cyclotron resonance mass spectrometry. MAbs 2019; 11:106-115. [PMID: 30230956 PMCID: PMC6343775 DOI: 10.1080/19420862.2018.1525253] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
The pharmaceutical industry's interest in monoclonal antibodies (mAbs) and their derivatives has spurred rapid growth in the commercial and clinical pipeline of these effective therapeutics. The complex micro-heterogeneity of mAbs requires in-depth structural characterization for critical quality attribute assessment and quality assurance. Currently, mass spectrometry (MS)-based methods are the gold standard in mAb analysis, primarily with a bottom-up approach in which immunoglobulins G (IgGs) and their variants are digested into peptides to facilitate the analysis. Comprehensive characterization of IgGs and the micro-variants remains challenging at the proteoform level. Here, we used both top-down and middle-down MS for in-depth characterization of a human IgG1 using ultra-high resolution Fourier transform MS. Our top-down MS analysis provided characteristic fingerprinting of the IgG1 proteoforms at unit mass resolution. Subsequently, the tandem MS analysis of intact IgG1 enabled the detailed sequence characterization of a representative IgG1 proteoform at the intact protein level. Moreover, we used the middle-down MS analysis to characterize the primary glycoforms and micro-variants. Micro-variants such as low-abundance glycoforms, C-terminal glycine clipping, and C-terminal proline amidation were characterized with bond cleavages higher than 44% at the subunit level. By combining top-down and middle-down analysis, 76% of bond cleavage (509/666 amino acid bond cleaved) of IgG1 was achieved. Taken together, we demonstrated the combination of top-down and middle-down MS as powerful tools in the comprehensive characterization of mAbs.
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Affiliation(s)
- Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ziqing Lin
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Qingge Xu
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cexiong Fu
- Process Analytical, AbbVie Inc, North Chicago, Illinois, USA
| | - Zhaorui Zhang
- Process Analytical, AbbVie Inc, North Chicago, Illinois, USA
| | - Qunying Zhang
- Process Analytical, AbbVie Inc, North Chicago, Illinois, USA
| | - Wayne A. Pritts
- Process Analytical, AbbVie Inc, North Chicago, Illinois, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Resemann A, Liu-Shin L, Tremintin G, Malhotra A, Fung A, Wang F, Ratnaswamy G, Suckau D. Rapid, automated characterization of disulfide bond scrambling and IgG2 isoform determination. MAbs 2018; 10:1200-1213. [PMID: 30277844 PMCID: PMC6284591 DOI: 10.1080/19420862.2018.1512328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human antibodies of the IgG2 subclass exhibit complex inter-chain disulfide bonding patterns that result in three structures, namely A, A/B, and B. In therapeutic applications, the distribution of disulfide isoforms is a critical product quality attribute because each configuration affects higher order structure, stability, isoelectric point, and antigen binding. The current standard for quantification of IgG2 disulfide isoform distribution is based on chromatographic or electrophoretic techniques that require additional characterization using mass spectrometry (MS)-based methods to confirm disulfide linkages. Detailed characterization of the IgG2 disulfide linkages often involve MS/MS approaches that include electrospray ionization or electron-transfer dissociation, and method optimization is often cumbersome due to the large size and heterogeneity of the disulfide-bonded peptides. As reported here, we developed a rapid LC-MALDI-TOF/TOF workflow that can both identify the IgG2 disulfide linkages and provide a semi-quantitative assessment of the distribution of the disulfide isoforms. We established signature disulfide-bonded IgG2 hinge peptides that correspond to the A, A/B, and B disulfide isoforms and can be applied to the fast classification of IgG2 isoforms in heterogeneous mixtures.
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Affiliation(s)
- Anja Resemann
- a BioPharma Solutions R&D , BALS, Bruker Daltonik , Bremen , Germany
| | - Lily Liu-Shin
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA.,c Department of Biochemistry and Molecular Biology , University of Miami Miller School of Medicine , Miami , FL , USA
| | | | - Arun Malhotra
- c Department of Biochemistry and Molecular Biology , University of Miami Miller School of Medicine , Miami , FL , USA
| | - Adam Fung
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA
| | - Fang Wang
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA
| | - Gayathri Ratnaswamy
- b Analytical and Formulation Development, Agensys, Inc., an affiliate of Astellas , Santa Monica , CA , USA
| | - Detlev Suckau
- a BioPharma Solutions R&D , BALS, Bruker Daltonik , Bremen , Germany
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50
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Háda V, Bagdi A, Bihari Z, Timári SB, Fizil Á, Szántay C. Recent advancements, challenges, and practical considerations in the mass spectrometry-based analytics of protein biotherapeutics: A viewpoint from the biosimilar industry. J Pharm Biomed Anal 2018; 161:214-238. [PMID: 30205300 DOI: 10.1016/j.jpba.2018.08.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/22/2023]
Abstract
The extensive analytical characterization of protein biotherapeutics, especially of biosimilars, is a critical part of the product development and registration. High-resolution mass spectrometry became the primary analytical tool used for the structural characterization of biotherapeutics. Its high instrumental sensitivity and methodological versatility made it possible to use this technique to characterize both the primary and higher-order structure of these proteins. However, even by using high-end instrumentation, analysts face several challenges with regard to how to cope with industrial and regulatory requirements, that is, how to obtain accurate and reliable analytical data in a time- and cost-efficient way. New sample preparation approaches, measurement techniques and data evaluation strategies are available to meet those requirements. The practical considerations of these methods are discussed in the present review article focusing on hot topics, such as reliable and efficient sequencing strategies, minimization of artefact formation during sample preparation, quantitative peptide mapping, the potential of multi-attribute methodology, the increasing role of mass spectrometry in higher-order structure characterization and the challenges of MS-based identification of host cell proteins. On the basis of the opportunities in new instrumental techniques, methodological advancements and software-driven data evaluation approaches, for the future one can envision an even wider application area for mass spectrometry in the biopharmaceutical industry.
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Affiliation(s)
- Viktor Háda
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary.
| | - Attila Bagdi
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Zsolt Bihari
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | | | - Ádám Fizil
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc, Hungary.
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