1
|
Rao VN, Coelho CH. Public antibodies: convergent signatures in human humoral immunity against pathogens. mBio 2025; 16:e0224724. [PMID: 40237455 PMCID: PMC12077206 DOI: 10.1128/mbio.02247-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2025] Open
Abstract
The human humoral immune system has evolved to recognize a vast array of pathogenic threats. This ability is primarily driven by the immense diversity of antibodies generated by gene rearrangement during B cell development. However, different people often produce strikingly similar antibodies when exposed to the same antigen-known as public antibodies. Public antibodies not only reflect the immune system's ability to consistently select for optimal B cells but can also serve as signatures of the humoral responses triggered by infection and vaccination. In this Minireview, we examine and compare public antibody identification methods, including the identification criteria used based on V(D)J gene usage and similarity in the complementarity-determining region three sequences, and explore the molecular features of public antibodies elicited against common pathogens, including viruses, protozoa, and bacteria. Finally, we discuss the evolutionary significance and potential applications of public antibodies in informing the design of germline-targeting vaccines, predicting escape mutations in emerging viruses, and providing insights into the process of affinity maturation. The ongoing discovery of public antibodies in response to emerging pathogens holds the potential to improve pandemic preparedness, accelerate vaccine design efforts, and deepen our understanding of human B cell biology.
Collapse
Affiliation(s)
- Vishal N. Rao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Camila H. Coelho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| |
Collapse
|
2
|
Khristenko NA, Nagornov KO, Garcia C, Gasilova N, Gant M, Druart K, Kozhinov AN, Menin L, Chamot-Rooke J, Tsybin YO. Top-Down and Middle-Down Mass Spectrometry of Antibodies. Mol Cell Proteomics 2025:100989. [PMID: 40368137 DOI: 10.1016/j.mcpro.2025.100989] [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: 01/15/2025] [Revised: 04/19/2025] [Accepted: 04/22/2025] [Indexed: 05/16/2025] Open
Abstract
Therapeutic antibodies, primarily immunoglobulin G-based monoclonal antibodies, are developed to treat cancer, autoimmune disorders, and infectious diseases. Their large size, structural complexity, and heterogeneity pose significant analytical challenges, requiring the use of advanced characterization techniques. This review traces the 30-year evolution of top-down (TD) and middle-down (MD) mass spectrometry (MS) for antibody analysis, beginning with their initial applications and highlighting key advances and challenges throughout this period. TD MS allows for the analysis of intact antibodies, and MD MS performs analysis of the antibody subunits, even in complex biological samples. Both approaches preserve critical quality attributes such as sequence integrity, post-translational modifications (PTMs), disulfide bonds, and glycosylation patterns. Key milestones in TD and MD MS of antibodies include the use of structure-specific enzymes for subunit generation, the implementation of high-resolution mass spectrometers, and the adoption of non-ergodic ion activation methods such as electron transfer dissociation (ETD), electron capture dissociation (ECD), ultraviolet photodissociation (UVPD), and matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD). The combination of complementary dissociation methods and the use of consecutive ion activation approaches has further enhanced TD/MD MS performance. The current TD MS record of antibody sequencing with terminal product ions is about 60% sequence coverage obtained using the activated ion-ETD approach on a high-resolution MS platform. Current MD MS analyses with about 95% sequence coverage were achieved using combinations of ion activation and dissociation techniques. The review explores TD and MD MS analysis of novel mAb modalities, including antibody-drug conjugates, bispecific antibodies, and endogenous antibodies from biofluids as well as immunoglobulin A and M-type classes. Content.
Collapse
Affiliation(s)
| | | | - Camille Garcia
- Institut Pasteur, Université Paris Cité, and CNRS UAR2024, Paris, France
| | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Megan Gant
- Institut Pasteur, Université Paris Cité, and CNRS UAR2024, Paris, France
| | - Karen Druart
- Institut Pasteur, Université Paris Cité, and CNRS UAR2024, Paris, France
| | | | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julia Chamot-Rooke
- Institut Pasteur, Université Paris Cité, and CNRS UAR2024, Paris, France
| | - Yury O Tsybin
- Spectrotech, 69006 Lyon, France; Spectroswiss, 1015 Lausanne, Switzerland.
| |
Collapse
|
3
|
Zhao Y, Wang S, Huang J, Meng B, An D, Fang X, Wei Y, Dai X. A transformer-based semi-autoregressive framework for high-speed and accurate de novo peptide sequencing. Commun Biol 2025; 8:234. [PMID: 39948275 PMCID: PMC11825679 DOI: 10.1038/s42003-025-07584-0] [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: 07/02/2024] [Accepted: 01/21/2025] [Indexed: 02/16/2025] Open
Abstract
De novo peptide sequencing directly identifies peptides from mass spectrometry data, playing a critical role in discovering novel proteins and analyzing complex biological samples without reliance on existing databases. To address challenges in both speed and accuracy, a transformer-based model, TSARseqNovo, incorporates two key innovations: a Semi-Autoregressive decoder for parallel prediction of multiple amino acids and a Masking Refinement decoder for refining low-confidence predictions. These features significantly enhance sequencing efficiency and accuracy. Evaluations on the Nine-Species, Aggregated, and Glycoproteomic datasets, demonstrate that TSARseqNovo outperforms state-of-the-art models, including CasaNovo, NovoB, InstaNovo + , and π-HelixNovo. Specifically, TSARseqNovo achieves up to a 2-fold speed increase over CasaNovo and π-HelixNovo, and approximately 10-fold over NovoB and InstaNovo + , while also showing substantial improvements in peptide prediction precision, especially for long peptides. These advancements position TSARseqNovo as a powerful tool for accelerating high-throughput proteomics research and addressing increasingly complex biological questions.
