{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T15:22:51Z","timestamp":1788535371237,"version":"build-2803163510"},"reference-count":48,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University","award":["RA(MF)14\/61"],"award-info":[{"award-number":["RA(MF)14\/61"]}]},{"name":"Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University","award":["RA(MF)45\/64"],"award-info":[{"award-number":["RA(MF)45\/64"]}]},{"name":"National Research Council of Thailand (NRCT) and Chulalongkorn University","award":["N42A670716"],"award-info":[{"award-number":["N42A670716"]}]},{"name":"Thailand Science Research and Innovation Fund, Chulalongkorn University","award":["HEA663000034"],"award-info":[{"award-number":["HEA663000034"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>This study profiles the personalized immunopeptidomes of 13 Thai patients with renal cell carcinoma (RCC), addressing a critical knowledge gap in Southeast Asian populations characterized by distinct HLA allele distributions. We combined whole-exome sequencing (WES)-based personalized proteome construction with liquid chromatography\u2013tandem mass spectrometry (LC\u2013MS\/MS), using both database-driven searches and de novo peptide sequencing. HLA typing identified several class I allotypes that are underrepresented in publicly available immunopeptidome resources, including seven alleles not previously represented in the databases examined; HLA-A*11:01 was the most frequent allele in this cohort. Database-based analysis identified a single tumor-specific neoantigen derived from a mutant JADE2 peptide in the patient with the highest tumor mutational burden, which was validated by a mutant-specific ELISPOT response. In contrast, de novo sequencing revealed numerous noncanonical peptides, a subset of which were supported by proteogenomic validation using PepQuery and detected exclusively in cancer proteomes but not in normal tissue data sets, indicating their potential as tumor-associated antigen candidates. Together, these results establish an integrated and scalable framework for identifying HLA-presented tumor-derived peptides and provide a foundational immunopeptidome resource to support personalized cancer immunotherapy development in Southeast Asia.<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00141","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T06:02:17Z","timestamp":1786687337000},"page":"4651-4664","source":"Crossref","is-referenced-by-count":0,"title":["Mass Spectrometry-Based\nProfiling of Personalized\nImmunopeptidomes in Thai Renal Cell Carcinoma"],"prefix":"10.1021","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7422-1135","authenticated-orcid":true,"given":"Poorichaya","family":"Somparn","sequence":"first","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sira","family":"Sriswasdi","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Piriya","family":"Wongkongkathep","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jirapat","family":"Techachakrit","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phijitra","family":"Muanwien","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saharat","family":"Nanthawong","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatchapon","family":"Apinan","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julin","family":"Opanuraks","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanop","family":"Shuangshoti","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nattiya","family":"Hirankarn","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sutpirat","family":"Moonmuang","sequence":"additional","affiliation":[{"name":"Chiang Mai University , , ,","place":["Chiang Mai, Thailand, 50200"]},{"name":"Chiang Mai University , , ,","place":["Chiang Mai, Thailand, 50200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanyaluck","family":"Kampoun","sequence":"additional","affiliation":[{"name":"Chiang Mai University , , ,","place":["Chiang Mai, Thailand, 50200"]},{"name":"Chiang Mai University , , ,","place":["Chiang Mai, Thailand, 50200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Parunya","family":"Chaiyawat","sequence":"additional","affiliation":[{"name":"Chiang Mai University , , ,","place":["Chiang Mai, Thailand, 50200"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6677-2271","authenticated-orcid":true,"given":"Trairak","family":"Pisitkun","sequence":"additional","affiliation":[{"name":"Chulalongkorn University , , ,","place":["Bangkok, Thailand, 10330"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,14]]},"reference":[{"issue":"2","key":"2026090409131111600_cit1","doi-asserted-by":"publisher","first-page":"166","DOI":"10.21037\/tau.2020.02.23","article-title":"Temporal trends of kidney cancer incidence and mortality from 1990\nto 2016 and projections to 2030","volume":"9","author":"Cai","year":"2020","journal-title":"Transl. Androl.