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Benazza R, Koutsopetras I, Vaur V, Chaubet G, Hernandez-Alba O, Cianférani S. SEC-MS in denaturing conditions (dSEC-MS) for in-depth analysis of rebridged monoclonal antibody-based formats. Talanta 2024; 272:125727. [PMID: 38364570 DOI: 10.1016/j.talanta.2024.125727] [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: 07/18/2023] [Revised: 12/04/2023] [Accepted: 01/27/2024] [Indexed: 02/18/2024]
Abstract
Disulfide rebridging methods are emerging recently as new ways to specifically modify antibody-based entities and produce future conjugates. Briefly, the solvent-accessible disulfide bonds of antibodies or antigen-binding fragments (Fab) thereof are reduced under controlled conditions and further covalently attached with a rebridging agent allowing the incorporation of one payload per disulfide bond. There are many examples of successful rebridging cases providing homogeneous conjugates due to the use of symmetrical reagents, such as dibromomaleimides. However, partial rebridging due to the use of unsymmetrical ones, containing functional groups with different reactivity, usually leads to the development of heterogeneous species that cannot be identified by a simple sodium dodecyl sulfate-polyacrylamide gel eletrophoresis (SDS-PAGE) due to its lack of sensitivity, resolution and low mass accuracy. Mass spectrometry coupled to liquid chromatography (LC-MS) approaches have already been demonstrated as highly promising alternatives for the characterization of newly developed antibody-drug-conjugate (ADC) and monoclonal antibody (mAb)-based formats. We report here the in-depth characterization of covalently rebridged antibodies and Fab fragments in-development, using size-exclusion chromatography hyphenated to mass spectrometry in denaturing conditions (denaturing SEC-MS, dSEC-MS). DSEC-MS was used to monitor closely the rebridging reaction of a conjugated trastuzumab, in addition to conjugated Fab fragments, which allowed an unambiguous identification of the covalently rebridged products along with the unbound species. This all-in-one approach allowed a straightforward analysis of the studied samples with precise mass measurement; critical quality attributes (CQAs) assessment along with rebridging efficiency determination.
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Affiliation(s)
- Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI-FR2048, 67087 Strasbourg, France
| | - Ilias Koutsopetras
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI-FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI-FR2048, 67087 Strasbourg, France.
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2
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Schachner LF, Mullen C, Phung W, Hinkle JD, Beardsley MI, Bentley T, Day P, Tsai C, Sukumaran S, Baginski T, DiCara D, Agard NJ, Masureel M, Gober J, ElSohly AM, Melani R, Syka JEP, Huguet R, Marty MT, Sandoval W. Exposing the molecular heterogeneity of glycosylated biotherapeutics. Nat Commun 2024; 15:3259. [PMID: 38627419 PMCID: PMC11021452 DOI: 10.1038/s41467-024-47693-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The heterogeneity inherent in today's biotherapeutics, especially as a result of heavy glycosylation, can affect a molecule's safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins or other heterogeneous biotherapeutics. Here, we present an approach to the molecular assessment of biotherapeutics that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact heterogeneous and/or glycosylated proteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment. For glycoproteins in particular, the method may offer insights into glycan composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug's pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.
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Affiliation(s)
- Luis F Schachner
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Christopher Mullen
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Wilson Phung
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua D Hinkle
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | | | - Tracy Bentley
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Day
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Christina Tsai
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Protein Analytical Development, Ascendis Pharma, Palo Alto, CA, USA
| | - Siddharth Sukumaran
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
- Translational Pharmacometrics, Janssen, Horsham, PA, USA
| | - Tomasz Baginski
- Pharmaceutical Technical Development, Genentech, Inc., South San Francisco, CA, USA
| | - Danielle DiCara
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Nicholas J Agard
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Joshua Gober
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Adel M ElSohly
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Rafael Melani
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - John E P Syka
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Romain Huguet
- Life Sciences Mass Spectrometry, Thermo Fisher Scientific, Inc., San Jose, CA, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA.
