1
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Chapman J, Paukner M, Leser M, Teng KW, Koide S, Holder M, Armache KJ, Becker C, Ueberheide B, Brenowitz M. Systematic Fe(II)-EDTA Method of Dose-Dependent Hydroxyl Radical Generation for Protein Oxidative Footprinting. Anal Chem 2023; 95:18316-18325. [PMID: 38049117 PMCID: PMC10734636 DOI: 10.1021/acs.analchem.3c02319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
Correlating the structure and dynamics of proteins with biological function is critical to understanding normal and dysfunctional cellular mechanisms. We describe a quantitative method of hydroxyl radical generation via Fe(II)-ethylenediaminetetraacetic acid (EDTA)-catalyzed Fenton chemistry that provides ready access to protein oxidative footprinting using equipment commonly found in research and process control laboratories. Robust and reproducible dose-dependent oxidation of protein samples is observed and quantitated by mass spectrometry with as fine a single residue resolution. An oxidation analysis of lysozyme provides a readily accessible benchmark for our method. The efficacy of our oxidation method is demonstrated by mapping the interface of a RAS-monobody complex, the surface of the NIST mAb, and the interface between PRC2 complex components. These studies are executed using standard laboratory tools and a few pennies of reagents; the mass spectrometry analysis can be streamlined to map the protein structure with single amino acid residue resolution.
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Affiliation(s)
- Jessica
R. Chapman
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
| | - Max Paukner
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Micheal Leser
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Kai Wen Teng
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
| | - Shohei Koide
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Marlene Holder
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Karim-Jean Armache
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Chris Becker
- Protein
Metrics Inc., Cupertino, California 95014, United States
| | - Beatrix Ueberheide
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Michael Brenowitz
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department
of Molecular Pharmacology, Albert Einstein
College of Medicine, Bronx, New York 10461, United States
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2
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Solomon TL, Chao K, Gingras G, Aubin Y, O'Dell WB, Marino JP, Brinson RG. Backbone NMR assignment of the yeast expressed Fab fragment of the NISTmAb reference antibody. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:75-81. [PMID: 36856943 DOI: 10.1007/s12104-023-10123-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/08/2023] [Indexed: 06/02/2023]
Abstract
The monoclonal antibody (mAb) protein class has become a primary therapeutic platform for the production of new life saving drug products. MAbs are comprised of two domains: the antigen-binding fragment (Fab) and crystallizable fragment (Fc). Despite the success in the clinic, NMR assignments of the complete Fab domain have been elusive, in part due to problems in production of properly folded, triply-labeled 2H,13C,15N Fab domain. Here, we report the successful recombinant expression of a triply-labeled Fab domain, derived from the standard IgG1κ known as NISTmAb, in yeast. Using the 2H,13C,15N Fab domain, we assigned 94% of the 1H, 13C, and 15N backbone atoms.
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Affiliation(s)
- Tsega L Solomon
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Kinlin Chao
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Genevieve Gingras
- Centre for Oncology, Radiopharmaceuticals and Research, Biologics and Radiotherapeutic Drugs Directorate, Health Canada, 251 Sir Frederick Banting Driveway, K1A 0K9, Ottawa, ON, Canada
| | - Yves Aubin
- Centre for Oncology, Radiopharmaceuticals and Research, Biologics and Radiotherapeutic Drugs Directorate, Health Canada, 251 Sir Frederick Banting Driveway, K1A 0K9, Ottawa, ON, Canada
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD, 20850, USA.
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3
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Solomon TL, Delaglio F, Giddens JP, Marino JP, Yu YB, Taraban MB, Brinson RG. Correlated analytical and functional evaluation of higher order structure perturbations from oxidation of NISTmAb. MAbs 2023; 15:2160227. [PMID: 36683157 PMCID: PMC9872951 DOI: 10.1080/19420862.2022.2160227] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The clinical efficacy and safety of protein-based drugs such as monoclonal antibodies (mAbs) rely on the integrity of the protein higher order structure (HOS) during product development, manufacturing, storage, and patient administration. As mAb-based drugs are becoming more prevalent in the treatment of many illnesses, the need to establish metrics for quality attributes of mAb therapeutics through high-resolution techniques is also becoming evident. To this end, here we used a forced degradation method, time-dependent oxidation by hydrogen peroxide, on the model biotherapeutic NISTmAb and evaluated the effects on HOS with orthogonal analytical methods and a functional assay. To monitor the oxidation process, the experimental workflow involved incubation of NISTmAb with hydrogen peroxide in a benchtop nuclear magnetic resonance spectrometer (NMR) that followed the reaction kinetics, in real-time through the water proton transverse relaxation rate R2(1H2O). Aliquots taken at defined time points were further analyzed by high-field 2D 1H-13C methyl correlation fingerprint spectra in parallel with other analytical techniques, including thermal unfolding, size-exclusion chromatography, and surface plasmon resonance, to assess changes in stability, heterogeneity, and binding affinities. The complementary measurement outputs from the different techniques demonstrate the utility of combining NMR with other analytical tools to monitor oxidation kinetics and extract the resulting structural changes in mAbs that are functionally relevant, allowing rigorous assessment of HOS attributes relevant to the efficacy and safety of mAb-based drug products.
