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Neutralizing antibodies against this infection have shown efficacy in in vivo studies. Thus, elucidation of the epitopes of neutralizing antibodies can aid in the design and development of effective vaccines against different strains of JEV. Here, we describe a combination of native mass spectrometry (native-MS) and hydrogen\/deuterium exchange mass spectrometry (HDX-MS) to complete screening of eight mouse monoclonal antibodies (MAbs) against JEV E-DIII to identify epitope regions. Native-MS was used as a first pass to identify the antibodies that formed a complex with the target antigen, and it revealed that seven of the eight monoclonal antibodies underwent binding. Native mass spectra of a MAb (JEV-27) known to be non-binding showed broad native-MS peaks and poor signal, suggesting the protein is a mixture or that there are impurities in the sample. We followed native-MS with HDX-MS to locate the binding sites for several of the complex-forming antibodies. This combination of two mass spectrometry-based approaches should be generally applicable and particularly suitable for screening of antigen\u2013antibody and other protein\u2013protein interactions when other traditional approaches give unclear results or are difficult, unavailable, or need to be validated.<\/jats:p>","DOI":"10.3390\/biom14030374","type":"journal-article","created":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T05:04:12Z","timestamp":1710911052000},"page":"374","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Epitope Mapping of Japanese Encephalitis Virus Neutralizing Antibodies by Native Mass Spectrometry and Hydrogen\/Deuterium Exchange"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6295-645X","authenticated-orcid":false,"given":"Jagat","family":"Adhikari","sequence":"first","affiliation":[{"name":"Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Heffernan","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa","family":"Edeling","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Estefania","family":"Fernandez","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7704-2810","authenticated-orcid":false,"given":"Prashant N.","family":"Jethva","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael S.","family":"Diamond","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA"},{"name":"Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63130, USA"},{"name":"Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63130, USA"},{"name":"Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daved H.","family":"Fremont","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA"},{"name":"Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA"},{"name":"Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael L.","family":"Gross","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"766","DOI":"10.2471\/BLT.10.085233","article-title":"Estimated global incidence of Japanese encephalitis: A systematic review","volume":"89","author":"Campbell","year":"2011","journal-title":"Bull. 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