{"doi":"10.1101/2021.07.20.453160","title":"Immunogenic SARS-CoV2 Epitopes Defined by Mass Spectrometry","abstract":"Abstract SARS-CoV-2 infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID19, the disease caused by SARS-CoV-2, T cell responses are important in mediating recovery and immune-protection. The identification of immunogenic epitopes that can elicit a meaningful T cell response can be elusive. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes; however, our previous studies find that ‘immunodominant’ SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing SARS-CoV-2. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined by directly analyzing peptides eluted from the peptide-MHC complex and then validating immunogenicity empirically by determining if such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes of SARS-CoV-2 derived not only from structural but also non-structural genes in regions highly conserved among SARS-CoV-2 strains including recently recognized variants. We report here, for the first time, several novel SARS-CoV-2 epitopes from membrane glycol-protein (MGP) and non-structure protein-13 (NSP13) defined by mass-spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity to induce T cell response. Significance Statement Current state of the art uses putative epitope peptides based on in silico prediction algorithms to evaluate the T cell response among COVID-19 patients. However, none of these peptides have been tested for immunogenicity, i.e. the ability to elicit a T cell response capable of recognizing endogenously presented peptide. In this study, we used MHC immune-precipitation, acid elution and tandem mass spectrometry to define the SARS-CoV-2 immunopeptidome for membrane glycol-protein and the non-structural protein. Furthermore, taking advantage of a highly robust endogenous T cell (ETC) workflow, we verify the immunogenicity of these MS-defined peptides by in vitro generation of MGP and NSP13 peptide-specific T cells and confirm T cell recognition of MGP or NSP13 endogenously expressing cell lines.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":216720,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9513,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":396322,"name":"Yulun Chiu","orcid":null,"position":1,"is_corresponding":false},{"id":380549,"name":"Eric Huang","orcid":"0000-0002-6444-1708","position":2,"is_corresponding":false},{"id":408649,"name":"Michelle Chen","orcid":"0000-0001-7028-9274","position":3,"is_corresponding":false},{"id":86256,"name":"Junmei Wang","orcid":"0000-0002-9607-8229","position":4,"is_corresponding":false},{"id":396320,"name":"Ivy Lai","orcid":null,"position":5,"is_corresponding":false},{"id":255858,"name":"Shailbala Singh","orcid":"0000-0002-0681-3948","position":6,"is_corresponding":false},{"id":677978,"name":"Rebecca Shaw","orcid":"0000-0002-3175-7423","position":7,"is_corresponding":false},{"id":79569,"name":"Michael J. MacCoss","orcid":"0000-0003-1853-0256","position":8,"is_corresponding":false},{"id":255864,"name":"Cassian Yee","orcid":"0000-0002-4429-7307","position":9,"is_corresponding":false},{"id":666247,"name":"Ke Pan","orcid":"0000-0002-0163-1045","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":null,"created_at":"2026-07-18T23:53:15.868165Z","pmid":"34312620","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}