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Affiliation(s)
- Tsega L. Solomon
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - John P. Giddens
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - John P. Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States
| | - Yihua Bruce Yu
- Bio- and Nano-Technology Center, University of Maryland School of Pharmacy, and Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States
| | - Marc B. Taraban
- Bio- and Nano-Technology Center, University of Maryland School of Pharmacy, and Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States
| | - Robert G. Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland, United States,CONTACT Robert G. Brinson Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, 9600 Gudelsky Drive Rockville, Rockville, Maryland20850, United States
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4
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Tajoddin NN, Konermann L. Structural Dynamics of a Thermally Stressed Monoclonal Antibody Characterized by Temperature-Dependent H/D Exchange Mass Spectrometry. Anal Chem 2022; 94:15499-15509. [DOI: 10.1021/acs.analchem.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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5
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Yandrofski K, Mouchahoir T, De Leoz ML, Duewer D, Hudgens JW, Anderson KW, Arbogast L, Delaglio F, Brinson RG, Marino JP, Phinney K, Tarlov M, Schiel JE. Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics. Front Mol Biosci 2022; 9:876780. [PMID: 35601836 PMCID: PMC9117750 DOI: 10.3389/fmolb.2022.876780] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 01/18/2023] Open
Abstract
Biopharmaceuticals such as monoclonal antibodies are required to be rigorously characterized using a wide range of analytical methods. Various material properties must be characterized and well controlled to assure that clinically relevant features and critical quality attributes are maintained. A thorough understanding of analytical method performance metrics, particularly emerging methods designed to address measurement gaps, is required to assure methods are appropriate for their intended use in assuring drug safety, stability, and functional activity. To this end, a series of interlaboratory studies have been conducted using NISTmAb, a biopharmaceutical-representative and publicly available monoclonal antibody test material, to report on state-of-the-art method performance, harmonize best practices, and inform on potential gaps in the analytical measurement infrastructure. Reported here is a summary of the study designs, results, and future perspectives revealed from these interlaboratory studies which focused on primary structure, post-translational modifications, and higher order structure measurements currently employed during biopharmaceutical development.
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Affiliation(s)
- Katharina Yandrofski
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
- *Correspondence: Katharina Yandrofski,
| | - Trina Mouchahoir
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | | | - David Duewer
- National Institute of Standards and Technology, Gaithersburg, MD, United States
| | - Jeffrey W. Hudgens
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | - Kyle W. Anderson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | - Luke Arbogast
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | - Robert G. Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | - John P. Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
| | - Karen Phinney
- National Institute of Standards and Technology, Gaithersburg, MD, United States
| | - Michael Tarlov
- National Institute of Standards and Technology, Gaithersburg, MD, United States
| | - John E. Schiel
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, MD, United States
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6
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Site-specific glycan-conjugated NISTmAb antibody drug conjugate mimetics: synthesis, characterization, and utility. Anal Bioanal Chem 2021; 413:4989-5001. [PMID: 34231000 DOI: 10.1007/s00216-021-03460-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 10/20/2022]
Abstract
Antibody drug conjugates (ADCs) represent a rapidly growing modality for the treatment of numerous oncology indications. The complexity of analytical characterization method development is increased due to the potential for synthetic intermediates and process-related impurities. In addition, the cytotoxicity of such materials provides an additional challenge with regard to handling products and/or sharing materials with analytical collaborators and/or vendors for technology development. Herein, we have utilized a site-specific chemoenzymatic glycoconjugation strategy for preparing ADC mimetics composed of the NIST monoclonal antibody (NISTmAb) conjugated to non-cytotoxic payloads representing both small molecules and peptides. The materials were exhaustively characterized with high-resolution mass spectrometry-based approaches to demonstrate the utility of each analytical method for confirming the conjugation fidelity as well as deep characterization of low-abundance synthetic intermediates and impurities arising from payload raw material heterogeneity. These materials therefore represent a widely available test metric to develop novel ADC analytical methods as well as a platform to discuss best practices for extensive characterization.
