{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T05:09:01Z","timestamp":1774674541367,"version":"3.50.1"},"reference-count":72,"publisher":"American Association for Cancer Research (AACR)","issue":"6","license":[{"start":{"date-parts":[[2023,6,2]],"date-time":"2023-06-02T00:00:00Z","timestamp":1685664000000},"content-version":"vor","delay-in-days":70,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-10-LABX-49-01"],"award-info":[{"award-number":["ANR-10-LABX-49-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-17-EURE-0003"],"award-info":[{"award-number":["ANR-17-EURE-0003"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002794","name":"Cancerfonden","doi-asserted-by":"crossref","award":["211709"],"award-info":[{"award-number":["211709"]}],"id":[{"id":"10.13039\/501100002794","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["UIDB\/00408\/2020"],"award-info":[{"award-number":["UIDB\/00408\/2020"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["UIDB\/00408\/2020"],"award-info":[{"award-number":["UIDB\/00408\/2020"]}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"crossref","award":["101017453"],"award-info":[{"award-number":["101017453"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"crossref","award":["EP\/S02431X\/1"],"award-info":[{"award-number":["EP\/S02431X\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100018536","name":"NuCana","doi-asserted-by":"crossref","award":["SMD0-ZIUN05"],"award-info":[{"award-number":["SMD0-ZIUN05"]}],"id":[{"id":"10.13039\/100018536","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100016338","name":"Imperial Experimental Cancer Medicine Centre","doi-asserted-by":"crossref","award":["ECMCQQR-2022\/100017"],"award-info":[{"award-number":["ECMCQQR-2022\/100017"]}],"id":[{"id":"10.13039\/100016338","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fundacja na rzecz Nauki Polskiej","award":["MAB\/3\/2017"],"award-info":[{"award-number":["MAB\/3\/2017"]}]},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"crossref","award":["264PRO"],"award-info":[{"award-number":["264PRO"]}],"id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000233","name":"Genome British Columbia","doi-asserted-by":"crossref","award":["264PRO"],"award-info":[{"award-number":["264PRO"]}],"id":[{"id":"10.13039\/501100000233","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["aacrjournals.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2023,6,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I\u2013associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.<\/jats:p>","DOI":"10.1158\/2326-6066.cir-22-0621","type":"journal-article","created":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T10:50:19Z","timestamp":1679655019000},"page":"747-762","update-policy":"https:\/\/doi.org\/10.1158\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I\u2013Associated Peptides"],"prefix":"10.1158","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3086-3742","authenticated-orcid":false,"given":"Georges","family":"Bedran","sequence":"first","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1274-4966","authenticated-orcid":false,"given":"Hans-Christof","family":"Gasser","sequence":"additional","affiliation":[{"name":"2School of Informatics, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8947-7793","authenticated-orcid":false,"given":"Kenneth","family":"Weke","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9237-156X","authenticated-orcid":false,"given":"Tongjie","family":"Wang","sequence":"additional","affiliation":[{"name":"2School of Informatics, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2263-2493","authenticated-orcid":false,"given":"Dominika","family":"Bedran","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7296-025X","authenticated-orcid":false,"given":"Alexander","family":"Laird","sequence":"additional","affiliation":[{"name":"3Urology Department, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom."},{"name":"4Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6849-7824","authenticated-orcid":false,"given":"Christophe","family":"Battail","sequence":"additional","affiliation":[{"name":"5CEA, Grenoble Alpes University, INSERM, IRIG, Biosciences and Bioengineering for Health Laboratory (BGE) - UA13 INSERM-CEA-UGA, Grenoble, France."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7301-3596","authenticated-orcid":false,"given":"Fabio Massimo","family":"Zanzotto","sequence":"additional","affiliation":[{"name":"6Department of Enterprise Engineering, University of Rome \u201cTor Vergata\u201d, Rome, Italy."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1847-9393","authenticated-orcid":false,"given":"Catia","family":"Pesquita","sequence":"additional","affiliation":[{"name":"7LASIGE, Faculdade de Ci\u00eancias, Universidade de Lisboa, Lisboa, Portugal."