Collapse
Affiliation(s)
- Yang Zhao
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China.
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
| | - Shuo Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Jinze Huang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Dong An
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
| | - Yaoguang Wei
- College of Information and Electrical Engineering, China Agricultural University, Beijing, 100083, China.
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
| |
Collapse
|
4
|
Malesys S, Torchet R, Saunier B, Maillet N. AntiBody Sequence Database. NAR Genom Bioinform 2024; 6:lqae171. [PMID: 39703430 PMCID: PMC11655285 DOI: 10.1093/nargab/lqae171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 11/13/2024] [Accepted: 11/19/2024] [Indexed: 12/21/2024] Open
Abstract
Antibodies play a crucial role in the humoral immune response against health threats, such as viral infections. Although the theoretical number of human immunoglobulins is well over a trillion, the total number of unique antibody protein sequences accessible in databases is much lower than the number found in a single individual. Training AI (Artificial Intelligence) models, for example to assist in developing serodiagnoses or antibody-based therapies, requires building datasets according to strict criteria to include as many standardized antibody sequences as possible. However, the available sequences are scattered across partially redundant databases, making it difficult to compile them into single non-redundant datasets. Here, we introduce ABSD (AntiBody Sequence Database, https://absd.pasteur.cloud), which contains data from major publicly available resources, creating the largest standardized, automatically updated and non-redundant source of public antibody sequences. This user-friendly and open website enables users to generate lists of antibodies based on selected criteria and download the unique sequence pairs of their variable regions.
Collapse
Affiliation(s)
- Simon Malesys
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 28 rue du Dr Roux, F-75015 Paris, France
| | - Rachel Torchet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 28 rue du Dr Roux, F-75015 Paris, France
| | - Bertrand Saunier
- Unité de Virologie Structurale, Institut Pasteur, Université Paris Cité, CNRS UMR 3569, 28 rue du Dr Roux, 75015 Paris, France
| | - Nicolas Maillet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 28 rue du Dr Roux, F-75015 Paris, France
| |
Collapse
|
5
|
Fridy PC, Rout MP, Ketaren NE. Nanobodies: From High-Throughput Identification to Therapeutic Development. Mol Cell Proteomics 2024; 23:100865. [PMID: 39433212 PMCID: PMC11609455 DOI: 10.1016/j.mcpro.2024.100865] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 10/08/2024] [Accepted: 10/13/2024] [Indexed: 10/23/2024] Open
Abstract
The camelid single-domain antibody fragment, commonly referred to as a nanobody, achieves the targeting power of conventional monoclonal antibodies (mAbs) at only a fraction of their size. Isolated from camelid species (including llamas, alpacas, and camels), their small size at ∼15 kDa, low structural complexity, and high stability compared with conventional antibodies have propelled nanobody technology into the limelight of biologic development. Nanobodies are proving themselves to be a potent complement to traditional mAb therapies, showing success in the treatment of, for example, autoimmune diseases and cancer, and more recently as therapeutic options to treat infectious diseases caused by rapidly evolving biological targets such as the SARS-CoV-2 virus. This review highlights the benefits of applying a proteomic approach to identify diverse nanobody sequences against a single antigen. This proteomic approach coupled with conventional yeast/phage display methods enables the production of highly diverse repertoires of nanobodies able to bind the vast epitope landscape of an antigen, with epitope sampling surpassing that of mAbs. Additionally, we aim to highlight recent findings illuminating the structural attributes of nanobodies that make them particularly amenable to comprehensive antigen sampling and to synergistic activity-underscoring the powerful advantage of acquiring a large, diverse nanobody repertoire against a single antigen. Lastly, we highlight the efforts being made in the clinical development of nanobodies, which have great potential as powerful diagnostic reagents and treatment options, especially when targeting infectious disease agents.
Collapse
Affiliation(s)
- Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA.
| |
Collapse
|
6
|
Vorauer C, Boniche-Alfaro C, Murphree T, Matsui T, Weiss T, Fries BC, Guttman M. Direct Mapping of Polyclonal Epitopes in Serum by HDX-MS. Anal Chem 2024; 96:16758-16767. [PMID: 39434663 PMCID: PMC11583827 DOI: 10.1021/acs.analchem.4c03274] [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: 10/23/2024]
Abstract
Elucidating the interactions that drive antigen recognition is central to understanding antibody-mediated protection and is vital for the rational design of immunogens. Often, structural knowledge of epitopes targeted by antibodies is derived from isolated studies of monoclonal antibodies, for which numerous structural techniques exist. In contrast, there are very few approaches capable of mapping the full scope of antigen surfaces targeted by polyclonal sera through the course of a natural antibody response. Here, we develop an approach using immobilized antigen coupled to hydrogen/deuterium exchange with mass spectrometry (HDX-MS) to probe epitope targeting in the context of the fully native serum environment. Using the well-characterized Staphylococcal enterotoxin B (SEB) as a model system, we show that complex combinations of epitopes can be detected and subtle differences across different antisera can be discerned. This work reveals new insight into how neutralizing antibodies and antisera target SEB and, more importantly, establishes a novel method for directly mapping the epitope landscape of polyclonal sera.
