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Khalikova M, Jireš J, Horáček O, Douša M, Kučera R, Nováková L. What is the role of current mass spectrometry in pharmaceutical analysis? MASS SPECTROMETRY REVIEWS 2024; 43:560-609. [PMID: 37503656 DOI: 10.1002/mas.21858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/02/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
The role of mass spectrometry (MS) has become more important in most application domains in recent years. Pharmaceutical analysis is specific due to its stringent regulation procedures, the need for good laboratory/manufacturing practices, and a large number of routine quality control analyses to be carried out. The role of MS is, therefore, very different throughout the whole drug development cycle. While it dominates within the drug discovery and development phase, in routine quality control, the role of MS is minor and indispensable only for selected applications. Moreover, its role is very different in the case of analysis of small molecule pharmaceuticals and biopharmaceuticals. Our review explains the role of current MS in the analysis of both small-molecule chemical drugs and biopharmaceuticals. Important features of MS-based technologies being implemented, method requirements, and related challenges are discussed. The differences in analytical procedures for small molecule pharmaceuticals and biopharmaceuticals are pointed out. While a single method or a small set of methods is usually sufficient for quality control in the case of small molecule pharmaceuticals and MS is often not indispensable, a large panel of methods including extensive use of MS must be used for quality control of biopharmaceuticals. Finally, expected development and future trends are outlined.
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Affiliation(s)
- Maria Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jakub Jireš
- Department of Analytical Chemistry, Faculty of Chemical Engineering, UCT Prague, Prague, Czech Republic
- Department of Development, Zentiva, k. s., Praha, Praha, Czech Republic
| | - Ondřej Horáček
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Michal Douša
- Department of Development, Zentiva, k. s., Praha, Praha, Czech Republic
| | - Radim Kučera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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2
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Yang J, Ostafe R, Bruening ML. In-Membrane Enrichment and Peptic Digestion to Facilitate Analysis of Monoclonal Antibody Glycosylation. Anal Chem 2024; 96:6347-6355. [PMID: 38607313 DOI: 10.1021/acs.analchem.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
The number of therapeutic monoclonal antibodies (mAbs) is growing rapidly due to their widespread use for treating various diseases and health conditions. Assessing the glycosylation profile of mAbs during production is essential to ensuring their safety and efficacy. This research aims to rapidly isolate and digest mAbs for liquid chromatography-tandem mass spectrometry (LC-MS/MS) identification of glycans and monitoring of glycosylation patterns, potentially during manufacturing. Immobilization of an Fc region-specific ligand, oFc20, in a porous membrane enables the enrichment of mAbs from cell culture supernatant and efficient elution with an acidic solution. Subsequent digestion of the mAb eluate occurred in a pepsin-modified membrane within 5 min. The procedure does not require alkylation and desalting, greatly shortening the sample preparation time. Subsequent LC-MS/MS analysis identified 11 major mAb N-glycan proteoforms and assessed the relative peak areas of the glycosylated peptides. This approach is suitable for the glycosylation profiling of various human IgG mAbs, including biosimilars and different IgG subclasses. The total time required for this workflow is less than 2 h, whereas the conventional enzymatic release and labeling of glycans can take much longer. Thus, the integrated membranes are suitable for facilitating the analysis of mAb glycosylation patterns.