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3
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Shaw J, Harvey S, Du C, Xu Z, Olmedillas E, Saphire EO, Wysocki VH. Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583498. [PMID: 38496594 PMCID: PMC10942452 DOI: 10.1101/2024.03.07.583498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Herein, we focus on native mass spectrometry (nMS) combined with a fast, tunable gas-phase charge reduction, electron capture charge reduction (ECCR), and illustrate its utility in the characterization of protein complex topology and glycoprotein heterogeneity. ECCR is illustrated to effectively spread the charge states of tetradecameric GroEL, illustrating Orbitrap m/z measurement out to greater than 100,000 m/z. For both the pentameric C-reactive protein and tetradecameric GroEL, our novel device combining ECCR with surface induced dissociation (SID) lowers the charge states and produces more topologically informative fragmentation. While more native-like fragmentation has previously been illustrated for complexes charge reduced by proton abstraction in solution, this is the first illustration that ECCR can lead to more native-like SID fragmentation of protein complexes. Application to protein glycosylation, one of the most common and diverse protein posttranslational modifications, is also illustrated because glycosylation is important for structural and functional properties and plays essential roles in many key biological processes. The immense heterogeneity resulting from variability in glycosylation sites and glycan composition and structure poses significant analytical challenges that hinder a mechanistic understanding of the biological role of glycosylation. Data for stabilized heavily glycosylated SARS-CoV-2 spike protein trimer and thyroglobulin dimer illustrate that ECCR enables significantly improved resolution of glycan heterogeneity. Without ECCR, the charge states of a glycoprotein complex are not resolved and average mass determination is available only through the use of charge detection mass spectrometry or mass photometry. With ECCR after narrow m/z selection, multiple glycoform m/z values are apparent, providing quick global, glycoform profiling and providing a future path for glycan localization on individual intact glycoforms (e.g., though top-down dissociation).
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Affiliation(s)
- Jared Shaw
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588
| | - Sophie Harvey
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
| | - Chen Du
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
| | - Zhixin Xu
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
| | - Eduardo Olmedillas
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92037
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
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4
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Dunham SD, Brodbelt JS. Enhancing Top-Down Analysis of Proteins by Combining Ultraviolet Photodissociation (UVPD), Proton-Transfer Charge Reduction (PTCR), and Gas-Phase Fractionation to Alleviate the Impact of Nondissociated Precursor Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:255-265. [PMID: 38150423 DOI: 10.1021/jasms.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Recent advances in top-down mass spectrometry strategies continue to improve the analysis of intact proteins. 193 nm ultraviolet photodissociation (UVPD) is one method well-suited for top-down analysis. UVPD is often performed using relatively low photon flux in order to limit multiple-generation dissociation of fragment ions and maximize sequence coverage. Consequently, a large portion of the precursor ion survives the UVPD process, dominates the spectrum, and may impede identification of fragment ions. Here, we explore the isolation of subpopulations of fragment ions lower and higher than the precursor ion after UVPD as a means to eliminate the impact of the surviving precursor ion on the detection of low abundance fragment ions. This gas-phase fractionation method improved sequence coverage harvested from fragment ions found in the m/z regions lower and higher than the precursor by an average factor of 1.3 and 2.3, respectively. Combining this gas-phase fractionation method with proton transfer charge reduction (PTCR) further increased the sequence coverage obtained from these m/z regions by another factor of 1.3 and 1.4, respectively. Implementing a post-UVPD fractionation + PTCR strategy with six fractionation events resulted in a sequence coverage of 75% for enolase, the highest reported for 193 nm UVPD.