\nUrol."},{"issue":"2","key":"2026090409131111600_cit2","doi-asserted-by":"publisher","first-page":"416","DOI":"10.20517\/cdr.2023.02","article-title":"Mechanisms\nand clinical implications in renal carcinoma resistance: narrative\nreview of immune checkpoint inhibitors","volume":"6","author":"Samnani","year":"2023","journal-title":"Cancer\nDrug Resist."},{"issue":"7662","key":"2026090409131111600_cit3","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1038\/nature22991","article-title":"An immunogenic\npersonal neoantigen vaccine for patients\nwith melanoma","volume":"547","author":"Ott","year":"2017","journal-title":"Nature"},{"key":"2026090409131111600_cit4","doi-asserted-by":"publisher","first-page":"13404","DOI":"10.1038\/ncomms13404","article-title":"Direct identification\nof clinically relevant neoepitopes presented on native human melanoma\ntissue by mass spectrometry","volume":"7","author":"Bassani-Sternberg","year":"2016","journal-title":"Nat. Commun."},{"issue":"7662","key":"2026090409131111600_cit5","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature23003","article-title":"Personalized RNA mutanome vaccines mobilize poly-specific\ntherapeutic immunity against cancer","volume":"547","author":"Sahin","year":"2017","journal-title":"Nature"},{"issue":"7738","key":"2026090409131111600_cit6","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1038\/s41586-018-0792-9","article-title":"Neoantigen\nvaccine generates intratumoral T cell responses in phase\nIb glioblastoma trial","volume":"565","author":"Keskin","year":"2019","journal-title":"Nature"},{"issue":"5","key":"2026090409131111600_cit7","doi-asserted-by":"publisher","first-page":"2056","DOI":"10.1172\/JCI99538","article-title":"Neoantigen identification\nstrategies enable personalized immunotherapy\nin refractory solid tumors","volume":"129","author":"Chen","year":"2019","journal-title":"J. Clin. Invest."},{"issue":"11","key":"2026090409131111600_cit8","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1038\/s41591-019-0639-4","article-title":"Evolutionary\ndivergence of HLA class I genotype impacts efficacy of cancer immunotherapy","volume":"25","author":"Chowell","year":"2019","journal-title":"Nat. Med."},{"issue":"4","key":"2026090409131111600_cit9","doi-asserted-by":"publisher","DOI":"10.1136\/jitc-2020-002071","article-title":"HLA Ligand\nAtlas: a benign reference of HLA-presented peptides to improve T-cell-based\ncancer immunotherapy","volume":"9","author":"Marcu","year":"2021","journal-title":"J. Immunother. Cancer"},{"issue":"46","key":"2026090409131111600_cit10","doi-asserted-by":"publisher","first-page":"E9942","DOI":"10.1073\/pnas.1707658114","article-title":"The immunopeptidomic landscape of ovarian carcinomas","volume":"114","author":"Schuster","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. 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Biol."},{"key":"2026090409131111600_cit12","doi-asserted-by":"publisher","first-page":"866407","DOI":"10.3389\/fgene.2023.866407","article-title":"An HLA map of the world:\nA comparison of HLA frequencies in 200 worldwide populations reveals\ndiverse patterns for class I and class II","volume":"14","author":"Arrieta-Bolanos","year":"2023","journal-title":"Front.\nGenet."},{"key":"2026090409131111600_cit13","doi-asserted-by":"publisher","first-page":"847756","DOI":"10.3389\/fimmu.2022.847756","article-title":"Unsupervised\nMining of HLA-I Peptidomes Reveals New\nBinding Motifs and Potential False Positives in the Community Database","volume":"13","author":"Sricharoensuk","year":"2022","journal-title":"Front. 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Protoc."},{"issue":"3","key":"2026090409131111600_cit23","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1007\/s42485-021-00066-x","article-title":"Digging deeper into the immunopeptidome:\ncharacterization of post-translationally modified peptides presented\nby MHC I","volume":"12","author":"Mangalaparthi","year":"2021","journal-title":"J. Protein Proteonomics"},{"issue":"D1","key":"2026090409131111600_cit24","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub\nfor mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2026090409131111600_cit25","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/978-1-4939-6747-6_23","article-title":"Data Conversion with ProteoWizard msConvert","volume":"1550","author":"Adusumilli","year":"2017","journal-title":"Methods Mol. 