1
|
Bailey AO, Durbin KR, Robey MT, Palmer LK, Russell WK. Filling the gaps in peptide maps with a platform assay for top-down characterization of purified protein samples. Proteomics 2024:e2400036. [PMID: 39004851 DOI: 10.1002/pmic.202400036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) intact mass analysis and LC-MS/MS peptide mapping are decisional assays for developing biological drugs and other commercial protein products. Certain PTM types, such as truncation and oxidation, increase the difficulty of precise proteoform characterization owing to inherent limitations in peptide and intact protein analyses. Top-down MS (TDMS) can resolve this ambiguity via fragmentation of specific proteoforms. We leveraged the strengths of flow-programmed (fp) denaturing online buffer exchange (dOBE) chromatography, including robust automation, relatively high ESI sensitivity, and long MS/MS window time, to support a TDMS platform for industrial protein characterization. We tested data-dependent (DDA) and targeted strategies using 14 different MS/MS scan types featuring combinations of collisional- and electron-based fragmentation as well as proton transfer charge reduction. This large, focused dataset was processed using a new software platform, named TDAcquireX, that improves proteoform characterization through TDMS data aggregation. A DDA-based workflow provided objective identification of αLac truncation proteoforms with a two-termini clipping search. A targeted TDMS workflow facilitated the characterization of αLac oxidation positional isomers. This strategy relied on using sliding window-based fragment ion deconvolution to generate composite proteoform spectral match (cPrSM) results amenable to fragment noise filtering, which is a fundamental enhancement relevant to TDMS applications generally.
Collapse
Affiliation(s)
- Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | | | - Lee K Palmer
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| |
Collapse
|
2
|
Duivelshof BL, Bouvarel T, Pirner S, Larraillet V, Knaupp A, Koll H, D’Atri V, Guillarme D. Enhancing Selectivity of Protein Biopharmaceuticals in Ion Exchange Chromatography through Addition of Organic Modifiers. Int J Mol Sci 2023; 24:16623. [PMID: 38068945 PMCID: PMC10706461 DOI: 10.3390/ijms242316623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Charge heterogeneity among therapeutic monoclonal antibodies (mAbs) is considered an important critical quality attribute and requires careful characterization to ensure safe and efficacious drug products. The charge heterogeneity among mAbs is the result of chemical and enzymatic post-translational modifications and leads to the formation of acidic and basic variants that can be characterized using cation exchange chromatography (CEX). Recently, the use of mass spectrometry-compatible salt-mediated pH gradients has gained increased attention to elute the proteins from the charged stationary phase material. However, with the increasing antibody product complexity, more and more selectivity is required. Therefore, in this study, we set out to improve the selectivity by using a solvent-enriched mobile phase composition for the analysis of a variety of mAbs and bispecific antibody products. It was found that the addition of the solvents to the mobile phase appeared to modify the hydrate shell surrounding the protein and alter the retention behavior of the studied proteins. Therefore, this work demonstrates that the use of solvent-enriched mobile phase composition could be an attractive additional method parameter during method development in CEX.
Collapse
Affiliation(s)
- Bastiaan Laurens Duivelshof
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Thomas Bouvarel
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
| | | | | | | | - Hans Koll
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Valentina D’Atri
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
| |
Collapse
|
3
|
Robey MT, Utley D, Greer JB, Fellers RT, Kelleher NL, Durbin KR. Advancing Intact Protein Quantitation with Updated Deconvolution Routines. Anal Chem 2023; 95:14954-14962. [PMID: 37750863 PMCID: PMC10840078 DOI: 10.1021/acs.analchem.3c02345] [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] [Indexed: 09/27/2023]
Abstract
Analysis of intact proteins by mass spectrometry enables direct quantitation of the specific proteoforms present in a sample and is an increasingly important tool for biopharmaceutical and academic research. Interpreting and quantifying intact protein species from mass spectra typically involves many challenges including mass deconvolution and peak processing as well as determining optimal spectral averaging parameters and matching masses to theoretical proteoforms. Each of these steps can present informatic hurdles, as parameters often need to be tailored specifically to the data sets. To reduce intact mass deconvolution data analysis burdens, we built upon the widely used "sliding window" mass deconvolution technique with several additional concepts. First, we found that how spectra are averaged and the overlap in spectral windows can be tuned to favor either sensitivity or speed. A multiple window averaging approach was found to be the most effective way to increase mass detection and yielded a >2-fold increase in the number of masses detected. We also developed a targeted feature-finding routine that boosted sensitivity by >2-fold, decreased coefficient of variation across replicates by 50%, and increased the quality of mass elution profiles through 3-fold more detected time points. Lastly, we furthered existing approaches for annotating detected masses with potential proteoforms through spectral fitting for possible proteoform family modifications and network viewing. These proteoform annotation approaches ultimately produced a more accurate way of finding related, but previously unknown proteoforms from intact mass-only data. Together, these quantitation workflow improvements advance the information obtainable from intact protein mass spectrometry analyses.