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Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
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5
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Shi RL, Dillon MA, Compton PD, Sawyer WS, Thorup JR, Kwong M, Chan P, Chiu CPC, Li R, Yadav R, Lee GY, Gober JG, Li Z, ElSohly AM, Ovacik AM, Koerber JT, Spiess C, Josephs JL, Tran JC. High-Throughput Analyses of Therapeutic Antibodies Using High-Field Asymmetric Waveform Ion Mobility Spectrometry Combined with SampleStream and Intact Protein Mass Spectrometry. Anal Chem 2023; 95:17263-17272. [PMID: 37956201 DOI: 10.1021/acs.analchem.3c03158] [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: 11/15/2023]
Abstract
Intact protein mass spectrometry (MS) coupled with liquid chromatography was applied to characterize the pharmacokinetics and stability profiles of therapeutic proteins. However, limitations from chromatography, including throughput and carryover, result in challenges with handling large sample numbers. Here, we combined intact protein MS with multiple front-end separations, including affinity capture, SampleStream, and high-field asymmetric waveform ion mobility spectrometry (FAIMS), to perform high-throughput and specific mass measurements of a multivalent antibody with one antigen-binding fragment (Fab) fused to an immunoglobulin G1 (IgG1) antibody. Generic affinity capture ensures the retention of both intact species 1Fab-IgG1 and the tentative degradation product IgG1. Subsequently, the analytes were directly loaded into SampleStream, where each injection occurs within ∼30 s. By separating ions prior to MS detection, FAIMS further offered improvement in signal-overnoise by ∼30% for denatured protein MS via employing compensation voltages that were optimized for different antibody species. When enhanced FAIMS transmission of 1Fab-IgG1 was employed, a qualified assay was established for spiked-in serum samples between 0.1 and 25 μg/mL, resulting in ∼10% accuracy bias and precision coefficient of variation. Selective FAIMS transmission of IgG1 as the degradation surrogate product enabled more sensitive detection of clipped species for intact 1Fab-IgG1 at 5 μg/mL in serum, generating an assay to measure 1Fab-IgG1 truncation between 2.5 and 50% with accuracy and precision below 20% bias and coefficient of variation. Our results revealed that the SampleStream-FAIMS-MS platform affords high throughput, selectivity, and sensitivity for characterizing therapeutic antibodies from complex biomatrices qualitatively and quantitatively.
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Affiliation(s)
- Rachel Liuqing Shi
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Michael A Dillon
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Philip D Compton
- Integrated Protein Technologies, Evanston, Illinois 60201, United States
| | - William S Sawyer
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - John R Thorup
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Mandy Kwong
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Pamela Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - Cecilia P C Chiu
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Ran Li
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, Genentech Inc., South San Francisco, California 94080, United States
| | - Rajbharan Yadav
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, Genentech Inc., South San Francisco, California 94080, United States
| | - Genee Y Lee
- Department of Molecular Oncology, Genentech Inc., South San Francisco, California 94080, United States
| | - Joshua G Gober
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | - Zhiyu Li
- The DMPK Service Department, WuXi AppTec Inc., Shanghai 200131, China
| | - Adel M ElSohly
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, United States
| | - Ayse Meric Ovacik
- Department of Preclinical and Translational Pharmacokinetics and Pharmacodynamics, Genentech Inc., South San Francisco, California 94080, United States
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Christoph Spiess
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, California 94080, United States
| | - Jonathan L Josephs
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
| | - John C Tran
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California 94080, United States
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6
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Gass DT, Cordes MS, Alberti SN, Kim HJ, Gallagher ES. Evidence of H/D Exchange within Metal-Adducted Carbohydrates after Ion/Ion-Dissociation Reactions. J Am Chem Soc 2023; 145:23972-23985. [PMID: 37874934 DOI: 10.1021/jacs.3c05793] [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: 10/26/2023]
Abstract
Tandem mass spectrometry (MS/MS) using fragmentation has become one of the most effective methods for gaining sequence and structural information on biomolecules. Ion/ion reactions are competitive reactions, where either proton transfer (PT) or electron transfer (ET) can occur from interactions between multiply charged cations and singly charged anions. Utilizing ion/ion reactions with fluoranthene has offered a unique method of fragment formation for the structural elucidation of biomolecules. Fluoranthene is considered an ideal anion reagent because it selectively causes electron-transfer dissociation (ETD) and minimizes PT when interacting with peptides. However, limited investigations have sought to understand how fluoranthene─the primary, commercially available anion reagent─interacts with other biomolecules. Here, we apply deuterium labeling to investigate ion/ion reaction mechanisms between fluoranthene and divalent, metal-adducted carbohydrates (Ca2+, Mg2+, Co2+, and Ni2+). Deuterium labeling of carbohydrates allowed us to observe evidence of hydrogen/deuterium exchange (HDX) occurring after ion/ion dissociation reactions. The extent of deuterium loss is dependent on several factors, including the physical properties of the metal ion and the fragment structure. Based on the deuterium labeling data, we have proposed ETD, PTD, and intermolecular PT─also described as HDX─mechanisms. This research provides a fundamental perspective of ion/ion and ion/molecule reaction mechanisms and illustrates properties that impact ion/ion and ion/molecule reactions for carbohydrates. Together, this could improve the capability to distinguish complex and heterogeneous biomolecules, such as carbohydrates.
