biostudies-literatureBraun ANational Psoriasis Foundation (NPF)Rebecca L. Cooper Medical Research FoundationDepartment of Health | National Health and Medical Research Council (NHMRC)7547https://www.ebi.ac.uk/biostudies/studies/S-EPMC11364864biostudies-literatureUnknown15(1)Most COVID-19 vaccines elicit immunity against the SARS-CoV-2 Spike protein. However, Spike protein mutations in emerging strains and immune evasion by the SARS-CoV-2 virus demonstrates the need to develop more broadly targeting vaccines. To facilitate this, we use mass spectrometry to identify immunopeptides derived from seven relatively conserved structural and non-structural SARS-CoV-2 proteins (N, E, Nsp1/4/5/8/9). We use two different B-lymphoblastoid cell lines to map Human Leukocyte Antigen (HLA) class I and class II immunopeptidomes covering some of the prevalent HLA types across the global human population. We employ DNA plasmid transfection and direct antigen delivery approaches to sample different antigens and find 248 unique HLA class I and HLA class II bound peptides with 71 dNature communicationsMapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes.PMC1136486411940362016596114336681790720263571173871PG2020775Scull KERowntree LCRossjohn JIlling PTPetersen JAyala RFaridi PKringelum JBraun ALittler DRRamarathinam SChung SPurcell AWThuesen NLi CCroft NPPandey KPersson GJappe Lange ESchantz Klausen MMifsud NAHuang ZRaji SKedzierska KNguyen THOSorensen ABfalseMapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes.Most COVID-19 vaccines elicit immunity against the SARS-CoV-2 Spike protein. However, Spike protein mutations in emerging strains and immune evasion by the SARS-CoV-2 virus demonstrates the need to develop more broadly targeting vaccines. To facilitate this, we use mass spectrometry to identify immunopeptides derived from seven relatively conserved structural and non-structural SARS-CoV-2 proteins (N, E, Nsp1/4/5/8/9). We use two different B-lymphoblastoid cell lines to map Human Leukocyte Antigen (HLA) class I and class II immunopeptidomes covering some of the prevalent HLA types across the global human population. We employ DNA plasmid transfection and direct antigen delivery approaches to sample different antigens and find 248 unique HLA class I and HLA class II bound peptides with 71 d2024-01-01T00:00:00Z2024 Aug2026-07-16T07:21:36.464Z2025-04-06T13:45:25.132ZS-EPMC113648643921499810.1038/s41467-024-51959-6