Collapse
Affiliation(s)
- Matthew T Robey
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
- Northwestern University, Evanston, Illinois 60208, United States
| | - Daisha Utley
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Joseph B Greer
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
- Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
- Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
- Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R Durbin
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
- Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
4
|
Di Marco F, Blöchl C, Esser-Skala W, Schäpertöns V, Zhang T, Wuhrer M, Sandra K, Wohlschlager T, Huber CG. Glycoproteomics of a Single Protein: Revealing Tens of Thousands of Myozyme Glycoforms by Hybrid HPLC-MS Approaches. Mol Cell Proteomics 2023; 22:100622. [PMID: 37478974 PMCID: PMC10470421 DOI: 10.1016/j.mcpro.2023.100622] [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: 01/31/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Characterization of highly glycosylated biopharma-ceuticals by mass spectrometry is challenging because of the huge chemical space of coexistent glycoforms present. Here, we report the use of an array of HPLC-mass spectrometry-based approaches at different structural levels of released glycan, glycopeptide, and hitherto unexplored intact glycoforms to scrutinize the biopharmaceutical Myozyme, containing the highly complex lysosomal enzyme recombinant acid α-glucosidase. The intrinsic heterogeneity of recombinant acid α-glucosidase glycoforms was unraveled using a novel strong anion exchange HPLC-mass spectrometry approach involving a pH-gradient of volatile buffers to facilitate chromatographic separation of glycoforms based on their degree of sialylation, followed by the acquisition of native mass spectra in an Orbitrap mass spectrometer. Upon considering the structures of 60 different glycans attached to seven glycosylation sites in the intact protein, the large set of interdependent data acquired at different structural levels was integrated using a set of bioinformatic tools and allowed the annotation of intact glycoforms unraveling more than 1,000,000 putative intact glycoforms. Detectable isoforms also included several mannose-6-phosphate variants, which are essential for directing the drug toward its target, the lysosomes. Finally, for the first time, we sought to validate the intact glycoform annotations by integrating experimental data on the enzymatically dissected proteoforms, which reduced the number of glycoforms supported by experimental evidence to 42,104. The latter verification clearly revealed the strengths but also intrinsic limitations of this approach for fully characterizing such highly complex glycoproteins by mass spectrometry.
Collapse
Affiliation(s)
- Fiammetta Di Marco
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Constantin Blöchl
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Salzburg, Austria; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wolfgang Esser-Skala
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria; Department of Biosciences and Medical Biology, Computational Systems Biology Group, University of Salzburg, Salzburg, Austria
| | - Veronika Schäpertöns
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Salzburg, Austria; Department of Biosciences and Medical Biology, Computational Systems Biology Group, University of Salzburg, Salzburg, Austria
| | - Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Koen Sandra
- Research Institute for Chromatography (RIC), Kortrijk, Belgium
| | - Therese Wohlschlager
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Salzburg, Austria.