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Affiliation(s)
- Junyan Yang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility; Purdue Institute for Inflammation, Immunology and Infection Diseases, Purdue University, West Lafayette, Indiana 47907, United States
| | - Merlin L Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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3
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [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: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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4
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Dai J, Ji C. In-depth size and charge variants characterization of monoclonal antibody with native mass spectrometry. Anal Chim Acta 2023; 1265:341360. [PMID: 37230578 DOI: 10.1016/j.aca.2023.341360] [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: 04/05/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Although the reversed-phase liquid chromatography (RPLC) is the most used separation front for mass spectrometry, many other separation modes are critical for enabling characterization of the protein therapeutics. Specifically, chromatographic separations under native conditions, such as those based on size exclusion chromatography (SEC) and ion-exchange chromatography (IEX), are used for characterizing important biophysical properties of protein variants in drug substance and drug product. Because most native state separation modes use non-volatile buffers with high salt concentration, optical detection has been traditionally used. However, there is an increasing need to understand and identify the optical underlying peaks by mass spectrometry for structure elucidation. For size variant separation by SEC, the native MS helps to understand the nature of the high molecular weight species, as well as clipping sites for low molecular weight fragments. For charge variant separation by IEX, native MS can reveal the post-translational modifications or other important factors contributing to charge heterogeneity at the intact level. Here, we demonstrate the power of native MS by direct coupling of SEC and IEX eluent to a time-of-flight mass spectrometer to characterize bevacizumab and NISTmAb. Our studies exemplify the effectiveness of native SEC-MS for characterizing bevacizumab's high molecular weight species at less than 0.3% (based on SEC/UV peak area%) and analyzing the fragment pathway with single amino acid difference for its low molecular weight species at less than 0.05%. Good IEX charge variant separation was obtained with consistent UV and MS profiles. The identity of separated acidic and basic variants were elucidated by native MS at intact level. We successfully differentiated several charge variants including glycoform variants that have not been reported before. In addition, native MS allowed identification of higher molecular weight species as late eluted variants. Overall, the SEC and IEX separation combined with high resolution and high sensitivity native MS, which is significantly different from the traditional RPLC-MS workflows, can be an effective tool that offers valuable insights for us to understand protein therapeutics at native state.
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Affiliation(s)
- Jun Dai
- NovaBioAssays LLC, 52 Dragon Ct, Suite 3B, Woburn, MA, 01801, USA.
| | - Chengjie Ji
- NovaBioAssays LLC, 52 Dragon Ct, Suite 3B, Woburn, MA, 01801, USA
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5
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Zhu Y, Liu J, Wu J, Feng H, Huang M, Lv H, Mei Y, Chen J, Pan Y, Zhou Y, Liu H. Discovery and characterization of hydroxylysine O-glycosylation in an engineered IL-2 fusion protein. Protein Expr Purif 2023; 205:106244. [PMID: 36737029 DOI: 10.1016/j.pep.2023.106244] [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: 11/23/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
In the present study, an engineered interleukin-2 (IL-2) fusion protein consisting of an anti-human serum albumin nanobody linked by ASTKG and a (G4S)2 linker to IL-2 was constructed. Liquid chromatography-mass spectrometry (LC-MS) characterization was performed on the intact molecule and at the peptide level. The LC-MS molecular mass analysis for the engineered fusion protein showed the appearance of unreported +340 Da peaks, apart from the expected O-glycosylation-related peaks in the IL-2 domain. Through a combination analysis of a K120R mutated molecule (The lysine at the position of 120 was mutated to arginine while the rest amino acid sequence remain unchanged), the possibility of a non-cleaved valine-histidine-serine signal peptide was ruled out and the presence of hydroxylysine (HyK) O-glycosylation in the ASTKG linker was confirmed. HyK O-glycosylation have been reported in other proteins such as collagen, which occurs in the conserved Gly-Xaa-HyK motif and is catalyzed by lysyl hydroxylase-3 complex. The present study showed high similar conserved motif of HyK-O-glycosylation in collagen, implying the HyK O-glycosylation in the engineered IL-2 possibly was catalyzed by the Chinese hamster ovary homolog of enzymes promoting HyK O-glycosylation in collagen. Bioactivity testing results revealed that HyK-O-glycosylation had no obvious effect on the in vitro activity of engineered IL-2. Our study is the first to report HyK-O-glycosylation modifications in therapeutic proteins through LC-MS characterization and in vitro activity analysis, which expands the scope of post-translational modification knowledge of therapeutic proteins.
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Affiliation(s)
- Yanping Zhu
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Jiyun Liu
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Jing Wu
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Hui Feng
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Min Huang
- Thermo Fisher Scientific Co. Ltd, Shanghai, China
| | - Haiyin Lv
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Yuanli Mei
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Jiaoyu Chen
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Yanping Pan
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Yu Zhou
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China
| | - Hongchuan Liu
- Shanghai Junshi Biosciences Co. Ltd, Shanghai, China.