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Affiliation(s)
- Darren T Gass
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sebastian N Alberti
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - H Jamie Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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7
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Lee H, Chofflet N, Liu J, Fan S, Lu Z, Resua Rojas M, Penndorf P, Bailey AO, Russell WK, Machius M, Ren G, Takahashi H, Rudenko G. Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function. J Biol Chem 2023; 299:104586. [PMID: 36889589 PMCID: PMC10131064 DOI: 10.1016/j.jbc.2023.104586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
MDGAs (MAM domain-containing glycosylphosphatidylinositol anchors) are synaptic cell surface molecules that regulate the formation of trans-synaptic bridges between neurexins (NRXNs) and neuroligins (NLGNs), which promote synaptic development. Mutations in MDGAs are implicated in various neuropsychiatric diseases. MDGAs bind NLGNs in cis on the postsynaptic membrane and physically block NLGNs from binding to NRXNs. In crystal structures, the six immunoglobulin (Ig) and single fibronectin III domains of MDGA1 reveal a striking compact, triangular shape, both alone and in complex with NLGNs. Whether this unusual domain arrangement is required for biological function or other arrangements occur with different functional outcomes is unknown. Here, we show that WT MDGA1 can adopt both compact and extended 3D conformations that bind NLGN2. Designer mutants targeting strategic molecular elbows in MDGA1 alter the distribution of 3D conformations while leaving the binding affinity between soluble ectodomains of MDGA1 and NLGN2 intact. In contrast, in a cellular context, these mutants result in unique combinations of functional consequences, including altered binding to NLGN2, decreased capacity to conceal NLGN2 from NRXN1β, and/or suppressed NLGN2-mediated inhibitory presynaptic differentiation, despite the mutations being located far from the MDGA1-NLGN2 interaction site. Thus, the 3D conformation of the entire MDGA1 ectodomain appears critical for its function, and its NLGN-binding site on Ig1-Ig2 is not independent of the rest of the molecule. As a result, global 3D conformational changes to the MDGA1 ectodomain via strategic elbows may form a molecular mechanism to regulate MDGA1 action within the synaptic cleft.
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Affiliation(s)
- Hubert Lee
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Nicolas Chofflet
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada; Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shanghua Fan
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhuoyang Lu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martin Resua Rojas
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada
| | - Patrick Penndorf
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mischa Machius
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Hideto Takahashi
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada; Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada.
| | - Gabby Rudenko
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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8
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Walker JN, Lam R, Brodbelt JS. Enhanced Characterization of Histones Using 193 nm Ultraviolet Photodissociation and Proton Transfer Charge Reduction. Anal Chem 2023; 95:5985-5993. [PMID: 36989418 DOI: 10.1021/acs.analchem.2c05765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Top-down characterization of histones, proteins that are critical participants in an array of DNA-dependent processes, offers the potential to examine the relationship between histone structure and mechanisms of genetic regulation. Mapping patterns of post-translational modifications (PTMs) of histones requires extensive backbone cleavages to bracket the sites of mass shifts corresponding to specific PTMs. Ultraviolet photodissociation (UVPD) causes substantial fragmentation of proteins, which is well-suited for PTM localization, but the resulting spectra are congested with fragment ions that may have overlapping isotopic distributions that confound deconvolution. Gas-phase proton transfer charge reduction (PTCR) decreases the charge states of highly charged ions, thus alleviating this congestion and facilitating the identification of additional sequence-determining and PTM-localizing fragment ions. By integrating UVPD with PTCR for histone proteoform analyses, sequence coverages up to 91% were achieved for calf thymus histone H4 containing acetylation marks at the N-terminus and Lys12 as well as a dimethylation at Arg3. UVPD-PTCR exhibited large gains in characterization for other histones, such as histone H2A, increasing the sequence coverage from 59 to 77% for monoacetylated H2A.