| |
Collapse
|
5
|
Durbin KR, Robey MT, Voong LN, Fellers RT, Lutomski CA, El-Baba TJ, Robinson CV, Kelleher NL. ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data. J Proteome Res 2023; 22:2660-2668. [PMID: 37436406 PMCID: PMC10407923 DOI: 10.1021/acs.jproteome.3c00171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 07/13/2023]
Abstract
Native mass spectrometry has recently moved alongside traditional structural biology techniques in its ability to provide clear insights into the composition of protein complexes. However, to date, limited software tools are available for the comprehensive analysis of native mass spectrometry data on protein complexes, particularly for experiments aimed at elucidating the composition of an intact protein complex. Here, we introduce ProSight Native as a start-to-finish informatics platform for analyzing native protein and protein complex data. Combining mass determination via spectral deconvolution with a top-down database search and stoichiometry calculations, ProSight Native can determine the complete composition of protein complexes. To demonstrate its features, we used ProSight Native to successfully determine the composition of the homotetrameric membrane complex Aquaporin Z. We also revisited previously published spectra and were able to decipher the composition of a heterodimer complex bound with two noncovalently associated ligands. In addition to determining complex composition, we developed new tools in the software for validating native mass spectrometry fragment ions and mapping top-down fragmentation data onto three-dimensional protein structures. Taken together, ProSight Native will reduce the informatics burden on the growing field of native mass spectrometry, enabling the technology to further its reach.
Collapse
Affiliation(s)
| | | | - Lilien N. Voong
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
| | - Ryan T. Fellers
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
- Northwestern
University, Evanston, Illinois 60208, United States
| | - Corinne A. Lutomski
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Tarick J. El-Baba
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, 12 Mansfield Rd. Oxford OX1 3TA, U.K.
- Kavli
Institute for NanoScience Discovery, Dorothy
Crowfoot Hodgkin Building University of Oxford, Oxford OX1 3QU, U.K.
| | - Neil L. Kelleher
- Proteinaceous,
Inc., Evanston, Illinois 60201, United States
- Northwestern
University, Evanston, Illinois 60208, United States
| |
Collapse
|
6
|
Kline JT, Belford MW, Huang J, Greer JB, Bergen D, Fellers RT, Greer SM, Horn DM, Zabrouskov V, Huguet R, Boeser CL, Durbin KR, Fornelli L. Improved Label-Free Quantification of Intact Proteoforms Using Field Asymmetric Ion Mobility Spectrometry. Anal Chem 2023; 95:9090-9096. [PMID: 37252723 PMCID: PMC11149911 DOI: 10.1021/acs.analchem.3c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The high-throughput quantification of intact proteoforms using a label-free approach is typically performed on proteins in the 0-30 kDa mass range extracted from whole cell or tissue lysates. Unfortunately, even when high-resolution separation of proteoforms is achieved by either high-performance liquid chromatography or capillary electrophoresis, the number of proteoforms that can be identified and quantified is inevitably limited by the inherent sample complexity. Here, we benchmark label-free quantification of proteoforms of Escherichia coli by applying gas-phase fractionation (GPF) via field asymmetric ion mobility spectrometry (FAIMS). Recent advances in Orbitrap instrumentation have enabled the acquisition of high-quality intact and fragmentation mass spectra without the need for averaging time-domain transients prior to Fourier transform. The resulting speed improvements allowed for the application of multiple FAIMS compensation voltages in the same liquid chromatography-tandem mass spectrometry experiment without increasing the overall data acquisition cycle. As a result, the application of FAIMS to label-free quantification based on intact mass spectra substantially increases the number of both identified and quantified proteoforms without penalizing quantification accuracy in comparison to traditional label-free experiments that do not adopt GPF.