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6
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Lignieres L, Legros V, Khelil M, Senecaut N, Lauber MA, Camadro JM, Chevreux G. Capillary liquid chromatography coupled with mass spectrometry for analysis of nanogram protein quantities on a wide-pore superficially porous particle column in top-down proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1214:123566. [PMID: 36516651 DOI: 10.1016/j.jchromb.2022.123566] [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: 10/06/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
In top-down proteomics experiments, intact protein ions are subjected to gas-phase fragmentation for MS analysis without prior digestion. This approach is used to characterize post-translational modifications and clipped forms of proteins, avoids several "inference" problems associated with bottom-up proteomics, and is well suited to the study of proteoforms. In the past decade, top-down proteomics has progressed rapidly, taking advantage of MS instrumentation improvements and the efforts of pioneering groups working to improve sample handling and data processing. The potential of this technology has been established through its successful use in a number of important biological studies. However, many challenges remain to be addressed like improving protein separation capabilities such that it might become possible to expand the dynamic range of whole proteome analysis, address co-elution and convoluted mass spectral data, and aid final data processing from peak identification to quantification. In this study, we investigated the use of a wide-pore silica-based superficially porous media with a high coverage phenyl bonding, commercially packed into customized capillary columns for the purpose of top-down proteomics. Protein samples of increasing complexity were tested, namely subunit digests of a monoclonal antibody, components of purified histones and proteins extracted from eukaryotic ribosomes. High quality mass spectra were obtained from only 100 ng of protein sample while using difluoroacetic acid as an ion pairing agent to improve peak shape and chromatographic resolution. A peak width at half height of about 15 s for a 45 min gradient time was observed on a complex mixture giving an estimated peak capacity close to 100. Most importantly, efficient separations were obtained for highly diverse proteins and there was no need to make method specific adjustments, suggesting this is a highly versatile and easy-to-use setup for top-down proteomics.
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Affiliation(s)
- Laurent Lignieres
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Manel Khelil
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nicolas Senecaut
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Matthew A Lauber
- Waters Corporation, 34, Maple Street, Milford, MA 01757-3696, United States
| | | | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France.
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7
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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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8
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Studying protein structure and function by native separation–mass spectrometry. Nat Rev Chem 2022; 6:215-231. [PMID: 37117432 DOI: 10.1038/s41570-021-00353-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 12/13/2022]
Abstract
Alterations in protein structure may have profound effects on biological function. Analytical techniques that permit characterization of proteins while maintaining their conformational and functional state are crucial for studying changes in the higher order structure of proteins and for establishing structure-function relationships. Coupling of native protein separations with mass spectrometry is emerging rapidly as a powerful approach to study these aspects in a reliable, fast and straightforward way. This Review presents the available native separation modes for proteins, covers practical considerations on the hyphenation of these separations with mass spectrometry and highlights the involvement of affinity-based separations to simultaneously obtain structural and functional information of proteins. The impact of these approaches is emphasized by selected applications addressing biomedical and biopharmaceutical research questions.
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9
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Matsuda Y, Mendelsohn BA. Recent Advances in Drug-Antibody Ratio Determination of Antibody-Drug Conjugates. Chem Pharm Bull (Tokyo) 2021; 69:976-983. [PMID: 34602579 DOI: 10.1248/cpb.c21-00258] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Antibody-drug conjugates (ADCs) are biopharmaceuticals produced by chemically linking small molecules (payloads) to antibodies that possess specific affinity for the target cell. The ADCs currently on the commercially market are the result of a stochastic conjugation of highly-potent payloads to multiple sites on the monoclonal antibody, resulting in a heterogeneous drug-antibody ratio (DAR) and drug distribution. The heterogeneity inherent to ADCs not produced site-specifically may not only be detrimental to the quality of the drug but also is less-desirable from the perspective of regulatory science. An ideal method or unified approach used to measure the DAR for ADCs, a critical aspect of their analysis and characterization, has not yet been established in the ADC field and remains an often-challenging issue for bioanalytical chemists. In this review we describe, compare, and evaluate the characteristics of various DAR determination methods for ADCs featuring recently reported technologies. The future landscape of bioconjugate DAR analysis is also discussed.