Collapse
Affiliation(s)
- Clint Vorauer
- Department of Medicinal Chemistry; University of Washington, Seattle, WA
| | - Camila Boniche-Alfaro
- Department of Medicine, Infectious Disease Division, Stony Brook University, Stony Brook, New York
- Veteran’s Administration Medical Center, Northport, New York
| | - Taylor Murphree
- Department of Medicinal Chemistry; University of Washington, Seattle, WA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Laboratory, SLAC, Menlo Park, CA
| | - Thomas Weiss
- Stanford Synchrotron Radiation Laboratory, SLAC, Menlo Park, CA
| | - Bettina C. Fries
- Department of Medicine, Infectious Disease Division, Stony Brook University, Stony Brook, New York
- Veteran’s Administration Medical Center, Northport, New York
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York
| | - Miklos Guttman
- Department of Medicinal Chemistry; University of Washington, Seattle, WA
| |
Collapse
|
7
|
Bernardes-Loch RM, Ribeiro AC, Ramírez-López CJ, Loch Gomes RA, Barros E, Filomeno Fontes EA, Baracat-Pereira MC. Human milk proteins differentiate over the sex of newborns and across stages of lactation. Clin Nutr ESPEN 2024; 62:144-156. [PMID: 38901936 DOI: 10.1016/j.clnesp.2024.05.013] [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: 12/18/2023] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND & AIMS Human milk (HM) is a complete food that meets the nutritional and energy demands of the newborns. It contains numerous bioactive components, including functional proteins. Variations in HM energy and lipid content have already been reported related to the newborn's sex, but differences between protein profiles are still scarce. This work aimed to identify differences between HM proteins produced by mothers of female and male newborns, in the lactation stages of colostrum and mature milk, and the metabolic pathways involved. METHODS A total of 98 HM samples were collected from 39 lactating women and classified according to the newborn's sex, stages of lactation, and three mothers' age groups, and evaluated about protein concentration and one-dimensional electrophoretic profile. Next, to assess samples with the greatest differences, the HM proteins regarding the newborn's sex and the stages of lactation were compared using nano-LC-MS/MS, in 24 HM samples randomly rearranged into four groups: female and male infants, and colostrum and mature milk. Functional classification, metabolic pathways, and protein interaction networks were analyzed by Gene Ontology, KEGG, and STRING, respectively. RESULTS The soluble protein content of HM decreased throughout lactation, with differences regarding isolated factors, such as mothers' age group, child's sex and stages of lactation, and also in terms of their interactions. A total of 146 proteins were identified, 42 of which showed different abundances over the sexes of newborns and 53 between the stages of lactation. In general, proteins related to metabolic processes were up-regulated for mothers of male infants and in the mature stage of lactation, while proteins related to defense were up-regulated in mothers of female infants and in the colostrum phase. CONCLUSION This study indicated that there are differentiated and specific nutritional and defense needs of newborns, by sex and by lactation phase, which is highly relevant for a more appropriate supply of food to infants receiving HM from donor mothers.
Collapse
Affiliation(s)
| | - Alessandra Casagrande Ribeiro
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG 36.570-900, Brazil; Department of Food Technology, Universidade Federal de Viçosa, Viçosa, MG 36.570-900, Brazil.
| | | | - Ruither Arthur Loch Gomes
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, MG 36.570-900, Brazil.
| | - Edvaldo Barros
- Nucleus for Biomolecule Analysis, Universidade Federal de Viçosa, Viçosa, MG 36.570-900, Brazil.
| | | | | |
Collapse
|
8
|
Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V. Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. NPJ Syst Biol Appl 2024; 10:73. [PMID: 38997321 PMCID: PMC11245537 DOI: 10.1038/s41540-024-00402-z] [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] [Received: 11/02/2023] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.
Collapse
Grants
- The Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to VG), UiO World-Leading Research Community (to VG), UiO: LifeScience Convergence Environment Immunolingo (to VG), EU Horizon 2020 iReceptorplus (#825821) (to VG), a Norwegian Cancer Society Grant (#215817, to VG), Research Council of Norway projects (#300740, (#311341, #331890 to VG), a Research Council of Norway IKTPLUSS project (#311341, to VG). This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 101007799 (Inno4Vac). This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA (to VG).
- Mass spectrometry-based proteomic analyses were performed by the Proteomics Core Facility, Department of Immunology, University of Oslo/Oslo University Hospital, which is supported by the Core Facilities program of the South-Eastern Norway Regional Health Authority. This core facility is also a member of the National Network of Advanced Proteomics Infrastructure (NAPI), which is funded by the Research Council of Norway INFRASTRUKTUR-program (project number: 295910).
