{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T22:32:10Z","timestamp":1784932330325,"version":"3.55.0"},"reference-count":62,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,7,9]],"date-time":"2025-07-09T00:00:00Z","timestamp":1752019200000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"The Major Project of Guangzhou National Laboratory","award":["GZNL2023A02007"],"award-info":[{"award-number":["GZNL2023A02007"]}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"publisher","award":["2024B1515020052"],"award-info":[{"award-number":["2024B1515020052"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"Guangdong Basic and Applied Basic Research Foundation","doi-asserted-by":"publisher","award":["2023A1515011783"],"award-info":[{"award-number":["2023A1515011783"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370972"],"award-info":[{"award-number":["32370972"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Graduate Innovation Project of Central South University","award":["2024XQLH056"],"award-info":[{"award-number":["2024XQLH056"]}]},{"name":"Scientific Research Foundation for Advanced Talents of Fujian Medical University","award":["XRCZX2022015"],"award-info":[{"award-number":["XRCZX2022015"]}]},{"name":"Excellent Youth Foundation of Hunan Scientific Committee","award":["2024JJ2084"],"award-info":[{"award-number":["2024JJ2084"]}]},{"name":"Science and Technology Innovation Program of Hunan province","award":["2023RC3080"],"award-info":[{"award-number":["2023RC3080"]}]},{"name":"The Scientific Research Fund of Hunan Provincial Education Department","award":["23B0023"],"award-info":[{"award-number":["23B0023"]}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32300528"],"award-info":[{"award-number":["32300528"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370821"],"award-info":[{"award-number":["32370821"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32300520"],"award-info":[{"award-number":["32300520"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>A fundamental principle of immunotherapy is that T cells are capable of detecting tumor epitopes presented on cancer cell surfaces. Immunopeptidomic strategies empowered by liquid chromatography\u2013tandem mass spectrometry have transformed tumor epitopes identification and provided novel insights into tumor immunology. It enables in-depth profiling of major histocompatibility complex (MHC) presented ligands, thereby offering valuable perspectives on the molecular dialog among tumor and T cells. Here, we developed an immune-ligand identification and analysis pipeline from large-scale immunopeptidomics data. Through an extensive collection and processing of 5821 immunopeptidomic samples, which amounted to 305.7 million MS2 spectra, we identified 24\u00a0380\u00a0595 peptide-spectrum matches from these samples and further detected a total of 1\u00a0017\u00a0731 unique MHC immune ligands. These ligands were deconvolved and classified to specific HLA alleles. In total, we detected 582\u00a0852 HLA-I peptides and 434\u00a0879 HLA-II peptides that can bind to 292 HLA alleles, thereby greatly expanding the cancer immunopeptidome. Additionally, we identified and annotated 372\u00a0720 tumor-associated post-translational modification (PTM) peptides, revealing the comprehensive landscape of PTM antigens. All ligands and annotations were aggregated into Ligand.MHC Atlas, a comprehensive repository dedicated to tumor-derived HLA-presented ligands across 26 major human cancers (54 subtypes). Overall, our study uniquely integrates batch-effect correction, leverages the optimized software with novel deconvolution approach for immunopeptidomics analysis and ligand identification, and provides a public web portal with a comprehensive HLA ligand repository. Ligand.MHC Atlas functions as an invaluable resource, offering crucial understandings into immunology investigations. It will accelerate the advancement of cancer vaccines and immunotherapies. Ligand.MHC Atlas is available at http:\/\/modinfor.com\/Ligand.MHC-Atlas\/.<\/jats:p>","DOI":"10.1093\/bib\/bbaf314","type":"journal-article","created":{"date-parts":[[2025,7,9]],"date-time":"2025-07-09T14:13:51Z","timestamp":1752070431000},"source":"Crossref","is-referenced-by-count":4,"title":["Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3840-797X","authenticated-orcid":false,"given":"Zhi","family":"Ran","sequence":"first","affiliation":[{"name":"Department of Orthopaedics, The Second Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]},{"name":"School of Life Science, Central South University , Changsha, Hunan 410011 ,","place":["China"]},{"name":"Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meilin","family":"Mu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, Hubei ,","place":["China"]},{"name":"Guangzhou National Laboratory , Guangzhou 510005 ,","place":["China"]},{"name":"State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1177-5480","authenticated-orcid":false,"given":"Shaofeng","family":"Lin","sequence":"additional","affiliation":[{"name":"Key Laboratory of Ministry of Education of Gastrointestinal Cancer, School of Basic Medical Science, Fujian Medical University , Fuzhou 350004 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Orthopaedics, The Second Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zeng","sequence":"additional","affiliation":[{"name":"Department of Orthopaedics, The Second Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lan","family":"Kuang","sequence":"additional","affiliation":[{"name":"Department of Orthopaedics, The Second Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6025-8957","authenticated-orcid":false,"given":"Kunqi","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Ministry of Education of Gastrointestinal Cancer, School of Basic Medical Science, Fujian Medical University , Fuzhou 350004 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengbao","family":"Suo","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , Guangzhou 510005 ,","place":["China"]},{"name":"State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7002-5703","authenticated-orcid":false,"given":"Kai","family":"Yuan","sequence":"additional","affiliation":[{"name":"School of Life Science, Central South University , Changsha, Hunan 410011 ,","place":["China"]},{"name":"Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2086-3893","authenticated-orcid":false,"given":"Haodong","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Orthopaedics, The Second Xiangya Hospital, Central South University , Changsha, Hunan 410011 ,","place":["China"]},{"name":"Center for Precision Health, School of Biomedical Informatics, UTHealth , Houston, TX 77030 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,7,9]]},"reference":[{"key":"2025070910134377600_ref1","doi-asserted-by":"publisher","first-page":"3801","DOI":"10.1038\/s41467-020-17670-y","article-title":"A decade of immune-checkpoint inhibitors in cancer therapy","volume":"11","author":"Robert","year":"2020","journal-title":"Nat Commun"},{"key":"2025070910134377600_ref2","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1016\/S0140-6736(21)01206-X","article-title":"Immune checkpoint inhibitors in melanoma","volume":"398","author":"Carlino","year":"2021","journal-title":"Lancet"},{"key":"2025070910134377600_ref3","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/s41571-021-00473-5","article-title":"PD-L1 as a biomarker of response to immune-checkpoint inhibitors","volume":"18","author":"Doroshow","year":"2021","journal-title":"Nat Rev Clin Oncol"},{"key":"2025070910134377600_ref4","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1016\/j.cell.2023.03.006","article-title":"Immune checkpoint therapy-current perspectives and future directions","volume":"186","author":"Sharma","year":"2023","journal-title":"Cell"},{"key":"2025070910134377600_ref5","doi-asserted-by":"publisher","first-page":"5309","DOI":"10.1016\/j.cell.2021.09.020","article-title":"Hallmarks of response, resistance, and toxicity to immune checkpoint blockade","volume":"184","author":"Morad","year":"2021","journal-title":"Cell"},{"key":"2025070910134377600_ref6","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1038\/s41571-022-00600-w","article-title":"Immune-checkpoint inhibitors: Long-term implications of toxicity","volume":"19","author":"Johnson","year":"2022","journal-title":"Nat Rev Clin Oncol"},{"key":"2025070910134377600_ref7","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/s41568-024-00705-7","article-title":"Defining clinically useful biomarkers of immune checkpoint inhibitors in solid tumours","volume":"24","author":"Holder","year":"2024","journal-title":"Nat Rev Cancer"},{"key":"2025070910134377600_ref8","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1038\/s41586-020-2537-9","article-title":"An RNA vaccine drives immunity in checkpoint-inhibitor-treated melanoma","volume":"585","author":"Sahin","year":"2020","journal-title":"Nature"},{"key":"2025070910134377600_ref9","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/s41586-023-06063-y","article-title":"Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer","volume":"618","author":"Rojas","year":"2023","journal-title":"Nature"},{"key":"2025070910134377600_ref10","doi-asserted-by":"publisher","first-page":"4511","DOI":"10.1158\/1078-0432.CCR-19-2881","article-title":"A pan-cancer clinical study of personalized neoantigen vaccine monotherapy in treating patients with various types of advanced solid tumors","volume":"26","author":"Fang","year":"2020","journal-title":"Clin Cancer Res"},{"key":"2025070910134377600_ref11","doi-asserted-by":"publisher","first-page":"2586","DOI":"10.1038\/s41591-024-03109-0","article-title":"Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: Phase 2 trial interim results","volume":"30","author":"Parkhurst","year":"2024","journal-title":"Nat Med"},{"key":"2025070910134377600_ref12","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1016\/S0140-6736(23)02268-7","article-title":"Individualised neoantigen therapy mRNA-4157 (V940) plus pembrolizumab versus pembrolizumab monotherapy in resected melanoma (KEYNOTE-942): A randomised, phase 2b study","volume":"403","author":"Weber","year":"2024","journal-title":"Lancet"},{"key":"2025070910134377600_ref13","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1038\/s41568-021-00339-z","article-title":"Antigen presentation in cancer: Insights into tumour immunogenicity and immune evasion","volume":"21","author":"Jhunjhunwala","year":"2021","journal-title":"Nat Rev Cancer"},{"key":"2025070910134377600_ref14","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41586-020-2229-5","article-title":"Autophagy promotes immune evasion of pancreatic cancer by degrading MHC-I","volume":"581","author":"Yamamoto","year":"2020","journal-title":"Nature"},{"key":"2025070910134377600_ref15","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"},{"key":"2025070910134377600_ref16","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/s41586-022-04839-2","article-title":"Deciphering the immunopeptidome in vivo reveals new tumour antigens","volume":"607","author":"Jaeger","year":"2022","journal-title":"Nature"},{"key":"2025070910134377600_ref17","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/35056572","article-title":"Antigen processing by the proteasome","volume":"2","author":"Kloetzel","year":"2001","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025070910134377600_ref18","doi-asserted-by":"publisher","first-page":"7976","DOI":"10.1073\/pnas.92.17.7976","article-title":"A mutated intron sequence codes for an antigenic peptide recognized by cytolytic T lymphocytes on a human melanoma","volume":"92","author":"Coulie","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025070910134377600_ref19","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/nri3818","article-title":"The ins and outs of MHC class II-mediated antigen processing and presentation","volume":"15","author":"Roche","year":"2015","journal-title":"Nat Rev Immunol"},{"key":"2025070910134377600_ref20","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1034\/j.1399-0039.2000.550314.x","article-title":"IMGT\/HLA database\u2014A sequence database for the human major histocompatibility complex","volume":"55","author":"Robinson","year":"2000","journal-title":"Tissue Antigens"},{"key":"2025070910134377600_ref21","doi-asserted-by":"publisher","first-page":"D1053","DOI":"10.1093\/nar\/gkac1011","article-title":"The IPD-IMGT\/HLA database","volume":"51","author":"Barker","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025070910134377600_ref22","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.artmed.2017.06.008","article-title":"iACP-GAEnsC: Evolutionary genetic algorithm based ensemble classification of anticancer peptides by utilizing hybrid feature space","volume":"79","author":"Akbar","year":"2017","journal-title":"Artif Intell Med"},{"key":"2025070910134377600_ref23","doi-asserted-by":"publisher","first-page":"102349","DOI":"10.1016\/j.artmed.2022.102349","article-title":"cACP-DeepGram: Classification of anticancer peptides via deep neural network and skip-gram-based word embedding model","volume":"131","author":"Akbar","year":"2022","journal-title":"Artif Intell Med"},{"key":"2025070910134377600_ref24","doi-asserted-by":"publisher","first-page":"103912","DOI":"10.1016\/j.chemolab.2019.103912","article-title":"cACP: Classifying anticancer peptides using discriminative intelligent model via Chou\u2019s 5-step rules and general pseudo components","volume":"196","author":"Akbar","year":"2020","journal-title":"Chemom Intel Lab Syst"},{"key":"2025070910134377600_ref25","doi-asserted-by":"publisher","first-page":"131939","DOI":"10.1109\/ACCESS.2020.3009125","article-title":"cACP-2LFS: Classification of anticancer peptides using sequential discriminative model of KSAAP and two-level feature selection approach","volume":"8","author":"Akbar","year":"2020","journal-title":"IEEE Access"},{"key":"2025070910134377600_ref26","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/s41598-024-84146-0","article-title":"pACP-HybDeep: Predicting anticancer peptides using binary tree growth based transformer and structural feature encoding with deep-hybrid learning","volume":"15","author":"Shahid","year":"2025","journal-title":"Sci Rep"},{"key":"2025070910134377600_ref27","doi-asserted-by":"publisher","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":"2025070910134377600_ref28","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.cels.2022.12.002","article-title":"Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8(+) T-cell