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van Schaick G, Domínguez-Vega E, Gstöttner C, van den Berg-Verleg JH, Schouten O, Akeroyd M, Olsthoorn MMA, Wuhrer M, Heck AJR, Abello N, Franc V. Native Structural and Functional Proteoform Characterization of the Prolyl-Alanyl-Specific Endoprotease EndoPro from Aspergillus niger. J Proteome Res 2021; 20:4875-4885. [PMID: 34515489 PMCID: PMC8491274 DOI: 10.1021/acs.jproteome.1c00663] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The prolyl-alanyl-specific
endoprotease (EndoPro) is an industrial
enzyme produced in Aspergillus niger. EndoPro is
mainly used for food applications but also as a protease in proteomics.
In-depth characterization of this enzyme is essential to understand
its structural features and functionality. However, there is a lack
of analytical methods capable of maintaining both the structural and
functional integrity of separated proteoforms. In this study, we developed
an anion exchange (AEX) method coupled to native mass spectrometry
(MS) for profiling EndoPro proteoforms. Moreover, we investigated
purified EndoPro proteoforms with complementary MS-based approaches,
including released N-glycan and glycopeptide analysis, to obtain a
comprehensive overview of the structural heterogeneity. We showed
that EndoPro has at least three sequence variants and seven N-glycosylation
sites occupied by high-mannose glycans that can be phosphorylated.
Each glycosylation site showed high microheterogeneity with ∼20
glycans per site. The functional characterization of fractionated
proteoforms revealed that EndoPro proteoforms remained active after
AEX-separation and the specificity of these proteoforms did not depend
on N-glycan phosphorylation. Nevertheless, our data confirmed a strong
pH dependence of EndoPro cleavage activity. Altogether, our study
demonstrates that AEX-MS is an excellent tool to characterize complex
industrial enzymes under native conditions.
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Affiliation(s)
- Guusje van Schaick
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Elena Domínguez-Vega
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christoph Gstöttner
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | | | - Olaf Schouten
- DSM Biotechnology Center, Center for Enabling Innovation, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Michiel Akeroyd
- DSM Biotechnology Center, Center for Enabling Innovation, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Maurien M A Olsthoorn
- DSM Biotechnology Center, Center for Enabling Innovation, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Nicolas Abello
- DSM Biotechnology Center, Center for Enabling Innovation, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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12
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Verscheure L, Cerdobbel A, Sandra P, Lynen F, Sandra K. Monoclonal antibody charge variant characterization by fully automated four-dimensional liquid chromatography-mass spectrometry. J Chromatogr A 2021; 1653:462409. [PMID: 34325295 DOI: 10.1016/j.chroma.2021.462409] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
Fully automated characterization of monoclonal antibody (mAb) charge variants using four-dimensional liquid chromatography-mass spectrometry (4D-LC-MS) is reported and illustrated. Charge variants resolved by cation-exchange chromatography (CEX) using a salt- or pH-gradient are collected in loops installed on a multiple heart-cutting valve and consequently subjected to online desalting, denaturation, reduction and trypsin digestion prior to LC-MS based peptide mapping. This innovation which substantially reduces turnaround time, sample manipulation, loss and artefacts and increases information gathering, is described in great technical detail, and applied to characterize the charge heterogeneity associated with three therapeutic mAbs. Sequence coverages > 95% are obtained for major and minor charge variants (> 1.0%). Post-translational modifications (PTMs) and modification sites are readily revealed in a repeatable manner including unstable succinimide intermediates which are not maintained when performing classical in-solution overnight digestion of offline collected CEX peaks.