Collapse
Affiliation(s)
- Khang Lê Quý
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Stensland
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sachin Singh
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | - Tuula A Nyman
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Igor Snapkow
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
9
|
Fiala J, Schuster D, Ollivier S, Pengelley S, Lubeck M, Busch F, Jankevics A, Raether O, Greisch JF, Heck AJR. Protein-Centric Analysis of Personalized Antibody Repertoires Using LC-MS-Based Fab-Profiling on a timsTOF. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1292-1300. [PMID: 38662593 PMCID: PMC11157643 DOI: 10.1021/jasms.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
Endogenous antibodies, or immunoglobulins (Igs), abundantly present in body fluids, represent some of the most challenging samples to analyze, largely due to the immense variability in their sequences and concentrations. It has been estimated that our body can produce billions of different Ig proteins with different isotypes, making their individual analysis seemingly impossible. However, recent advances in protein-centric proteomics using LC-MS coupled to Orbitrap mass analyzers to profile intact Fab fragments formed by selective cleavage at the IgG-hinge revealed that IgG repertoires may be less diverse, albeit unique for each donor. Serum repertoires seem to be dominated by a few hundred clones that cumulatively make up 50-95% of the total IgG content. Enabling such analyses required careful optimization of the chromatography and mass analysis, as all Fab analytes are highly alike in mass (46-51 kDa) and sequence. To extend the opportunities of this mass-spectrometry-based profiling of antibody repertoires, we here report the optimization and evaluation of an alternative MS platform, namely, the timsTOF, for antibody repertoire profiling. The timsTOF mass analyzer has gained traction in recent years for peptide-centric proteomics and found wide applicability in plasma proteomics, affinity proteomics, and HLA peptidomics, to name a few. However, for protein-centric analysis, this platform has been less explored. Here, we demonstrate that the timsTOF platform can be adapted to perform protein-centric LC-MS-based profiling of antibody repertoires. In a side-by-side comparison of the timsTOF and the Orbitrap we demonstrate that the extracted serum antibody repertoires are alike qualitatively and quantitatively, whereby in particular the sensitivity of the timsTOF platform excels. Future incorporation of advanced top-down capabilities on the timsTOF may make this platform a very valuable alternative for protein-centric proteomics and top-down proteomics and thus also for personalized antibody repertoire profiling.
Collapse
Affiliation(s)
- Jan Fiala
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Dina Schuster
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simon Ollivier
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Stuart Pengelley
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Markus Lubeck
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Florian Busch
- Bruker
Switzerland AG, 8117 Fällanden, Zurich Switzerland
| | - Andris Jankevics
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Oliver Raether
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | | | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
10
|
Townsend DR, Towers DM, Lavinder JJ, Ippolito GC. Innovations and trends in antibody repertoire analysis. Curr Opin Biotechnol 2024; 86:103082. [PMID: 38428225 DOI: 10.1016/j.copbio.2024.103082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/07/2023] [Accepted: 01/28/2024] [Indexed: 03/03/2024]
Abstract
Monoclonal antibodies have revolutionized the treatment of human diseases, which has made them the fastest-growing class of therapeutics, with global sales expected to reach $346.6 billion USD by 2028. Advances in antibody engineering and development have led to the creation of increasingly sophisticated antibody-based therapeutics (e.g. bispecific antibodies and chimeric antigen receptor T cells). However, approaches for antibody discovery have remained comparatively grounded in conventional yet reliable in vitro assays. Breakthrough developments in high-throughput single B-cell sequencing and immunoglobulin proteomic serology, however, have enabled the identification of high-affinity antibodies directly from endogenous B cells or circulating immunoglobulin produced in vivo. Moreover, advances in artificial intelligence offer vast potential for antibody discovery and design with large-scale repertoire datasets positioned as the optimal source of training data for such applications. We highlight advances and recent trends in how these technologies are being applied to antibody repertoire analysis.
Collapse
Affiliation(s)
- Douglas R Townsend
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Dalton M Towers
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
11
|
Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
Collapse
Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| |
Collapse
|
12
|
Houen G. Peptide Antibodies: Current Status. Methods Mol Biol 2024; 2821:1-8. [PMID: 38997476 DOI: 10.1007/978-1-0716-3914-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Peptide antibodies have become one of the most important classes of reagents in molecular biology and clinical diagnostics. For this reason, methods for their production and characterization continue to be developed, including basic peptide synthesis protocols, peptide-conjugate production and characterization, conformationally restricted peptides, immunization procedures, etc. Detailed mapping of peptide antibody epitopes has yielded important information on antibody-antigen interaction in general and specifically in relation to antibody cross-reactivity and theories of molecular mimicry. This information is essential for detailed understanding of paratope-epitope dynamics, design of antibodies for research, design of peptide-based vaccines, development of therapeutic peptide antibodies, and de novo design of antibodies with predetermined specificity.
Collapse
Affiliation(s)
- Gunnar Houen
- Department of Neurology and Translational Research Center, Rigshospitalet, Glostrup, Denmark.
| |
Collapse
|
13
|
Walter J, Eludin Z, Drabovich AP. Redefining serological diagnostics with immunoaffinity proteomics. Clin Proteomics 2023; 20:42. [PMID: 37821808 PMCID: PMC10568870 DOI: 10.1186/s12014-023-09431-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lack of universal reference standards, potential cross-reactivity, and challenges with multiplexing the complete panel of human immunoglobulin isotypes and subclasses. Redesign of conventional serological tests to include multiplex quantification of immunoglobulin isotypes and subclasses, utilize universal reference standards, and minimize cross-reactivity and non-specific binding will facilitate the development of assays with higher diagnostic specificity. Improved serological assays with higher diagnostic specificity will enable screenings of asymptomatic populations and may provide earlier detection of infectious diseases, autoimmune disorders, and cancer. In this review, we present the major clinical needs for serological diagnostics, overview conventional immunoassay detection techniques, present the emerging immunoassay detection technologies, and discuss in detail the advantages and limitations of mass spectrometry and immunoaffinity proteomics for serological diagnostics. Finally, we explore the design of novel immunoaffinity-proteomic assays to evaluate cell-mediated immunity and advance the sequencing of clinically relevant immunoglobulins.
