{"entity": "researcher", "timestamp": "2026-08-20T20:49:07.563Z", "family": "Snijder", "given": "Joost", "initials": "J", "orcid": "0000-0002-9310-8226", "affiliations": ["Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan, Utrecht, Netherlands."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0"}}, "publications": [{"entity": "publication", "iuid": "d8c9aa48568e4a64a848ccfd196dbfc2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d8c9aa48568e4a64a848ccfd196dbfc2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d8c9aa48568e4a64a848ccfd196dbfc2"}}, "title": "Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry", "authors": [{"family": "Schulte", "given": "Douwe", "initials": "D"}, {"family": "\u0160iborov\u00e1", "given": "Marta", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Snijder", "given": "Joost", "initials": "J", "orcid": "0000-0002-9310-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0.json"}}], "type": "journal-article", "published": "2025-04-23", "journal": {"issn": "2050-084X", "volume": "14", "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.101322.3", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:51:03.972Z", "modified": "2026-08-20T13:51:04.047Z"}, {"entity": "publication", "iuid": "e8d5450e7fa24f618378b9c3a1a15e6d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e8d5450e7fa24f618378b9c3a1a15e6d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e8d5450e7fa24f618378b9c3a1a15e6d"}}, "title": "Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry.", "authors": [{"family": "Schulte", "given": "Douwe", "initials": "D"}, {"family": "\u0160iborov\u00e1", "given": "Marta", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Snijder", "given": "Joost", "initials": "J", "orcid": "0000-0002-9310-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0.json"}}], "type": "journal article", "published": "2025-04-23", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "14", "issn-l": "2050-084X"}, "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.", "doi": "10.7554/eLife.101322", "pmid": "40266252", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12017766"}, {"db": "pii", "key": "101322"}], "notes": [], "created": "2026-08-20T13:50:56.173Z", "modified": "2026-08-20T13:50:56.248Z"}, {"entity": "publication", "iuid": "21a8d3e13f23496193c8105214eb4439", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/21a8d3e13f23496193c8105214eb4439.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/21a8d3e13f23496193c8105214eb4439"}}, "title": "Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry \u2013 a perspective", "authors": [{"family": "Schulte", "given": "Douwe", "initials": "D", "orcid": "0000-0003-0594-0993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c6ad74fbd500482591b08a885e861caa.json"}}, {"family": "\u0160iborov\u00e1", "given": "Marta", "initials": "M", "orcid": "0000-0002-6879-5247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b902ba7871a42aa80297ce50aee55e6.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Snijder", "given": "Joost", "initials": "J", "orcid": "0000-0002-9310-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0.json"}}], "type": "peer-review", "published": "2025-03-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.101322.2.sa0", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:51:01.920Z", "modified": "2026-08-20T13:51:01.993Z"}, {"entity": "publication", "iuid": "8770f4bc45d54bcda6091cba4ead9123", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8770f4bc45d54bcda6091cba4ead9123.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8770f4bc45d54bcda6091cba4ead9123"}}, "title": "Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry \u2013 a perspective", "authors": [{"family": "Schulte", "given": "Douwe", "initials": "D", "orcid": "0000-0003-0594-0993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c6ad74fbd500482591b08a885e861caa.json"}}, {"family": "\u0160iborov\u00e1", "given": "Marta", "initials": "M", "orcid": "0000-0002-6879-5247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b902ba7871a42aa80297ce50aee55e6.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Snijder", "given": "Joost", "initials": "J", "orcid": "0000-0002-9310-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0.json"}}], "type": "posted-content", "published": "2025-03-18", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.101322.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:51:00.076Z", "modified": "2026-08-20T13:51:00.121Z"}, {"entity": "publication", "iuid": "f1d3015bfe124dbb9dd2fb84537c4b57", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f1d3015bfe124dbb9dd2fb84537c4b57.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f1d3015bfe124dbb9dd2fb84537c4b57"}}, "title": "Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry \u2013 a perspective", "authors": [{"family": "Schulte", "given": "Douwe", "initials": "D", "orcid": "0000-0003-0594-0993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c6ad74fbd500482591b08a885e861caa.json"}}, {"family": "\u0160iborov\u00e1", "given": "Marta", "initials": "M", "orcid": "0000-0002-6879-5247", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3b902ba7871a42aa80297ce50aee55e6.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Snijder", "given": "Joost", "initials": "J", "orcid": "0000-0002-9310-8226", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eaf244f006c744cea77ba2addf983ff0.json"}}], "type": "posted-content", "published": "2025-01-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.101322.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:58.087Z", "modified": "2026-08-20T13:50:58.268Z"}]}