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Affiliation(s)
- Liesa Verscheure
- RIC group, President Kennedypark 26, Kortrijk 8500, Belgium; Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, Ghent B-9000, Belgium
| | - An Cerdobbel
- RIC group, President Kennedypark 26, Kortrijk 8500, Belgium
| | - Pat Sandra
- RIC group, President Kennedypark 26, Kortrijk 8500, Belgium; Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, Ghent B-9000, Belgium
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, Ghent B-9000, Belgium
| | - Koen Sandra
- RIC group, President Kennedypark 26, Kortrijk 8500, Belgium; Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, Ghent B-9000, Belgium.
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13
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Kimerer LK, Niu B, Pabst TM, Zhai W, Hunter AK, Carta G. Chromatographic and adsorptive behavior of a bivalent bispecific antibody and associated fragments. J Chromatogr A 2021; 1648:462181. [PMID: 33989897 DOI: 10.1016/j.chroma.2021.462181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 10/01/2022]
Abstract
The elution and adsorptive behavior of a bivalent bispecific antibody (BiSAb), comprising an IgG1 framework with a scFv domain genetically fused to each heavy chain C-terminus via flexible linkers, and of two associated fragments were studied on two cation exchange chromatography media - ProPac WCX-10, which is pellicular and suitable for analytical use, and Nuvia HR-S, which is macroporous and suitable for preparative and process scale uses. Both fragments were identified by MS as missing one of the two scFv domains and its flexible linker, but one of them also contains an additional C-terminal lysine. The separation of these fragments on both resins occurs as a result of differences in non-specific ligand-protein interactions that are modulated by the salt concentration. For the ProPac WCX-10 column, complex, multipeak elution behaviors are observed, since, as a result of the linker flexibility, both the intact molecule and the fragments appear to exist in multiple binding configurations with each scFv domains either collapsed onto the IgG framework or extended away from it. With a residence time of 2.5 min and at 21 °C, two peak elution is observed for the fragments which contain a single linked scFv and three peak elution for the intact molecule which contains two linked scFvs. This behavior is affected by residence time, temperature, and hold time. Increasing the residence time to 25 min or increasing temperature to 40°C results in elution of a single, merged peak for each of the protein species. For Nuvia HR-S, the broader peaks, obtained as a result of mass transfer limitations, tend to obscure the multipeak elution behavior. Nevertheless, even for this resin, the effects of configurational flexibility are still manifested at the single-particle scale and affect the evolution of the patterns of protein binding within individual resin particles as evident from confocal microscopy observations.
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Affiliation(s)
- Lucas K Kimerer
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Ben Niu
- Analytical Sciences, BioPharmaceuticals Development, AstraZeneca, Gaithersburg, MD, USA
| | - Timothy M Pabst
- Purification Process Sciences, BioPharmaceuticals Development, AstraZeneca, Gaithersburg, MD, USA
| | - Weiguo Zhai
- Analytical Sciences, BioPharmaceuticals Development, AstraZeneca, Gaithersburg, MD, USA
| | - Alan K Hunter
- Purification Process Sciences, BioPharmaceuticals Development, AstraZeneca, Gaithersburg, MD, USA
| | - Giorgio Carta
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA.
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14
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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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15
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van Schaick G, Gstöttner C, Büttner A, Reusch D, Wuhrer M, Domínguez-Vega E. Anion exchange chromatography – Mass spectrometry for monitoring multiple quality attributes of erythropoietin biopharmaceuticals. Anal Chim Acta 2021; 1143:166-172. [DOI: 10.1016/j.aca.2020.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022]
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16
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Verscheure L, Oosterlynck M, Cerdobbel A, Sandra P, Lynen F, Sandra K. Middle-up characterization of monoclonal antibodies by online reduction liquid chromatography-mass spectrometry. J Chromatogr A 2020; 1637:461808. [PMID: 33385741 DOI: 10.1016/j.chroma.2020.461808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
This study describes the fully automated middle-up characterization of monoclonal antibodies (mAbs) and next-generation variants by online reduction liquid chromatography-mass spectrometry (LC-MS). Proteins were trapped on-column and subjected to online desalting, denaturation and reduction prior to reversed phase elution of the created subunits in the MS. The evaluation of more than 20 different therapeutic proteins including full length mAbs (subclasses IgG1, IgG2 and IgG4), bispecific antibodies, antibody fragments, fusion proteins and antibody-drug conjugates (ADC) revealed that the online reduction method is as powerful as the widely applied offline sample preparation with dithiothreitol (DTT) as reducing agent and guanidine hydrochloride (Gnd.HCl) as denaturant and tackles some major disadvantages associated with the latter method, i.e. corrosion of stainless steel components, adduct formation impacting spectral quality and sample stability. The value of the online reduction LC-MS method is also enforced by its ability to reveal unstable antibody variants such as succinimide intermediates of asparagine deamidation and aspartic acid isomerization which are often lost when using the offline sample preparation method. The performance of the online reduction LC-MS set-up was verified and it was revealed that the method is precise with RSD values below 0.25% and 3.0% for retention time and area, respectively. Carry-over is within acceptable limits (< 0.5%) and the reducing buffer is stable up to 24 hours.