Collapse
Affiliation(s)
- Jonathan Walter
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zicki Eludin
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
| |
Collapse
|
14
|
Pandeswari PB, Isaac AE, Sabareesh V. Database Creator for Mass Analysis of Peptides and Proteins, DC-MAPP: A Standalone Tool for Simplifying Manual Analysis of Mass Spectral Data to Identify Peptide/Protein Sequences. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1962-1969. [PMID: 37526995 DOI: 10.1021/jasms.3c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Proteomic studies typically involve the use of different types of software for annotating experimental tandem mass spectrometric data (MS/MS) and thereby simplifying the process of peptide and protein identification. For such annotations, these softwares calculate the m/z values of the peptide/protein precursor and fragment ions, for which a database of protein sequences must be provided as an input file. The calculated m/z values are stored as another database, which the user usually cannot view. Database Creator for Mass Analysis of Peptides and Proteins (DC-MAPP) is a novel standalone software that can create custom databases for "viewing" the calculated m/z values of precursor and fragment ions, prior to the database search. It contains three modules. Peptide/Protein sequences as per user's choice can be entered as input to the first module for creating a custom database. In the second module, m/z values must be queried-in, which are searched within the custom database to identify protein/peptide sequences. The third module is suited for peptide mass fingerprinting, which can be used to analyze both ESI and MALDI mass spectral data. The feature of "viewing" the custom database can be helpful not only for better understanding the search engine processes, but also for designing multiple reaction monitoring (MRM) methods. Post-translational modifications and protein isoforms can also be analyzed. Since, DC-MAPP relies on the protein/peptide "sequences" for creating custom databases, it may not be applicable for the searches involving spectral libraries. Python language was used for implementation, and the graphical user interface was built with Page/Tcl, making this tool more user-friendly. It is freely available at https://vit.ac.in/DC-MAPP/.
Collapse
Affiliation(s)
- Pandi Boomathi Pandeswari
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014, India
| | - Arnold Emerson Isaac
- Bioinformatics Programming Laboratory, School of Bio Sciences & Technology (SBST), VIT, Vellore, Tamil Nadu - 632014, India
| | - Varatharajan Sabareesh
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu - 632014, India
| |
Collapse
|
15
|
Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
Collapse
Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| |
Collapse
|
16
|
Zavialova M, Kamaeva D, Kazieva L, Skvortsov VS, Smirnova L. Some structural features of the peptide profile of myelin basic protein-hydrolyzing antibodies in schizophrenic patients. PeerJ 2023; 11:e15584. [PMID: 37431466 PMCID: PMC10329820 DOI: 10.7717/peerj.15584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/26/2023] [Indexed: 07/12/2023] Open
Abstract
The antibodies of schizophrenic patients that hydrolyze myelin basic protein (MBP) have been actively studied recently, but the mechanism of the catalytic properties of immunoglobulin molecules remains unknown. Determination of specific immunoglobulin sequences associated with the high activity of MBP proteolysis will help to understand the mechanisms of abzyme catalysis. In the course of comparative mass spectrometric analysis of IgG peptides from the blood serum of patients with acute schizophrenia and healthy people, 12 sequences were identified, which were found only in antibodies that hydrolyze MBP. These sequences belong to IgG heavy chains and κ- and λ-type light chains, with eight of them belonging to variable domains. The content of peptides from the variable regions of the light chains does not correlate with the proteolytic activity of IgG to MBP in patients with schizophrenia, whereas for two sequences from the variable regions of the heavy chains (FQ(+0.98)GWVTMTR and *LYLQMN(+0.98)SLR), an increase in activity with increasing their concentration. The results suggest that these sequences may be involved in one way or another in MBP hydrolysis.
Collapse
Affiliation(s)
| | - Daria Kamaeva
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | | | | | - Liudmila Smirnova
- Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| |
Collapse
|
17
|
Troelnikov A, Armour B, Putty T, Aggarwal A, Akerman A, Milogiannakis V, Chataway T, King J, Turville SG, Gordon TP, Wang JJ. Immunoglobulin repertoire restriction characterizes the serological responses of patients with predominantly antibody deficiency. J Allergy Clin Immunol 2023; 152:290-301.e7. [PMID: 36965845 DOI: 10.1016/j.jaci.2023.02.033] [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: 08/22/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/27/2023]
Abstract
BACKGROUND Predominantly antibody deficiency (PAD) is the most common category of inborn errors of immunity and is underpinned by impaired generation of appropriate antibody diversity and quantity. In the clinic, responses are interrogated by assessment of vaccination responses, which is central to many PAD diagnoses. However, the composition of the generated antibody repertoire is concealed from traditional quantitative measures of serological responses. Leveraging modern mass spectrometry-based proteomics (MS-proteomics), it is possible to elaborate the molecular features of specific antibody repertoires, which may address current limitations of diagnostic vaccinology. OBJECTIVES We sought to evaluate serum antibody responses in patients with PAD following vaccination with a neo-antigen (severe acute respiratory syndrome coronavirus-2 vaccination) using MS-proteomics. METHODS Following severe acute respiratory syndrome coronavirus-2 vaccination, serological responses in individuals with PAD and healthy controls (HCs) were assessed by anti-S1 subunit ELISA and neutralization assays. Purified anti-S1 subunit IgG and IgM was profiled by MS-proteomics for IGHV subfamily usage and somatic hypermutation analysis. RESULTS Twelve patients with PAD who were vaccine-responsive were recruited with 11 matched vaccinated HCs. Neutralization and end point anti-S1 titers were lower in PAD. All subjects with PAD demonstrated restricted anti-S1 IgG antibody repertoires, with usage of <5 IGHV subfamilies (median: 3; range 2-4), compared to ≥5 for the 11 HC subjects (P < .001). IGHV3-7 utilization was far less common in patients with PAD than in HCs (2 of 12 vs 10 of 11; P = .001). Amino acid substitutions due to somatic hypermutation per subfamily did not differ between groups. Anti-S1 IgM was present in 64% and 50% of HC and PAD cohorts, respectively, and did not differ significantly between HCs and patients with PAD. CONCLUSIONS This study demonstrates the breadth of anti-S1 antibodies elicited by vaccination at the proteome level and identifies stereotypical restriction of IGHV utilization in the IgG repertoire in patients with PAD compared with HC subjects. Despite uniformly pauci-clonal antibody repertoires some patients with PAD generated potent serological responses, highlighting a possible limitation of traditional serological techniques. These findings suggest that IgG repertoire restriction is a key feature of antibody repertoires in PAD.
