De novo protein sequencing of antibodies for identification of neutralizing antibodies in human plasma post SARS-CoV-2 vaccination
peer-reviewed · Nature Communications · 2024
| Date | 2024-10-10 |
| Type | peer-reviewed |
| Venue | Nature Communications |
| Publisher | Springer Science and Business Media LLC |
| Contribution | downstream-application |
| DOI | 10.1038/s41467-024-53105-8 |
| Citations (OpenAlex) | 18 |
| Venue 2-year citedness | 17.60 |
Preprint version: de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination (2024-03-15, bioRxiv)
Abstract
The antibody response to vaccination and infection is a key component of the immune response to pathogens. Sequencing of peripheral B cells may not represent the complete B cell receptor repertoire. Here we present a method for sequencing human plasma-derived polyclonal IgG using a combination of mass spectrometry and B-cell sequencing. We investigate the IgG response to the Moderna Spikevax COVID-19 vaccine. From the sequencing data of the natural polyclonal response to vaccination, we generate 12 recombinant antibodies. Six derived recombinant antibodies, including four generated with de novo protein sequencing, exhibit similar or higher binding affinities than the original natural polyclonal antibody. Neutralization tests reveal that the six antibodies possess neutralizing capabilities against the target antigen. This research provides insights into sequencing polyclonal IgG antibodies and the potential of our approach in generating recombinant antibodies with robust binding affinity and neutralization capabilities. Directly examining the circulating IgG pool is crucial due to potential misrepresentations by B-cell analysis alone.
Methods and tools
- Polyclonal IgG neutralizing antibody discovery: Sequencing the circulating antibody repertoire itself rather than the B cells that make it. Human plasma-derived polyclonal IgG is sequenced by combining mass spectrometry with B-cell sequencing, applied to the IgG response to the Moderna Spikevax COVID-19 vaccine. Twelve recombinant antibodies were generated from the natural polyclonal response; six of them, including four derived by de novo protein sequencing, bound at least as well as the original polyclonal antibody, and all six neutralised the target antigen. The argument for the approach is that sequencing peripheral B cells may not represent the complete receptor repertoire, so the circulating IgG pool has to be examined directly. Notable as antibody discovery carried out end to end by a commercial de novo sequencing service.
Data deposited
- de novo Protein Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plas (MSV000093480) (as deposited) · MSV000093480
- de novo Protein Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 V (as deposited) · MSV000094953
Data used
- de novo Protein Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 V (as deposited) · MSV000094953
Cites (11)
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Cited by (13)
- From polyclonal to monoclonal: de novo sequencing of goat antibodies for a standardized ApoA-I immunoturbidimetric assay (2026) both
- Mass Spectrometry-based Antibody Sequencing Technologies (2026) both
- Deep coverage and extended sequence reads obtained with a single archaeal protease expedite de novo protein sequencing by mass spectrometry (2026) both
- Generalizable Direct Protein Sequencing With InstaNexus (2026) both
- XA-Novo: an accurate and high-throughput mass spectrometry-based de novo sequencing technology for monoclonal antibodies and antibody mixtures (2026) both
- AbNovoBench: a resource and benchmarking platform for monoclonal antibody de novo sequencing (2026) both
- Identification of Unknown Biological Toxin Proteins Using Mass Spectrometry: A Case Study on De Novo Sequencing of Ricin (2025) both
- Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle–Down, and De Novo Bottom–Up Mass Spectrometry (2025) both
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2025) both
- Identification of broadly inhibitory anti-PfEMP1 antibodies by mass spectrometry sequencing of plasma IgG from a malaria-exposed child (2025) both
- Generalizable direct protein sequencing with InstaNexus (2025) crossref
- Cumulating MS Signal enables polyclonal antibody analysis (2025) both
- Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (2024) crossref