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Affiliation(s)
- Liesa Verscheure
- Research Institute for Chromatography (RIC), President Kennedypark 26, 8500 Kortrijk, Belgium; Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Marie Oosterlynck
- Chemistry Department, KU Leuven, Celestijnenlaan 200F, bus 2404, 3001 Leuven, Belgium
| | - An Cerdobbel
- Research Institute for Chromatography (RIC), President Kennedypark 26, 8500 Kortrijk, Belgium
| | - Pat Sandra
- Research Institute for Chromatography (RIC), President Kennedypark 26, 8500 Kortrijk, Belgium; Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium
| | - Koen Sandra
- Research Institute for Chromatography (RIC), President Kennedypark 26, 8500 Kortrijk, Belgium; Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium.
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17
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Jaag S, Shirokikh M, Lämmerhofer M. Charge variant analysis of protein-based biopharmaceuticals using two-dimensional liquid chromatography hyphenated to mass spectrometry. J Chromatogr A 2020; 1636:461786. [PMID: 33326927 DOI: 10.1016/j.chroma.2020.461786] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/16/2020] [Accepted: 12/06/2020] [Indexed: 01/04/2023]
Abstract
The profile of charge variants represents an important critical quality attribute of protein-based biopharmaceuticals, in particular of monoclonal antibodies, and must therefore becontrolled. In this work, 2D-LC methods for charge variant analysis were developed using a strong cation-exchange chromatography (SCX) as first dimension (1D) separation. Non-porous SCX (3 µm) particle columns and different mobile phases were evaluated using a test mixture of some standard proteins of different size and pI (comprising myoglobin, bovine serum albumin, cytochrome c, lysozyme and β-lactoglobulin) and two monoclonal IgG1 antibodies (NIST mAb and Secukinumab). The most promising 1D eluent for SCX was a salt-mediated pH-gradient system using a ternary mobile phase system with 2-(N-morpholino)ethanesulfonic acid, 1,3-diamino-2-propanol and sodium chloride. For the second dimension (2D), a desalting reversed-phase liquid chromatography (RP-LC) was chosen to enable the hyphenation of the charge variant separation with mass spectrometric (MS) detection. While for intact mAbs the 2D just served for desalting without additional selectivity, the 2D contributed some orthogonal selectivity for the mAb fragment separation. Various core-shell and monolithic columns were tested and variables such as gradient time and flow rate systematically optimized. Unexpectedly, a C4 400 Å column (3.4 µm diameter with 0.2 µm porous shell) provided higher peak capacities compared to the same 1000 Å column (2.7 µm diameter with 0.5 µm porous shell). A thinner shell appeared to be more advantageous than wider pores under high flow regime. An ultra-fast RP-LC method with a run time of one minute was developed using trifluoroacetic acid which was later replaced by formic acid as additive for better MS compatibility. The successful hyphenation of the two orthogonal separation modes, SCX and RP-LC, could be demonstrated in the multiple heart-cutting and the full comprehensive mode. MS analysis using a high-resolution quadrupole time-of-flight instrument enabled to identify different glycoforms and some major charge variants of the antibody at the intact protein level as well as on the subunit level (Fc/2, Lc, Fd') in a middle-up approach by 2D-LC-ESI-MS analysis.