Collapse
Affiliation(s)
- Alexander Troelnikov
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia.
| | - Bridie Armour
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia
| | - Trishni Putty
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia
| | | | | | | | - Tim Chataway
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Jovanka King
- SA Pathology, Adelaide, Australia; Women's and Children's Hospital Network, Adelaide, Australia; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | | | - Tom P Gordon
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia; Flinders Medical Centre, Bedford Park, Australia
| | - Jing Jing Wang
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia
| |
Collapse
|
18
|
Polak J, Wagnerberger JH, Torsetnes SB, Lindeman I, Høglund RAA, Vartdal F, Sollid LM, Lossius A. Single-cell transcriptomics combined with proteomics of intrathecal IgG reveal transcriptional heterogeneity of oligoclonal IgG-secreting cells in multiple sclerosis. Front Cell Neurosci 2023; 17:1189709. [PMID: 37362001 PMCID: PMC10285169 DOI: 10.3389/fncel.2023.1189709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
The phenotypes of B lineage cells that produce oligoclonal IgG in multiple sclerosis have not been unequivocally determined. Here, we utilized single-cell RNA-seq data of intrathecal B lineage cells in combination with mass spectrometry of intrathecally synthesized IgG to identify its cellular source. We found that the intrathecally produced IgG matched a larger fraction of clonally expanded antibody-secreting cells compared to singletons. The IgG was traced back to two clonally related clusters of antibody-secreting cells, one comprising highly proliferating cells, and the other consisting of more differentiated cells expressing genes associated with immunoglobulin synthesis. These findings suggest some degree of heterogeneity among cells that produce oligoclonal IgG in multiple sclerosis.
Collapse
Affiliation(s)
- Justyna Polak
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Johanna H. Wagnerberger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Ida Lindeman
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Rune A. Aa. Høglund
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Frode Vartdal
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Ludvig M. Sollid
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andreas Lossius
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| |
Collapse
|
19
|
Emmenegger M, Worth R, Fiedler S, Devenish SRA, Knowles TPJ, Aguzzi A. Protocol to determine antibody affinity and concentration in complex solutions using microfluidic antibody affinity profiling. STAR Protoc 2023; 4:102095. [PMID: 36853663 PMCID: PMC9925161 DOI: 10.1016/j.xpro.2023.102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/24/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
Conventional methods of measuring affinity are limited by artificial immobilization, large sample volumes, and homogeneous solutions. This protocol describes microfluidic antibody affinity profiling on complex human samples in solution to obtain a fingerprint reflecting both affinity and active concentration of the target protein. To illustrate the protocol, we analyze the antibody response in SARS-CoV-2 omicron-naïve samples against different SARS-CoV-2 variants of concern. However, the protocol and the technology are amenable to a broad spectrum of biomedical questions. For complete details on the use and execution of this protocol, please refer to Emmenegger et al. (2022),1 Schneider et al. (2022),2 and Fiedler et al. (2022).3.
Collapse
Affiliation(s)
- Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland.
| | - Roland Worth
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Sebastian Fiedler
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Sean R A Devenish
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland.
| |
Collapse
|
20
|
Kazieva LS, Farafonova TE, Zgoda VG. [Antibody proteomics]. BIOMEDITSINSKAIA KHIMIIA 2023; 69:5-18. [PMID: 36857423 DOI: 10.18097/pbmc20236901005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Antibodies represent an essential component of humoral immunity; therefore their study is important for molecular biology and medicine. The unique property of antibodies to specifically recognize and bind a certain molecular target (an antigen) determines their widespread application in treatment and diagnostics of diseases, as well as in laboratory and biotechnological practices. High specificity and affinity of antibodies is determined by the presence of primary structure variable regions, which are not encoded in the human genome and are unique for each antibody-producing B cell clone. Hence, there is little or no information about amino acid sequences of the variable regions in the databases. This differs identification of antibody primary structure from most of the proteomic studies because it requires either B cell genome sequencing or de novo amino acid sequencing of the antibody. The present review demonstrates some examples of proteomic and proteogenomic approaches and the methodological arsenal that proteomics can offer for studying antibodies, in particular, for identification of primary structure, evaluation of posttranslational modifications and application of bioinformatics tools for their decoding.