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Immunol."},{"issue":"2","key":"2026090409131111600_cit38","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/S0198-8859(96)00284-4","article-title":"HLA-A, -B, -DRB1, -DQA1, and -DQB1\npolymorphism in\nThais","volume":"53","author":"Chandanayingyong","year":"1997","journal-title":"Hum. Immunol."},{"issue":"D1","key":"2026090409131111600_cit39","doi-asserted-by":"publisher","first-page":"D783","DOI":"10.1093\/nar\/gkz1029","article-title":"Allele frequency net\ndatabase (AFND) 2020 update: gold-standard data classification, open\naccess genotype data and new query tools","volume":"48","author":"Gonzalez-Galarza","year":"2019","journal-title":"Nucleic\nAcids Res."},{"issue":"1","key":"2026090409131111600_cit40","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1038\/s41467-020-14968-9","article-title":"Integrated proteogenomic deep sequencing and\nanalytics accurately identify non-canonical peptides in tumor immunopeptidomes","volume":"11","author":"Chong","year":"2020","journal-title":"Nat. Commun."},{"issue":"23","key":"2026090409131111600_cit41","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1182\/blood.V126.23.1851.1851","article-title":"Patient-Specific\nMutation-Derived Tumor Antigens as Targets for Cancer Immunotherapy\nin Multiple Myeloma","volume":"126","author":"Perumal","year":"2015","journal-title":"Blood"},{"issue":"9","key":"2026090409131111600_cit42","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.1016\/j.jtho.2020.05.019","article-title":"The Promises and Challenges of Tumor Mutation Burden\nas an Immunotherapy Biomarker: A Perspective from the International\nAssociation for the Study of Lung Cancer Pathology Committee","volume":"15","author":"Sholl","year":"2020","journal-title":"J. Thorac. Oncol."},{"issue":"43","key":"2026090409131111600_cit43","doi-asserted-by":"publisher","first-page":"28817","DOI":"10.1074\/jbc.M801407200","article-title":"Role of\nJade-1 in the histone acetyltransferase (HAT) HBO1 complex","volume":"283","author":"Foy","year":"2008","journal-title":"J. Biol. Chem."},{"issue":"1","key":"2026090409131111600_cit44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.gene.2016.05.002","article-title":"Structure,\nfunction and regulation of jade family PHD finger 1 (JADE1)","volume":"589","author":"Panchenko","year":"2016","journal-title":"Gene"},{"issue":"7528","key":"2026090409131111600_cit45","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1038\/nature14001","article-title":"Predicting immunogenic tumour mutations by\ncombining mass spectrometry and exome sequencing","volume":"515","author":"Yadav","year":"2014","journal-title":"Nature"},{"issue":"1_Supplement","key":"2026090409131111600_cit46","doi-asserted-by":"publisher","first-page":"217.16","DOI":"10.4049\/jimmunol.204.Supp.217.16","article-title":"Proteogenomics and de novo sequencing\nbased approach for neoantigen discovery from the immunopeptidomes\nof patient CRC liver metastases using Mass Spectrometry","volume":"204","author":"shah","year":"2020","journal-title":"J. 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Commun."}],"container-title":["Journal of Proteome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jproteome.6c00141","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/9\/4651\/66541463\/acs.jproteome.6c00141.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jprobs\/article-pdf\/25\/9\/4651\/66541463\/acs.jproteome.6c00141.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T14:52:45Z","timestamp":1788533565000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jprobs\/article\/25\/9\/4651\/5255178\/Mass-Spectrometry-Based-Profiling-of-Personalized"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,14]]},"references-count":48,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,8,14]]},"published-print":{"date-parts":[[2026,9,4]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jproteome.6c00141","relation":{},"ISSN":["1535-3893","1535-3907"],"issn-type":[{"value":"1535-3893","type":"print"},{"value":"1535-3907","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,14]]}}}