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7749-5043","authenticated-orcid":false,"given":"H\u00e5kan","family":"Axelson","sequence":"additional","affiliation":[{"name":"8Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3765-3075","authenticated-orcid":false,"given":"Ajitha","family":"Rajan","sequence":"additional","affiliation":[{"name":"2School of Informatics, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9041-9988","authenticated-orcid":false,"given":"David J.","family":"Harrison","sequence":"additional","affiliation":[{"name":"9School of Medicine, University of St Andrews, St Andrews, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3140-8469","authenticated-orcid":false,"given":"Aleksander","family":"Palkowski","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3419-7262","authenticated-orcid":false,"given":"Maciej","family":"Pawlik","sequence":"additional","affiliation":[{"name":"10Academic Computer Centre CYFRONET, AGH University of Science and Technology, Cracow, Poland."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4456-3369","authenticated-orcid":false,"given":"Maciej","family":"Parys","sequence":"additional","affiliation":[{"name":"11Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2230-7137","authenticated-orcid":false,"given":"J. Robert","family":"O'Neill","sequence":"additional","affiliation":[{"name":"12Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7347-830X","authenticated-orcid":false,"given":"Paul M.","family":"Brennan","sequence":"additional","affiliation":[{"name":"13Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9892-9314","authenticated-orcid":false,"given":"Stefan N.","family":"Symeonides","sequence":"additional","affiliation":[{"name":"4Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8045-8200","authenticated-orcid":false,"given":"David R.","family":"Goodlett","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."},{"name":"14Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada."},{"name":"15University of Victoria Genome BC Proteome Centre, Victoria, Canada."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3725-0914","authenticated-orcid":false,"given":"Kevin","family":"Litchfield","sequence":"additional","affiliation":[{"name":"16Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom."},{"name":"17Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0402-8492","authenticated-orcid":false,"given":"Robin","family":"Fahraeus","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."},{"name":"18Inserm UMRS1131, Institut de G\u00e9n\u00e9tique Mol\u00e9culaire, Universit\u00e9 Paris 7, Paris, France."}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0391-0352","authenticated-orcid":false,"given":"Ted R.","family":"Hupp","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."},{"name":"4Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2431-9935","authenticated-orcid":false,"given":"Sachin","family":"Kote","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5553-6991","authenticated-orcid":false,"given":"Javier A.","family":"Alfaro","sequence":"additional","affiliation":[{"name":"1International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland."},{"name":"2School of Informatics, University of Edinburgh, Edinburgh, United Kingdom."},{"name":"14Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada."}]}],"member":"1086","published-online":{"date-parts":[[2023,3,24]]},"reference":[{"key":"2025112607311063400_bib1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms13404","article-title":"Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry","volume":"7","author":"Bassani-Sternberg","year":"2016","journal-title":"Nat Commun"},{"key":"2025112607311063400_bib2","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1186\/s40425-019-0769-8","article-title":"Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment","volume":"7","author":"Newey","year":"2019","journal-title":"J Immunother Cancer"},{"key":"2025112607311063400_bib3","doi-asserted-by":"crossref","first-page":"e129152","DOI":"10.1172\/jci.insight.129152","article-title":"Mass spectrometry\u2013driven exploration reveals nuances of neoepitope-driven tumor rejection","volume":"4","author":"Ebrahimi-Nik","year":"2019","journal-title":"JCI Insight"},{"key":"2025112607311063400_bib4","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41571-020-00460-2","article-title":"Advances in the development of personalized neoantigen-based therapeutic cancer vaccines","volume":"18","author":"Blass","year":"2021","journal-title":"Nat Rev Clin Oncol"},{"key":"2025112607311063400_bib5","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/s43018-021-00210-y","article-title":"Targeting public neoantigens for cancer immunotherapy","volume":"2","author":"Pearlman","year":"2021","journal-title":"Nat Cancer"},{"key":"2025112607311063400_bib6","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/s41467-020-14968-9","article-title":"Integrated proteogenomic deep sequencing and analytics accurately identify noncanonical peptides in tumor immunopeptidomes","volume":"11","author":"Chong","year":"2020","journal-title":"Nat Commun"},{"key":"2025112607311063400_bib7","doi-asserted-by":"crossref","first-page":"e06722","DOI":"10.7554\/eLife.06722","article-title":"Quality control of transcription start site selection by nonsense-mediated-mRNA