Collapse
Affiliation(s)
- L Sh Kazieva
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|
21
|
Beslic D, Tscheuschner G, Renard BY, Weller MG, Muth T. Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly. Brief Bioinform 2023; 24:bbac542. [PMID: 36545804 PMCID: PMC9851299 DOI: 10.1093/bib/bbac542] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody-antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69-99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
Collapse
Affiliation(s)
- Denis Beslic
- Robert Koch Institute, MF1, Nordufer 20, 13353 Berlin
| | - Georg Tscheuschner
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin
| | - Bernhard Y Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 Potsdam
| | - Michael G Weller
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin
| | - Thilo Muth
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin
| |
Collapse
|
22
|
Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
Collapse
Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
23
|
Creech M, Carvalho L, McCoy H, Jacobs J, Hinson HE. Mass Spectrometry-Based Approaches for Clinical Biomarker Discovery in Traumatic Brain Injury. Curr Treat Options Neurol 2022; 24:605-618. [PMID: 37025501 PMCID: PMC10072855 DOI: 10.1007/s11940-022-00742-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2022] [Indexed: 11/28/2022]
Abstract
Purpose of Review Precision treatments to address the multifaceted pathophysiology of traumatic brain injury (TBI) are desperately needed, which has led to the intense study of fluid-based protein biomarkers in TBI. Mass Spectrometry (MS) is increasingly being applied to biomarker discovery and quantification in neurological disease to explore the proteome, allowing for more flexibility in biomarker discovery than commonly encountered antibody-based assays. In this narrative review, we will provide specific examples of how MS technology has advanced translational research in traumatic brain injury (TBI) focusing on clinical studies, and looking ahead to promising emerging applications of MS to the field of Neurocritical Care. Recent Findings Proteomic biomarker discovery using MS technology in human subjects has included the full range of injury severity in TBI, though critically ill patients can offer more options to biofluids given the need for invasive monitoring. Blood, urine, cerebrospinal fluid, brain specimens, and cerebral extracellular fluid have all been sources for analysis. Emerging evidence suggests there are distinct proteomic profiles in radiographic TBI subtypes, and that biomarkers may be used to distinguish patients sustaining TBI from healthy controls. Metabolomics may offer a window into the perturbations of ongoing cerebral insults in critically ill patients after severe TBI. Summary Emerging MS technologies may offer biomarker discovery and validation opportunities not afforded by conventional means due to its ability to handle the complexities associated with the proteome. While MS techniques are relatively early in development in the neurosciences space, the potential applications to TBI and neurocritical care are likely to accelerate in the coming decade.
Collapse
Affiliation(s)
- Matthew Creech
- Department of Neurology, Oregon Health and Science University, Portland OR
| | - Lindsey Carvalho
- Department of Neurology, Oregon Health and Science University, Portland OR
| | - Heather McCoy
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA
| | - Jon Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA
| | - H E Hinson
- Department of Neurology, Oregon Health and Science University, Portland OR
- Department of Emergency Medicine, Oregon Health and Science University, Portland OR
| |
Collapse
|
24
|
Dekker PM, Azad MB, Boeren S, Mandhane PJ, Moraes TJ, Simons E, Subbarao P, Turvey SE, Saccenti E, Hettinga KA. The human milk proteome and allergy of mother and child: Exploring associations with protein abundances and protein network connectivity. Front Immunol 2022; 13:977470. [PMID: 36311719 PMCID: PMC9613325 DOI: 10.3389/fimmu.2022.977470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background The human milk proteome comprises a vast number of proteins with immunomodulatory functions, but it is not clear how this relates to allergy of the mother or allergy development in the breastfed infant. This study aimed to explore the relation between the human milk proteome and allergy of both mother and child. Methods Proteins were analyzed in milk samples from a subset of 300 mother-child dyads from the Canadian CHILD Cohort Study, selected based on maternal and child allergy phenotypes. For this selection, the definition of "allergy" included food allergy, eczema, allergic rhinitis, and asthma. Proteins were analyzed with non-targeted shotgun proteomics using filter-aided sample preparation (FASP) and nanoLC-Orbitrap-MS/MS. Protein abundances, based on label-free quantification, were compared using multiple statistical approaches, including univariate, multivariate, and network analyses. Results Using univariate analysis, we observed a trend that milk for infants who develop an allergy by 3 years of age contains higher abundances of immunoglobulin chains, irrespective of the allergy status of the mother. This observation suggests a difference in the milk's immunological potential, which might be related to the development of the infant's immune system. Furthermore, network analysis showed overall increased connectivity of proteins in the milk of allergic mothers and milk for infants who ultimately develop an allergy. This difference in connectivity was especially noted for proteins involved in the protein translation machinery and may be due to the physiological status of the mother, which is reflected in the interconnectedness of proteins in her milk. In addition, it was shown that network analysis complements the other methods for data analysis by revealing complex associations between the milk proteome and mother-child allergy status. Conclusion Together, these findings give new insights into how the human milk proteome, through differences in the abundance of individual proteins and protein-protein associations, relates to the allergy status of mother and child. In addition, these results inspire new research directions into the complex interplay of the mother-milk-infant triad and allergy.