epitopes","volume":"14","author":"Gfeller","year":"2023","journal-title":"Cell Syst"},{"key":"2025070910134377600_ref29","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/978-1-0716-3874-3_14","article-title":"How to predict binding specificity and ligands for new MHC-II alleles with MixMHC2pred","volume":"2809","author":"Racle","year":"2024","journal-title":"Methods Mol Biol"},{"key":"2025070910134377600_ref30","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.cels.2020.06.010","article-title":"MHCflurry 2.0: Improved pan-allele prediction of MHC class I-presented peptides by incorporating antigen processing","volume":"11","author":"O\u2019Donnell","year":"2020","journal-title":"Cell Syst"},{"key":"2025070910134377600_ref31","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1158\/2326-6066.CIR-19-0464","article-title":"High-throughput prediction of MHC class I and II neoantigens with MHCnuggets","volume":"8","author":"Shao","year":"2020","journal-title":"Cancer Immunol Res"},{"key":"2025070910134377600_ref32","doi-asserted-by":"publisher","first-page":"13268","DOI":"10.1073\/pnas.0404740101","article-title":"Comparative immunopeptidomics of humans and their pathogens","volume":"101","author":"Istrail","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025070910134377600_ref33","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/348252a0","article-title":"Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells","volume":"348","author":"R\u00f6tzschke","year":"1990","journal-title":"Nature"},{"key":"2025070910134377600_ref34","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1158\/2326-6066.CIR-19-0894","article-title":"Spliced peptides and cytokine-driven changes in the Immunopeptidome of melanoma","volume":"8","author":"Faridi","year":"2020","journal-title":"Cancer Immunol Res"},{"key":"2025070910134377600_ref35","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.omto.2018.12.010","article-title":"Measles virus-based treatments trigger a pro-inflammatory cascade and a distinctive immunopeptidome in glioblastoma","volume":"12","author":"Rajaraman","year":"2019","journal-title":"Mol Ther Oncolytics"},{"key":"2025070910134377600_ref36","doi-asserted-by":"publisher","first-page":"100032","DOI":"10.1074\/mcp.RA120.002201","article-title":"CIITA-transduced glioblastoma cells uncover a rich repertoire of clinically relevant tumor-associated HLA-II antigens","volume":"20","author":"Forlani","year":"2021","journal-title":"Mol Cell Proteomics"},{"key":"2025070910134377600_ref37","doi-asserted-by":"publisher","first-page":"110916","DOI":"10.1016\/j.celrep.2022.110916","article-title":"Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides","volume":"39","author":"Bont\u00e9","year":"2022","journal-title":"Cell Rep"},{"key":"2025070910134377600_ref38","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1038\/s43018-023-00548-5","article-title":"The immunopeptidome landscape associated with T cell infiltration, inflammation and immune editing in lung cancer","volume":"4","author":"Kraemer","year":"2023","journal-title":"Nat Cancer"},{"key":"2025070910134377600_ref39","doi-asserted-by":"publisher","first-page":"1121973","DOI":"10.3389\/fimmu.2023.1121973","article-title":"PRAME and CTCFL-reactive TCRs for the treatment of ovarian cancer","volume":"14","author":"Amerongen","year":"2023","journal-title":"Front Immunol"},{"key":"2025070910134377600_ref40","doi-asserted-by":"publisher","first-page":"645770","DOI":"10.3389\/fimmu.2021.645770","article-title":"IFN\u03b3 modulates the Immunopeptidome of triple negative breast cancer cells by enhancing and diversifying antigen processing and presentation","volume":"12","author":"Goncalves","year":"2021","journal-title":"Front Immunol"},{"key":"2025070910134377600_ref41","doi-asserted-by":"publisher","DOI":"10.1172\/JCI166740","article-title":"Breast cancer immunopeptidomes contain numerous shared tumor antigens","volume":"134","author":"Kina","year":"2024","journal-title":"J Clin Invest"},{"key":"2025070910134377600_ref42","doi-asserted-by":"publisher","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":"L\u00f6ffler","year":"2019","journal-title":"Genome Med"},{"key":"2025070910134377600_ref43","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/s41467-023-44460-z","article-title":"MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer","volume":"15","author":"Liao","year":"2024","journal-title":"Nat Commun"},{"key":"2025070910134377600_ref44","doi-asserted-by":"publisher","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":"2025070910134377600_ref45","doi-asserted-by":"publisher","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-based cancer immunotherapy","volume":"9","author":"Marcu","year":"2021","journal-title":"J Immunother Cancer"},{"key":"2025070910134377600_ref46","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1007\/978-1-0716-0327-7_12","article-title":"The