decay","volume":"4","author":"Malabat","year":"2015","journal-title":"eLife"},{"key":"2025112607311063400_bib8","doi-asserted-by":"crossref","first-page":"e03528","DOI":"10.7554\/eLife.03528","article-title":"Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq","volume":"3","author":"Aspden","year":"2014","journal-title":"eLife"},{"key":"2025112607311063400_bib9","doi-asserted-by":"crossref","first-page":"6689","DOI":"10.1038\/s41467-021-26936-y","article-title":"Proteogenomic discovery of neoantigens facilitates personalized multi-antigen targeted T-cell immunotherapy for brain tumors","volume":"12","author":"Rivero-Hinojosa","year":"2021","journal-title":"Nat Commun"},{"key":"2025112607311063400_bib10","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nbt.4239","article-title":"Intron retention is a source of neoepitopes in cancer","volume":"36","author":"Smart","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2025112607311063400_bib11","doi-asserted-by":"crossref","first-page":"6928","DOI":"10.4049\/jimmunol.176.11.6928","article-title":"Epitopes derived by incidental translational frameshifting give rise to a protective CTL response","volume":"176","author":"Zook","year":"2006","journal-title":"J Immunol"},{"key":"2025112607311063400_bib12","doi-asserted-by":"crossref","first-page":"748820","DOI":"10.3389\/fimmu.2021.748820","article-title":"Novel tumor-specific antigens for immunotherapy identified from multi-omics profiling in thymic carcinomas","volume":"12","author":"Fang","year":"2021","journal-title":"Front Immunol"},{"key":"2025112607311063400_bib13","doi-asserted-by":"crossref","first-page":"10238","DOI":"10.1038\/ncomms10238","article-title":"Global proteogenomic analysis of human MHC class I\u2014associated peptides derived from noncanonical reading frames","volume":"7","author":"Laumont","year":"2016","journal-title":"Nat Commun"},{"key":"2025112607311063400_bib14","doi-asserted-by":"crossref","first-page":"eaau5516","DOI":"10.1126\/scitranslmed.aau5516","article-title":"Noncoding regions are the main source of targetable tumor-specific antigens","volume":"10","author":"Laumont","year":"2018","journal-title":"Sci Transl Med"},{"key":"2025112607311063400_bib15","doi-asserted-by":"crossref","first-page":"108815","DOI":"10.1016\/j.celrep.2021.108815","article-title":"Most noncanonical proteins uniquely populate the proteome or immunopeptidome","volume":"34","author":"Ruiz","year":"2021","journal-title":"Cell Rep"},{"key":"2025112607311063400_bib16","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/s41587-021-01021-3","article-title":"Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer","volume":"40","author":"Ouspenskaia","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2025112607311063400_bib17","doi-asserted-by":"crossref","first-page":"1700410","DOI":"10.1002\/pmic.201700410","article-title":"T-cell immunopeptidomes reveal cell subtype surface markers derived from intracellular proteins","volume":"18","author":"Olsson","year":"2018","journal-title":"Proteomics"},{"key":"2025112607311063400_bib18","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.1021\/acs.jproteome.8b00821","article-title":"Pre-fractionation extends but also creates a bias in the detectable HLA Class \u0399 ligandome","volume":"18","author":"Demmers","year":"2019","journal-title":"J Proteome Res"},{"key":"2025112607311063400_bib19","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1182\/blood-2018-06-845156","article-title":"B-cell lymphomas present immunoglobulin neoantigens","volume":"133","author":"Khodadoust","year":"2019","journal-title":"Blood"},{"key":"2025112607311063400_bib20","doi-asserted-by":"crossref","first-page":"1700248","DOI":"10.1002\/pmic.201700248","article-title":"Cell surface MHC class I expression is limited by the availability of peptide-receptive \u201cempty\u201d molecules rather than by the supply of peptide ligands","volume":"18","author":"Komov","year":"2018","journal-title":"Proteomics"},{"key":"2025112607311063400_bib21","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s40478-018-0521-5","article-title":"CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival","volume":"6","author":"Zeiner","year":"2018","journal-title":"Acta Neuropathol Commun"},{"key":"2025112607311063400_bib22","doi-asserted-by":"crossref","first-page":"3876","DOI":"10.1021\/acs.jproteome.9b00313","article-title":"MHCquant: automated and reproducible data analysis for immunopeptidomics","volume":"18","author":"Bichmann","year":"2019","journal-title":"J Proteome Res"},{"key":"2025112607311063400_bib23","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1074\/mcp.TIR117.000383","article-title":"High-throughput and sensitive immunopeptidomics platform reveals profound interferon\u03b3-mediated remodeling of the human leukocyte antigen (HLA) ligandome","volume":"17","author":"Chong","year":"2018","journal-title":"Mol Cell Proteomics"},{"key":"2025112607311063400_bib24","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1007\/s00262-019-02358-0","article-title":"Editing the immunopeptidome of melanoma cells using a potent inhibitor of endoplasmic reticulum aminopeptidase 1 (ERAP1)","volume":"68","author":"Koumantou","year":"2019","journal-title":"Cancer Immunol