Collapse
Affiliation(s)
- Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | - Jingjing Huang
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Joseph B. Greer
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | - David Bergen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ryan T. Fellers
- Proteinaceous, Inc., Evanston, Illinois 60208, United States
| | | | - David M. Horn
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | | | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| |
Collapse
|
7
|
Böttinger K, Esser-Skala W, Segl M, Herwig C, Huber CG. At-line quantitative profiling of monoclonal antibody products during bioprocessing using HPLC-MS. Anal Chim Acta 2022; 1207:339813. [DOI: 10.1016/j.aca.2022.339813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 11/01/2022]
|
8
|
Abstract
Intact protein, top-down, and native mass spectrometry (MS) generally requires the deconvolution of electrospray ionization (ESI) mass spectra to assign the mass of components from their charge state distribution. For small, well-resolved proteins, the charge can usually be assigned based on the isotope distribution. However, it can be challenging to determine charge states with larger proteins that lack isotopic resolution, in complex mass spectra with overlapping charge states, and in native spectra that show adduction. To overcome these challenges, UniDec uses Bayesian deconvolution to assign charge states and to create a zero-charge mass distribution. UniDec is fast, user-friendly, and includes a range of advanced tools to assist in intact protein, top-down, and native MS data analysis. This chapter provides a step-by-step protocol and an in-depth explanation of the UniDec algorithm, and highlights the parameters that affect the deconvolution. It also covers advanced data analysis tools, such as macromolecular mass defect analysis and tools for assigning potential PTMs and bound ligands. Overall, this chapter provides users with a deeper understanding of UniDec, which will enhance the quality of deconvolutions and allow for more intricate MS experiments.
Collapse
Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.
- Bio5 Institute, University of Arizona, Tucson, AZ, USA.
| |
Collapse
|
9
|
Murisier A, Duivelshof BL, Fekete S, Bourquin J, Schmudlach A, Lauber MA, Nguyen JM, Beck A, Guillarme D, D'Atri V. Towards a simple on-line coupling of ion exchange chromatography and native mass spectrometry for the detailed characterization of monoclonal antibodies. J Chromatogr A 2021; 1655:462499. [PMID: 34487883 DOI: 10.1016/j.chroma.2021.462499] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
This work describes the direct hyphenation of cation exchange chromatography (CEX) with a compact, easy-to-use benchtop Time of Flight mass spectrometer (ToF/MS) for the analytical characterization of monoclonal antibodies (mAbs). For this purpose, a wide range of commercial mAb products (including expired samples and mAb biosimilars) were selected to draw reliable conclusions. From a chromatographic point of view, various buffers and column dimensions were tested. When considering pH response, buffer stability over time and MS compatibility, the best compromise is represented by the following recipe: 50 mM ammonium acetate, titrated to pH 5.0 (mobile phase A) and 160 mM ammonium acetate, titrated to pH 8.5 (mobile phase B). Despite the broader peaks observed with the 2.1 mm i.d. CEX column, this was preferentially selected for CEX-MS operation, since the efficiency loss (caused by extra-column dispersion) was still acceptable while MS compatibility was strongly enhanced (thanks to low flow rate). In terms of MS, it was important to avoid the use of glass-bottled mobile phases, laboratory glassware and glass vials to minimize loss of MS resolution, sensitivity, and mass accuracy due to metal contaminants. With this new CEX-MS setup, straightforward and rapid analysis (in less than 10 min) of charge variants was possible, allowing the separation and identification of several charge variants.
Collapse
Affiliation(s)
- Amarande Murisier
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Bastiaan L Duivelshof
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Szabolcs Fekete
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Julien Bourquin
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Andrew Schmudlach
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Matthew A Lauber
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Jennifer M Nguyen
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Alain Beck
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 5 Avenue Napoléon III, BP 60497 Saint-Julien-en-Genevois, France
| | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Valentina D'Atri
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, 1211 Geneva 4, Switzerland.