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Affiliation(s)
- Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Raymond Lam
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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9
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Wang X, Mayorga-Flores M, Bien KG, Bailey AO, Iwahara J. DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein. J Biol Chem 2022; 298:102577. [DOI: 10.1016/j.jbc.2022.102577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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10
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Chen Q, Dai R, Yao X, Chaihu L, Tong W, Huang Y, Wang G. Improving Accuracy in Mass Spectrometry-Based Mass Determination of Intact Heterogeneous Protein Utilizing the Universal Benefits of Charge Reduction and Alternative Gas-Phase Reactions. Anal Chem 2022; 94:13869-13878. [PMID: 36170625 DOI: 10.1021/acs.analchem.2c02586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In mass analysis of proteins, mass spectrometry directly measures the mass to charge ratios of ionized proteins and promises higher accuracy than that of indirect approaches measuring other physicochemical properties, provided that the charge states of detected ions are determined. Accurate mass determination of heterogeneously glycosylated proteins is often hindered by unreliable charge determination due to the insufficient resolution of signals from different charge states and inconsistency among mass profiles of ions in individual charge states. Limited charge reduction of a subpopulation of proteoforms using electron transfer/capture reactions (ETnoD/ETnoD) solves this problem by narrowing the mass distribution of examined proteoforms and preserving the mass profile of the precursor charge state in the reduced charge states. However, the limited availability of ETnoD/ETnoD function in commercial instruments limits the application of this approach. Here, utilizing a range of charge-dependent and accuracy-affecting spectral features revealed by a systematic evaluation at levels of both the ensemble and subpopulation of proteoforms based on theoretical models and experiments, we developed a limited charge reduction workflow that enables using collision-induced dissociation and higher energy collisional dissociation, two widely available reactions, as alternatives to ETnoD/ETnoD while providing adequate accuracy. Alternatively, substituting proton transfer charge reduction for ETnoD/ETnoD provides higher accuracy of mass determination. Performing mass selection in a window-sliding manner improves the accuracy and allows profiling of the whole proteoform distribution. The proposed workflow may facilitate the development of universal characterization strategies for more complex and heterogeneous protein systems.
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Affiliation(s)
- Qingrong Chen
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Rongrong Dai
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaopeng Yao
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Lingxiao Chaihu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Wenjun Tong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yanyi Huang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
| | - Guanbo Wang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
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Yang W, Ivanov DG, Kaltashov IA. Extending the capabilities of intact-mass analyses to monoclonal immunoglobulins of the E-isotype (IgE). MAbs 2022; 14:2103906. [PMID: 35895856 PMCID: PMC9336480 DOI: 10.1080/19420862.2022.2103906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mass spectrometry (MS) has become an indispensable tool in structural characterization and quality control of monoclonal antibodies (mAbs). Intact-mass analysis is a particularly attractive option that provides a powerful and cost-effective means to not only confirm the structural integrity of the protein, but also probe its interactions with therapeutic targets. To a certain extent, this success can be attributed to relatively modest glycosylation levels exhibited by IgG molecules, which limits their structural heterogeneity and enables straightforward mass measurements at the intact molecule level. The recent surge of interest in expanding the repertoire of mAbs to include other classes of immunoglobulins places a premium on efforts to adapt the IgG-tailored experimental strategies to other classes of antibodies, but their dramatically higher levels of glycosylation may create insurmountable obstacles. The monoclonal murine IgE antibody explored in this work provides a challenging model system, as its glycosylation level exceeds that of conventional IgG mAbs by a factor of nine. The commercial sample, which included various IgE fragments, yields a poorly resolved ionic signal in intact-mass measurements, from which little useful information can be extracted. However, coupling MS measurements with the limited charge reduction of select polycationic species in the gas phase gives rise to well-defined charge ladders, from which both ionic masses and charges can be readily determined. The measurements reveal significant variation of the extent of glycosylation within intact IgE molecules, as well as the presence of low-molecular weight impurities in the commercial IgE sample. Furthermore, incubation of the monoclonal IgE with its antigen (ovalbumin) gives rise to the formation of complexes with varying stoichiometries, which can also be uniquely identified using a combination of native MS, limited charge reduction in the gas phase and data fitting procedures. This work demonstrates that following appropriate modifications, intact-mass analysis measurements can be successfully applied to mAbs beyond the IgG isotype, providing a wealth of information not only on the mass distribution of the intact IgE molecules, but also their large-scale conformational integrity, the integrity of their covalent structure, and their interactions with antigens.
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Affiliation(s)
- Wenhua Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.,College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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