Immunother"},{"key":"2025112607311063400_bib25","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1021\/acs.jproteome.6b00528","article-title":"Arginine (Di)methylated human leukocyte antigen class I peptides are favorably presented by HLA-B*07","volume":"16","author":"Marino","year":"2017","journal-title":"J Proteome Res"},{"key":"2025112607311063400_bib26","doi-asserted-by":"crossref","first-page":"e0219547","DOI":"10.1371\/journal.pone.0219547","article-title":"Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin","volume":"14","author":"Narayan","year":"2019","journal-title":"PLoS One"},{"key":"2025112607311063400_bib27","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1074\/mcp.M116.060350","article-title":"Human leukocyte antigen (HLA) peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy","volume":"15","author":"Shraibman","year":"2016","journal-title":"Mol Cell Proteomics"},{"key":"2025112607311063400_bib28","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.immuni.2017.02.007","article-title":"Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction","volume":"46","author":"Abelin","year":"2017","journal-title":"Immunity"},{"key":"2025112607311063400_bib29","first-page":"2639","article-title":"Unveiling the peptide motifs of HLA-C and HLA-G from naturally presented peptides and generation of binding prediction matrices","volume":"199","author":"Di Marco","year":"2017","journal-title":"J Immunol Baltim Md 1950"},{"key":"2025112607311063400_bib30","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1074\/mcp.M114.042812","article-title":"Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation","volume":"14","author":"Bassani-Sternberg","year":"2015","journal-title":"Mol Cell Proteomics MCP"},{"key":"2025112607311063400_bib31","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/nature21433","article-title":"Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens","volume":"543","author":"Khodadoust","year":"2017","journal-title":"Nature"},{"key":"2025112607311063400_bib32","doi-asserted-by":"crossref","first-page":"e1800357","DOI":"10.1002\/pmic.201800357","article-title":"MS-Rescue: a computational pipeline to increase the quality and yield of immunopeptidomics experiments","volume":"19","author":"Andreatta","year":"2019","journal-title":"Proteomics"},{"key":"2025112607311063400_bib33","doi-asserted-by":"crossref","first-page":"e1005725","DOI":"10.1371\/journal.pcbi.1005725","article-title":"Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity","volume":"13","author":"Bassani-Sternberg","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2025112607311063400_bib34","doi-asserted-by":"crossref","first-page":"e1700465","DOI":"10.1002\/pmic.201700465","article-title":"Immunopeptidomic profiling of HLA-A2\u2013positive triple-negative breast cancer identifies potential immunotherapy target antigens","volume":"18","author":"Ternette","year":"2018","journal-title":"Proteomics"},{"key":"2025112607311063400_bib35","doi-asserted-by":"crossref","first-page":"4690","DOI":"10.1172\/JCI88590","article-title":"MHC class I\u2013associated peptides derive from selective regions of the human genome","volume":"126","author":"Pearson","year":"2016","journal-title":"J Clin Invest"},{"key":"2025112607311063400_bib36","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nmeth.4631","article-title":"Improved Ribo-seq enables identification of cryptic translation events","volume":"15","author":"Erhard","year":"2018","journal-title":"Nat Methods"},{"key":"2025112607311063400_bib37","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s13073-019-0636-8","article-title":"Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma","volume":"11","author":"Loffler","year":"2019","journal-title":"Genome Med"},{"key":"2025112607311063400_bib38","doi-asserted-by":"crossref","first-page":"e002071","DOI":"10.1136\/jitc-2020-002071","article-title":"HLA ligand atlas: a benign reference of HLA-presented peptides to improve T cell\u2013based cancer immunotherapy","volume":"9","author":"Marcu","year":"2021","journal-title":"J Immunother Cancer"},{"key":"2025112607311063400_bib39","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41587-019-0322-9","article-title":"A large peptidome dataset improves HLA class I epitope prediction across most of the human population","volume":"38","author":"Sarkizova","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2025112607311063400_bib40","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1038\/s41592-020-0912-y","article-title":"Philosopher: a versatile toolkit for shotgun proteomics data analysis","volume":"17","author":"da Veiga Leprevost","year":"2020","journal-title":"Nat Methods"},{"key":"2025112607311063400_bib41","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the catalogue of somatic mutations in cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025112607311063400_bib42","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry\u2013based proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat Methods"},{"key":"2025112607311063400_bib43","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1074\/mcp.RA118.000812","article-title":"PTMiner: localization and quality control of protein