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Affiliation(s)
- Simon Jaag
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Marina Shirokikh
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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18
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Yan Y, Xing T, Wang S, Li N. Versatile, Sensitive, and Robust Native LC-MS Platform for Intact Mass Analysis of Protein Drugs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2171-2179. [PMID: 32865416 DOI: 10.1021/jasms.0c00277] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over the past several years, hyphenation of native (nondenaturing) liquid chromatography (nLC) methods, such as size exclusion chromatography (SEC), ion exchange chromatography (IEX), and hydrophobic interaction chromatography (HIC) with mass spectrometry (MS) have become increasingly popular to study the size, charge, and structural heterogeneity of protein drug products. Despite the availability of a wide variety of nLC-MS methods, an integrated platform that can accommodate different applications is still lacking. In this study, we described the development of a versatile, sensitive, and robust nLC-MS platform that can support various nLC-MS applications. In particular, the developed platform can tolerate a wide range of LC flow rates and high salt concentrations, which are critical for accommodating different nLC methods. In addition, a dopant-modified desolvation gas can be readily applied on this platform to achieve online charge-reduction native MS, which improves the characterization of both heterogeneous and labile biomolecules. Finally, we demonstrated that this nLC-MS platform is highly sensitive and robust and can be routinely applied in protein drug characterization.
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Affiliation(s)
- Yuetian Yan
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Tao Xing
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Shunhai Wang
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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19
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Matsuda Y, Kliman M, Mendelsohn BA. Application of Native Ion Exchange Mass Spectrometry to Intact and Subunit Analysis of Site-Specific Antibody-Drug Conjugates Produced by AJICAP First Generation Technology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1706-1712. [PMID: 32608232 DOI: 10.1021/jasms.0c00129] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibody-drug conjugates (ADCs) are at the forefront of the next generation of oncology biopharmaceuticals. Conventional ADCs involve stochastic conjugation of the antibody to a cytotoxic drug, creating a highly heterogeneous product. The resulting stochastic distribution often leads to a narrow therapeutic index and makes it difficult to analyze the composition of heterogeneous ADCs. With the goal of overcoming these issues, we developed a site-specific conjugation technology, named AJICAP, for production of low heterogeneity ADCs. For analysis of these site-specific ADCs, we report herein strong cation exchange chromatography coupled with UV and mass spectrometry detection (SCX-UV-MS). Retention time reproducibility after SCX column equilibration enabled monitoring of important changes in product quality. SCX-UV-MS performed with MS-compatible mobile phases was conducted for intact native ADC analysis, allowing drug-antibody ratio characterization and charge variant characterization in single analysis. Furthermore, subunit analysis of the site-specific ADCs by native SCX-UV-MS confirmed the Fc site selectivity of ADCs generated by AJICAP conjugation.
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Affiliation(s)
- Yutaka Matsuda
- Ajinomoto Bio-Pharma Services, 11040 Roselle Street, San Diego, California 92121, United States
| | - Michal Kliman
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Brian A Mendelsohn
- Ajinomoto Bio-Pharma Services, 11040 Roselle Street, San Diego, California 92121, United States
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20
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Farsang E, Guillarme D, Veuthey JL, Beck A, Lauber M, Schmudlach A, Fekete S. Coupling non-denaturing chromatography to mass spectrometry for the characterization of monoclonal antibodies and related products. J Pharm Biomed Anal 2020; 185:113207. [DOI: 10.1016/j.jpba.2020.113207] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 01/31/2023]
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21
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Pérez-Robles R, Cuadros-Rodríguez L, Salmerón-García A, Cabeza-Barrera J, Navas N. Intact charge variant analysis of ziv-aflibercept by cationic exchange liquid chromatography as a proof of concept: Comparison between volatile and non-volatile salts in the mobile phase. J Pharm Biomed Anal 2020; 185:113233. [DOI: 10.1016/j.jpba.2020.113233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/15/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022]
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22
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Characterization of charge variants for antibody-based biopharmaceuticals by mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1134-1135:121879. [DOI: 10.1016/j.jchromb.2019.121879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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