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7
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Rincon Pabon JP, Kochert BA, Liu YH, Richardson DD, Weis DD. Protein A does not induce allosteric structural changes in an IgG1 antibody during binding. J Pharm Sci 2021; 110:2355-2361. [PMID: 33640336 DOI: 10.1016/j.xphs.2021.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
Affinity chromatography is widely used for antibody purification in biopharmaceutical production. Although there is evidence suggesting that affinity chromatography might induce structural changes in antibodies, allosteric changes in structure have not been well-explored. Here, we used hydrogen exchange-mass spectrometry (HX-MS) to reveal conformational changes in the NIST mAb upon binding with a protein A (ProA) matrix. HX-MS measurements of NIST mAb bound to in-solution and resin forms of ProA revealed regions of the CH2 and CH3 domains with increased protection from HX upon ProA binding, consistent with the known ProA binding region. In-solution ProA experiments revealed regions in the Fab with increased HX uptake when the ProA:mAb molar ratio was increased to 2:1, suggesting an allosterically induced increase in backbone flexibility. Such effects were not observed with lower ProA concentration (1:1 molar ratio) or when ProA resin was used, suggesting some kind of change in binding mode. Since all pharmaceutical processes use ProA bound to resin, our results rule out reversible allosteric effects on the NIST mAb during interaction with resin ProA. However, irreversible effects cannot be ruled out since the NIST mAb was previously exposed to ProA during its original purification.
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Affiliation(s)
- Juan P Rincon Pabon
- Department of Chemistry and the Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Brent A Kochert
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yan-Hui Liu
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Douglas D Richardson
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - David D Weis
- Department of Chemistry and the Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, United States.
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8
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Arbogast LW, Delaglio F, Brinson RG, Marino JP. Assessment of the Higher-Order Structure of Formulated Monoclonal Antibody Therapeutics by 2D Methyl Correlated NMR and Principal Component Analysis. ACTA ACUST UNITED AC 2021; 100:e105. [PMID: 32407007 DOI: 10.1002/cpps.105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Characterization of the higher-order structure (HOS) of protein therapeutics, and in particular of monoclonal antibodies, by 2D 1 H-13 C methyl correlated NMR has been demonstrated as precise and robust. Such characterization can be greatly enhanced when collections of spectra are analyzed using multivariate approaches such as principal component analysis (PCA), allowing for the detection and identification of small structural differences in drug substance that may otherwise fall below the limit of detection of conventional spectral analysis. A major limitation to this approach is the presence of aliphatic signals from formulation or excipient components, which result in spectral interference with the protein signal of interest; however, the recently described Selective Excipient Reduction and Removal (SIERRA) filter greatly reduces this issue. Here we will outline how basic 2D 1 H-13 C methyl-correlated NMR may be combined with the SIERRA approach to collect 'clean' NMR spectra of formulated monoclonal antibody therapeutics (i.e., drug substance spectra free of interfering component signals), and how series of such spectra may be used for HOS characterization by direct PCA of the series spectral matrix. © 2020 U.S. Government. Basic Protocol 1: NMR data acquisition Basic Protocol 2: Full spectral matrix data processing and analysis Support Protocol: Data visualization and cluster analysis.
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Affiliation(s)
- Luke W Arbogast
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, Rockville, Maryland
| | - Frank Delaglio
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, Rockville, Maryland
| | - Robert G Brinson
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, Rockville, Maryland
| | - John P Marino
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, Rockville, Maryland
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9
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Groves K, Cryar A, Cowen S, Ashcroft AE, Quaglia M. Mass Spectrometry Characterization of Higher Order Structural Changes Associated with the Fc-glycan Structure of the NISTmAb Reference Material, RM 8761. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:553-564. [PMID: 32008322 DOI: 10.1021/jasms.9b00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
As monoclonal antibodies (mAbs) rapidly emerge as a dominant class of therapeutics, so does the need for suitable analytical technologies to monitor for changes in protein higher order structure (HOS) of these biomolecules. Reference materials (RM) serve a key analytical purpose of benchmarking the suitability and robustness of both established and emerging analytical procedures for both drug producers and regulators. Here, two simple enzymatic protocols for generating Fc-glycan variants from the NISTmAb RM are described and both global and localized changes in HOS between the RM and these Fc-glycan variants are characterized using hydrogen deuterium exchange-mass spectrometry (HDX-MS) and ion mobility spectrometry-mass spectrometry (IMS-MS) measurements. An alternative statistical approach is described where measurement thresholds that differentiate between measurement variability and significant structural changes were established on the basis of experimental data. Measurements revealed decreases in structural stability correlating with the degree of Fc-glycan structure loss, especially at the CH2/CH3 domain interface. These data promote the use of this RM and these Fc-glycan variants for establishing the sensitivity of and validating analytical methods for the detection of HOS measurements of mAbs.