modifications detected in an open search and its application to comprehensive","volume":"18","author":"An","year":"2019","journal-title":"Mol Cell Proteomics"},{"key":"2025112607311063400_bib44","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/s42256-021-00304-3","article-title":"Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices","volume":"3","author":"Qiao","year":"2021","journal-title":"Nat Mach Intell"},{"key":"2025112607311063400_bib45","doi-asserted-by":"crossref","first-page":"1800280","DOI":"10.1002\/pmic.201800280","article-title":"Scavager: a versatile postsearch validation algorithm for shotgun proteomics based on gradient boosting","volume":"19","author":"Ivanov","year":"2019","journal-title":"Proteomics"},{"key":"2025112607311063400_bib46","first-page":"656","article-title":"BLAT\u2014The BLAST-Like Alignment Tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2025112607311063400_bib47","doi-asserted-by":"crossref","first-page":"i234","DOI":"10.1093\/bioinformatics\/btx247","article-title":"TITER: predicting translation initiation sites by deep learning","volume":"33","author":"Zhang","year":"2017","journal-title":"Bioinformatics"},{"key":"2025112607311063400_bib48","doi-asserted-by":"crossref","first-page":"3423","DOI":"10.1093\/bioinformatics\/btr539","article-title":"Pybedtools: a flexible Python library for manipulating genomic datasets and annotations","volume":"27","author":"Dale","year":"2011","journal-title":"Bioinformatics"},{"key":"2025112607311063400_bib49","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1158\/2326-6066.CIR-19-0886","article-title":"Identification of the cryptic HLA-I immunopeptidome","volume":"8","author":"Erhard","year":"2020","journal-title":"Cancer Immunol Res"},{"key":"2025112607311063400_bib50","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1186\/1471-2105-11-237","article-title":"ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data","volume":"11","author":"Zhu","year":"2010","journal-title":"BMC Bioinf"},{"key":"2025112607311063400_bib51","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1089\/bio.2015.0032","article-title":"A novel approach to high-quality postmortem tissue procurement: The GTEx Project","volume":"13","author":"Carithers","year":"2015","journal-title":"Biopreservation Biobanking"},{"key":"2025112607311063400_bib52","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","author":"Uhl\u00e9n","year":"2015","journal-title":"Science"},{"key":"2025112607311063400_bib53","doi-asserted-by":"crossref","first-page":"5277","DOI":"10.1038\/ncomms6277","article-title":"MS-GF+ makes progress towards a universal database search tool for proteomics","volume":"5","author":"Kim","year":"2014","journal-title":"Nat Commun"},{"key":"2025112607311063400_bib54","doi-asserted-by":"crossref","first-page":"8020","DOI":"10.1002\/jcp.30483","article-title":"Cognizance of posttranslational modifications in vaccines: a way to enhanced immunogenicity","volume":"236","author":"Ojha","year":"2021","journal-title":"J Cell Physiol"},{"key":"2025112607311063400_bib55","doi-asserted-by":"crossref","first-page":"27979","DOI":"10.1074\/jbc.M114.573402","article-title":"The cellular redox environment alters antigen presentation","volume":"289","author":"Trujillo","year":"2014","journal-title":"J Biol Chem"},{"key":"2025112607311063400_bib56","doi-asserted-by":"crossref","first-page":"109179","DOI":"10.1016\/j.celrep.2021.109179","article-title":"Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells","volume":"35","author":"Parker","year":"2021","journal-title":"Cell Rep"},{"key":"2025112607311063400_bib57","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025112607311063400_bib58","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1084\/jem.184.4.1319","article-title":"Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames","volume":"184","author":"Bullock","year":"1996","journal-title":"J Exp Med"},{"key":"2025112607311063400_bib59","doi-asserted-by":"crossref","first-page":"aad3867","DOI":"10.1126\/science.aad3867","article-title":"Translation from the 5\u2032 untranslated region shapes the integrated stress response","volume":"351","author":"Starck","year":"2016","journal-title":"Science"},{"key":"2025112607311063400_bib60","doi-asserted-by":"crossref","first-page":"5670","DOI":"10.1073\/pnas.1402670111","article-title":"Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3\u2032 UTR","volume":"111","author":"Goodenough","year":"2014","journal-title":"Proc Natl Acad Sci"},{"key":"2025112607311063400_bib61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2172-9-1","article-title":"HLA class I supertypes: a revised and updated classification","volume":"9","author":"Sidney","year":"2008","journal-title":"BMC Immunol"},{"key":"2025112607311063400_bib62","doi-asserted-by":"crossref","first-page":"103107","DOI":"10.1016\/j.isci.2021.103107","article-title":"caAtlas: an immunopeptidome atlas of human cancer","volume":"24","author":"Yi","year":"2021","journal-title":"iScience"},{"key":"2025112607311063400_bib63","doi-asserted-by":"crossref","first-page":"10800","DOI":"10.3390\/ijms221910800","article-title":"Ubiquitination