| |
Collapse
|
10
|
Nagornov KO, Gasilova N, Kozhinov AN, Virta P, Holm P, Menin L, Nesatyy VJ, Tsybin YO. Drug-to-Antibody Ratio Estimation via Proteoform Peak Integration in the Analysis of Antibody-Oligonucleotide Conjugates with Orbitrap Fourier Transform Mass Spectrometry. Anal Chem 2021; 93:12930-12937. [PMID: 34519496 DOI: 10.1021/acs.analchem.1c02247] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The therapeutic efficacy and pharmacokinetics of antibody-drug conjugates (ADCs) in general, and antibody-oligonucleotide conjugates (AOCs) in particular, depend on the drug-to-antibody ratio (DAR) distribution and average value. The DAR is considered a critical quality attribute, and information pertaining to it needs to be gathered during ADC/AOC development, production, and storage. However, because of the high structural complexity of ADC/AOC samples, particularly in the initial drug-development stages, the application of the current state-of-the-art mass spectrometric approaches can be limited for DAR analysis. Here, we demonstrate a novel approach for the analysis of complex ADC/AOC samples, following native size-exclusion chromatography Orbitrap Fourier transform mass spectrometry (FTMS). The approach is based on the integration of the proteoform-level mass spectral peaks in order to provide an estimate of the DAR distribution and its average value with less than 10% error. The peak integration is performed via a truncation of the Orbitrap's unreduced time-domain ion signals (transients) before mass spectra generation via FT processing. Transient recording and processing are undertaken using an external data acquisition system, FTMS Booster X2, coupled to a Q Exactive HF Orbitrap FTMS instrument. This approach has been applied to the analysis of whole and subunit-level trastuzumab conjugates with oligonucleotides. The obtained results indicate that ADC/AOC sample purification or simplification procedures, for example, deglycosylation, could be omitted or minimized prior to the DAR analysis, streamlining the drug-development process.
Collapse
Affiliation(s)
| | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Pasi Virta
- Department of Chemistry, University of Turku, 20014 Turku, Finland
| | - Patrik Holm
- Protein and Antibody Engineering Unit, Orion Pharma, 20380 Turku, Finland
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Victor J Nesatyy
- Protein and Antibody Engineering Unit, Orion Pharma, 20380 Turku, Finland
| | | |
Collapse
|
11
|
Di Marco F, Berger T, Esser-Skala W, Rapp E, Regl C, Huber CG. Simultaneous Monitoring of Monoclonal Antibody Variants by Strong Cation-Exchange Chromatography Hyphenated to Mass Spectrometry to Assess Quality Attributes of Rituximab-Based Biotherapeutics. Int J Mol Sci 2021; 22:9072. [PMID: 34445776 PMCID: PMC8396523 DOI: 10.3390/ijms22169072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Different manufacturing processes and storage conditions of biotherapeutics can lead to a significant variability in drug products arising from chemical and enzymatic post-translational modifications (PTMs), resulting in the co-existence of a plethora of proteoforms with different physicochemical properties. To unravel the heterogeneity of these proteoforms, novel approaches employing strong cation-exchange (SCX) high-performance liquid chromatography (HPLC) hyphenated to mass spectrometry (MS) using a pH gradient of volatile salts have been developed in recent years. Here, we apply an established SCX-HPLC-MS method to characterize and compare two rituximab-based biotherapeutics, the originator MabThera® and its Indian copy product Reditux™. The study assessed molecular differences between the two drug products in terms of C-terminal lysine variants, glycosylation patterns, and other basic and acidic variants. Overall, MabThera® and Reditux™ displayed differences at the molecular level. MabThera® showed a higher degree of galactosylated and sialylated glycoforms, while Reditux™ showed increased levels of oligomannose and afucosylated glycoforms. Moreover, the two drug products showed differences in terms of basic variants such as C-terminal lysine and N-terminal truncation, present in Reditux™ but not in MabThera®. This study demonstrates the capability of this fast SCX-HPLC-MS approach to compare different drug products and simultaneously assess some of their quality attributes.
Collapse
Affiliation(s)
- Fiammetta Di Marco
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria; (F.D.M.); (T.B.); (W.E.-S.); (C.R.)
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Thomas Berger
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria; (F.D.M.); (T.B.); (W.E.-S.); (C.R.)
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Wolfgang Esser-Skala
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria; (F.D.M.); (T.B.); (W.E.-S.); (C.R.)
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Department of Biosciences, Computational Systems Biology Group, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Erdmann Rapp
- glyXera GmbH, Brenneckestraße 20—ZENIT, 39120 Magdeburg, Germany;
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Christof Regl
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria; (F.D.M.); (T.B.); (W.E.-S.); (C.R.)
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria; (F.D.M.); (T.B.); (W.E.-S.); (C.R.)
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| |
Collapse
|