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Affiliation(s)
- Kate Groves
- LGC, Queens Road, Teddington TW11 0LY, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam Cryar
- LGC, Queens Road, Teddington TW11 0LY, UK
| | | | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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10
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem 2019; 91:7336-7345. [PMID: 31045344 PMCID: PMC6745711 DOI: 10.1021/acs.analchem.9b01100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ sLab⟩ ≤ (0.15 ± 0.01) Da (1σx̅). All laboratories achieved ⟨sLab⟩ ≤ 0.4 Da. For immersions of protein at THDX = (3.6 to 25) °C and for D2O exchange times of tHDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σreproducibility15 Laboratories( tHDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at THDX = 25 °C exhibited reproducibility of σreproducibility25C cohort( tHDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.
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Affiliation(s)
- Jeffrey W Hudgens
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States
- Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Elyssia S Gallagher
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States
- Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Ioannis Karageorgos
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States
- Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Kyle W Anderson
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States
- Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - James J Filliben
- Statistical Engineering Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - George M Bou-Assaf
- Analytical Development , Biogen Inc. , 225 Binney Street , Cambridge , Massachusetts 02142 , United States
| | - Alfonso Espada
- Centro de Investigación Lilly S.A. , 28108 Alcobendas , Spain
| | - Michael J Chalmers
- Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | - Hui-Min Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Benjamin T Walters
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jennifer Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - John Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
- Joint Center for Structural Genomics , La Jolla , California 92037 , United States
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Xiaojun Lu
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Ratnesh Pandey
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Arun Chandramohan
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Sasidhar N Nirudodhi
- Vaccine R&D , Pfizer Inc. , 401 N Middletown Rd , Pearl River, New York 10965 , United States
| | - Justin B Sperry
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Jason C Rouse
- Analytical R&D , Pfizer Inc. , 1 Burtt Road , Andover , Massachusetts 01810 , United States
| | - James A Carroll
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Ulrike Leurs
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - David D Weis
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Mohammed A Al-Naqshabandi
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
- Department of General Science , Soran University , Kawa Street , Soran , Kurdistan Region, Iraq
| | - Tyler S Hageman
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Malvina Papanastasiou
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - Sheng Li
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Sarah Urata
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2019; 124:1-7. [PMID: 34877153 PMCID: PMC7339623 DOI: 10.6028/jres.124.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/10/2019] [Indexed: 06/13/2023]
Abstract
The spreadsheet file reported herein provides centroid data, descriptive of
deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as
measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS)
method. The protein sample was incubated in deuterium-rich solutions under uniform
pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging
over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic
peptide fragments were measured by mass spectrometry. These data were reported by
fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass
spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide
sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage.
In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide
sequences of the Fc fragment. The instrumentation and physical and chemical
conditions under which these data were acquired are documented.
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Affiliation(s)
- Jeffrey W Hudgens
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Elyssia S Gallagher
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Ioannis Karageorgos
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Kyle W Anderson
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Richard Y-C Huang
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - Guodong Chen
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - George M Bou-Assaf
- Biogen Inc., Analytical Development, 225 Binney Street, Cambridge, MA 02142, USA
| | - Alfonso Espada
- Centro de Investigación Lilly S.A., 28108-Alcobendas, Spain
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Hui-Min Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jennifer Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Venable
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
- Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Xiaojun Lu
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ratnesh Pandey
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Arun Chandramohan
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | - Ganesh Srinivasan Anand
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | | | - Justin B Sperry
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Jason C Rouse
- Pfizer Inc., Analytical R&D, 1 Burtt Road, Andover, MA 01810, USA
| | - James A Carroll
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Kasper D Rand
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ulrike Leurs
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - David D Weis
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Mohammed A Al-Naqshabandi
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
- Soran University, Department of General Science, Kawa Street, Soran, Kurdistan Region, Iraq
| | - Tyler S Hageman
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Daniel Deredge
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Patrick L Wintrode
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Malvina Papanastasiou
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - John D Lambris
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - Sheng Li
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sarah Urata
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
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