in T-cell activation and checkpoint inhibition: new avenues for targeted cancer immunotherapy","volume":"22","author":"Gavali","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2025112607311063400_bib64","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1021\/acs.jproteome.6b00496","article-title":"Identification and characterization of complex glycosylated peptides presented by the MHC class II processing pathway in melanoma","volume":"16","author":"Malaker","year":"2017","journal-title":"J Proteome Res"},{"key":"2025112607311063400_bib65","doi-asserted-by":"crossref","first-page":"723566","DOI":"10.3389\/fimmu.2021.723566","article-title":"Tumor-infiltrating lymphocytes target HLA-I phosphopeptides derived from cancer signaling in colorectal cancer","volume":"12","author":"Penny","year":"2021","journal-title":"Front Immunol"},{"key":"2025112607311063400_bib66","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1038\/s41467-017-02763-y","article-title":"T cells specific for posttranslational modifications escape intrathymic tolerance induction","volume":"9","author":"Raposo","year":"2018","journal-title":"Nat Commun"},{"key":"2025112607311063400_bib67","first-page":"239","article-title":"Posttranslational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors","volume-title":"Nat Biotechnol","author":"Kacen","year":"2022"},{"key":"2025112607311063400_bib68","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/BF01888363","article-title":"Complete amino acid sequence of Proteus mirabilis PR catalase. Occurrence of a methionine sulfone in the close proximity of the active site","volume":"14","author":"Buzy","year":"1995","journal-title":"J Protein Chem"},{"key":"2025112607311063400_bib69","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.jiph.2019.03.021","article-title":"A comparative analysis of infection in patients with malignant cancer: a clinical pharmacist consultation study","volume":"12","author":"Lin","year":"2019","journal-title":"J Infect Public Health"},{"key":"2025112607311063400_bib70","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.4049\/jimmunol.162.3.1303","article-title":"Isolation of MHC class I\u2014restricted tumor antigen peptide and its precursors associated with heat shock proteins hsp70, hsp90, and gp96","volume":"162","author":"Ishii","year":"1999","journal-title":"J Immunol"},{"key":"2025112607311063400_bib71","doi-asserted-by":"crossref","first-page":"3575","DOI":"10.1158\/1078-0432.CCR-16-1369","article-title":"Autologous heat shock protein peptide vaccination for newly diagnosed glioblastoma: impact of peripheral PD-L1 expression on response to therapy","volume":"23","author":"Bloch","year":"2017","journal-title":"Clin Cancer Res"},{"key":"2025112607311063400_bib72","doi-asserted-by":"crossref","first-page":"103814","DOI":"10.1016\/j.cellimm.2018.05.007","article-title":"Immunosurveillance of cancer and the heat shock protein-CD91 pathway","volume":"343","author":"Binder","year":"2019","journal-title":"Cell Immunol"}],"container-title":["Cancer Immunology Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/aacrjournals.org\/cancerimmunolres\/article-pdf\/doi\/10.1158\/2326-6066.CIR-22-0621\/3285889\/cir-22-0621.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/aacrjournals.org\/cancerimmunolres\/article-pdf\/doi\/10.1158\/2326-6066.CIR-22-0621\/3328064\/cir-22-0621.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/aacrjournals.org\/cancerimmunolres\/article-pdf\/11\/6\/747\/3332462\/747.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/aacrjournals.org\/cancerimmunolres\/article-pdf\/11\/6\/747\/3332462\/747.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T12:31:29Z","timestamp":1764160289000},"score":1,"resource":{"primary":{"URL":"https:\/\/aacrjournals.org\/cancerimmunolres\/article\/11\/6\/747\/726531\/The-Immunopeptidome-from-a-Genomic-Perspective"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,24]]},"references-count":72,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,3,24]]},"published-print":{"date-parts":[[2023,6,2]]}},"URL":"https:\/\/doi.org\/10.1158\/2326-6066.cir-22-0621","relation":{"has-preprint":[{"id-type":"doi","id":"10.1158\/2326-6066.22732005.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283486.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732020.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283453","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732020","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283453.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.c.6626538.v3","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283465.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732023","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283450","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732011.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.c.6626538.v2","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.c.6626538","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732017.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732002","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283459.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283444.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283459","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732005","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283456","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283483.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732002.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732008.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283468.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732008","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732023.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283441","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283465","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283450.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283489.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283471.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732011","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283477.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732014","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283441.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283456.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283447","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732014.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283447.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.22732017","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283438.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283444","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.c.6626538.v1","asserted-by":"object"}],"is-supplemented-by":[{"id-type":"doi","id":"10.1158\/2326-6066.27026378","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283468","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283444","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283441.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026375.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283447","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720630","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026375","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283471","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283468.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283447.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026390.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026396.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283459.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720627","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283453.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283486.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283486","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026384.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026384","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283438.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283438","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720624","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283465","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283489","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283441","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026381","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720621","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026393.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283456","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720618","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283471.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283477.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026378.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026387","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283483","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283465.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283444.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026390","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283459","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283456.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720615","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283450.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283489.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283450","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026387.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026396","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026381.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283483.v1","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720612","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283453","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.23283477","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.27026393","asserted-by":"object"},{"id-type":"doi","id":"10.1158\/2326-6066.30720609","asserted-by":"object"}]},"ISSN":["2326-6066","2326-6074"],"issn-type":[{"value":"2326-6066","type":"print"},{"value":"2326-6074","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,24]]}}}