SysteMHC atlas: A computational pipeline, a website, and a data repository for immunopeptidomic analyses","volume":"2120","author":"Shao","year":"2020","journal-title":"Methods Mol Biol"},{"key":"2025070910134377600_ref47","doi-asserted-by":"publisher","first-page":"D1062","DOI":"10.1093\/nar\/gkad1068","article-title":"The SysteMHC atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics","volume":"52","author":"Huang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025070910134377600_ref48","doi-asserted-by":"publisher","first-page":"981","DOI":"10.1038\/s41592-020-0955-0","article-title":"MassIVE.Quant: A community resource of quantitative mass spectrometry-based proteomics datasets","volume":"17","author":"Choi","year":"2020","journal-title":"Nat Methods"},{"key":"2025070910134377600_ref49","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1021\/acs.jproteome.3c00591","article-title":"The 2023 report on the proteome from the HUPO human proteome project","volume":"23","author":"Omenn","year":"2024","journal-title":"J Proteome Res"},{"key":"2025070910134377600_ref50","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: A hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025070910134377600_ref51","doi-asserted-by":"publisher","first-page":"D1211","DOI":"10.1093\/nar\/gky869","article-title":"iProX: An integrated proteome resource","volume":"47","author":"Ma","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025070910134377600_ref52","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1007\/978-1-0716-1178-4_20","article-title":"The jPOST repository as a public data repository for shotgun proteomics","volume":"2259","author":"Watanabe","year":"2021","journal-title":"Methods Mol Biol"},{"key":"2025070910134377600_ref53","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1038\/nbt.4236","article-title":"Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine","volume":"36","author":"Chi","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2025070910134377600_ref54","doi-asserted-by":"publisher","first-page":"207","DOI":"10.52601\/bpr.2021.210004","article-title":"How to use open-pFind in deep proteomics data analysis?\u2014A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data","volume":"7","author":"Shao","year":"2021","journal-title":"Biophys Rep"},{"key":"2025070910134377600_ref55","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1002\/pmic.200300744","article-title":"Unimod: Protein modifications for mass spectrometry","volume":"4","author":"Creasy","year":"2004","journal-title":"Proteomics"},{"key":"2025070910134377600_ref56","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nmeth1019","article-title":"Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry","volume":"4","author":"Elias","year":"2007","journal-title":"Nat Methods"},{"key":"2025070910134377600_ref57","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1016\/j.immuni.2023.03.009","article-title":"Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes","volume":"56","author":"Racle","year":"2023","journal-title":"Immunity"},{"key":"2025070910134377600_ref58","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1093\/bioinformatics\/btad031","article-title":"Cytoscape.Js 2023 update: A graph theory library for visualization and analysis","volume":"39","author":"Franz","year":"2023","journal-title":"Bioinformatics"},{"key":"2025070910134377600_ref59","doi-asserted-by":"publisher","first-page":"100133","DOI":"10.1016\/j.mcpro.2021.100133","article-title":"Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples","volume":"20","author":"Klaeger","year":"2021","journal-title":"Mol Cell Proteomics"},{"key":"2025070910134377600_ref60","doi-asserted-by":"publisher","first-page":"3108","DOI":"10.1038\/s41467-022-30867-7","article-title":"A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics","volume":"13","author":"Xin","year":"2022","journal-title":"Nat Commun"},{"key":"2025070910134377600_ref61","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1016\/j.immuni.2019.08.012","article-title":"Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction","volume":"51","author":"Abelin","year":"2019","journal-title":"Immunity"},{"key":"2025070910134377600_ref62","doi-asserted-by":"publisher","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"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/4\/bbaf314\/63711467\/bbaf314.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/4\/bbaf314\/63711467\/bbaf314.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,9]],"date-time":"2025-07-09T14:13:53Z","timestamp":1752070433000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf314\/8195344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":62,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf314","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,7]]},"article-number":"bbaf314"}}