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bioRxiv · 10.1101/2024.06.21.600107

Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry - a perspective.

Schulte, D.·Siborova, M.·Kall, L.·Snijder, J.
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Abstract

Antibodies are a major component of adaptive immunity against invading pathogens. Here we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in convalescent serum. This approach aims to perform simultaneous antibody sequencing and epitope mapping using a combination of single particle cryo-electron microscopy (cryoEM) and bottom-up proteomics techniques based on mass spectrometry (LC-MS/MS). We evaluate the performance of the deep-learning tool ModelAngelo in determining de novo antibody sequences directly from reconstructed 3D volumes of antibody-antigen complexes. We demonstrate that while map quality is a critical bottleneck, it is possible to sequence antibody variable domains from cryoEM reconstructions with accuracies of up to 80-90%. While the rate of errors exceeds the typical levels of somatic hypermutation, we show that the ModelAngelo-derived sequences can be used to assign the used V-genes. This provides a functional guide to assemble de novo peptides from LC-MS/MS data more accurately and improves the tolerance to a background of polyclonal antibody sequences. Following this proof-of-principle, we discuss the feasibility and future directions of this approach to characterize antigen-specific antibody repertoires.

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Schulte, D., Siborova, M., Kall, L., Snijder, J.. 2024-06-22. Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry - a perspective.. https://doi.org/10.1101/2024.06.21.600107

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