Collapse
Affiliation(s)
- Pieter M. Dekker
- Food Quality and Design Group, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Meghan B. Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Interdisciplinary Lactation Centre (MILC), Children’s Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | | | - Theo J. Moraes
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Interdisciplinary Lactation Centre (MILC), Children’s Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Padmaja Subbarao
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Stuart E. Turvey
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Kasper A. Hettinga
- Food Quality and Design Group, Wageningen University and Research, Wageningen, Netherlands
| |
Collapse
|
25
|
Extrapolating missing antibody-virus measurements across serological studies. Cell Syst 2022; 13:561-573.e5. [PMID: 35798005 DOI: 10.1016/j.cels.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 05/03/2022] [Accepted: 06/10/2022] [Indexed: 01/25/2023]
Abstract
The development of new vaccines, as well as our understanding of key processes that shape viral evolution and host antibody repertoires, relies on measuring multiple antibody responses against large panels of viruses. Given the enormous diversity of circulating virus strains and antibody responses, comprehensively testing all antibody-virus interactions is infeasible. Even within individual studies with limited panels, exhaustive testing is not always performed, and there is no common framework for combining information across studies with partially overlapping panels, especially when the assay type or host species differ. Prior studies have demonstrated that antibody-virus interactions can be characterized in a vastly simpler and lower dimensional space, suggesting that relatively few measurements could predict unmeasured antibody-virus interactions. Here, we apply matrix completion to several large-scale influenza and HIV-1 studies. We explore how prediction accuracy evolves as the number of measurements changes and approximates the number of additional measurements necessary in several highly incomplete datasets (suggesting ∼250,000 measurements could be saved). In addition, we show how the method can combine disparate datasets, even when the number of available measurements is below the theoretical limit that guarantees successful prediction. This approach can be readily generalized to other viruses or more broadly to other low-dimensional biological datasets.
Collapse
|
26
|
Ionov S, Lee J. An Immunoproteomic Survey of the Antibody Landscape: Insights and Opportunities Revealed by Serological Repertoire Profiling. Front Immunol 2022; 13:832533. [PMID: 35178051 PMCID: PMC8843944 DOI: 10.3389/fimmu.2022.832533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Immunoproteomics has emerged as a versatile tool for analyzing the antibody repertoire in various disease contexts. Until recently, characterization of antibody molecules in biological fluids was limited to bulk serology, which identifies clinically relevant features of polyclonal antibody responses. The past decade, however, has seen the rise of mass-spectrometry-enabled proteomics methods that have allowed profiling of the antibody response at the molecular level, with the disease-specific serological repertoire elucidated in unprecedented detail. In this review, we present an up-to-date survey of insights into the disease-specific immunological repertoire by examining how quantitative proteomics-based approaches have shed light on the humoral immune response to infection and vaccination in pathogenic illnesses, the molecular basis of autoimmune disease, and the tumor-specific repertoire in cancer. We address limitations of this technology with a focus on emerging potential solutions and discuss the promise of high-resolution immunoproteomics in therapeutic discovery and novel vaccine design.
Collapse
Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
| |
Collapse
|
27
|
Broketa M, Bruhns P. Single-Cell Technologies for the Study of Antibody-Secreting Cells. Front Immunol 2022; 12:821729. [PMID: 35173713 PMCID: PMC8841722 DOI: 10.3389/fimmu.2021.821729] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Antibody-secreting cells (ASC), plasmablasts and plasma cells, are terminally differentiated B cells responsible for large-scale production and secretion of antibodies. ASC are derived from activated B cells, which may differentiate extrafollicularly or form germinal center (GC) reactions within secondary lymphoid organs. ASC therefore consist of short-lived, poorly matured plasmablasts that generally secrete lower-affinity antibodies, or long-lived, highly matured plasma cells that generally secrete higher-affinity antibodies. The ASC population is responsible for producing an immediate humoral B cell response, the polyclonal antibody repertoire, as well as in parallel building effective humoral memory and immunity, or potentially driving pathology in the case of autoimmunity. ASC are phenotypically and transcriptionally distinct from other B cells and further distinguishable by morphology, varied lifespans, and anatomical localization. Single cell analyses are required to interrogate the functional and transcriptional diversity of ASC and their secreted antibody repertoire and understand the contribution of individual ASC responses to the polyclonal humoral response. Here we summarize the current and emerging functional and molecular techniques for high-throughput characterization of ASC with single cell resolution, including flow and mass cytometry, spot-based and microfluidic-based assays, focusing on functional approaches of the secreted antibodies: specificity, affinity, and secretion rate.
Collapse
Affiliation(s)
- Matteo Broketa
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
| |
Collapse
|
28
|
Bondt A, Dingess KA, Hoek M, van Rijswijck DMH, Heck AJR. A Direct MS-Based Approach to Profile Human Milk Secretory Immunoglobulin A (IgA1) Reveals Donor-Specific Clonal Repertoires With High Longitudinal Stability. Front Immunol 2021; 12:789748. [PMID: 34938298 PMCID: PMC8685336 DOI: 10.3389/fimmu.2021.789748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/17/2021] [Indexed: 12/29/2022] Open
Abstract
Recently, a mass spectrometry-based approach was introduced to directly assess the IgG1 immunoglobulin clonal repertoires in plasma. Here we expanded upon this approach by describing a mass spectrometry-based technique to assess specifically the clonal repertoire of another important class of immunoglobulin molecules, IgA1, and show it is efficiently and robustly applicable to either milk or plasma samples. Focusing on two individual healthy donors, whose milk was sampled longitudinally during the first 16 weeks of lactation, we demonstrate that the total repertoire of milk sIgA1 is dominated by only 50-500 clones, even though the human body theoretically can generate several orders of magnitude more clones. We show that in each donor the sIgA1 repertoire only changes marginally and quite gradually over the monitored 16-week period of lactation. Furthermore, the observed overlap in clonal repertoires between the two individual donors is close to non-existent. Mothers provide protection to their newborn infants directly by the transfer of antibodies via breastfeeding. The approach introduced here, can be used to visualize the clonal repertoire transferred from mother to infant and to detect changes in-time in that repertoire adapting to changes in maternal physiology.
Collapse
Affiliation(s)
- Albert Bondt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Kelly A Dingess
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Danique M H van Rijswijck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| |
Collapse
|