{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T22:46:30Z","timestamp":1776293190967,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,2,24]],"date-time":"2020-02-24T00:00:00Z","timestamp":1582502400000},"content-version":"vor","delay-in-days":54,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Neoantigens can function as actual antigens to facilitate tumor rejection, which play a crucial role in cancer immunology and immunotherapy. Emerging evidence revealed that neoantigens can be used to develop personalized, cancer-specific vaccines. To date, large numbers of immunogenomic peptides have been computationally predicted to be potential neoantigens. However, experimental validation remains the gold standard for potential clinical application. Experimentally validated neoantigens are rare and mostly appear scattered among scientific papers and various databases. Here, we constructed dbPepNeo, a specific database for human leukocyte antigen class I (HLA-I) binding neoantigen peptides based on mass spectrometry (MS) validation or immunoassay in human tumors. According to the verification methods of these neoantigens, the collection of peptides was classified as 295 high confidence, 247 medium confidence and 407\u2009794 low confidence neoantigens, respectively. This can serve as a valuable resource to aid further screening for effective neoantigens, optimize a neoantigen prediction pipeline and study T-cell receptor (TCR) recognition. Three applications of dbPepNeo are shown. In summary, this work resulted in a platform to promote the screening and confirmation of potential neoantigens in cancer immunotherapy.<\/jats:p>\n               <jats:p>Database URL: www.biostatistics.online\/dbPepNeo\/.<\/jats:p>","DOI":"10.1093\/database\/baaa004","type":"journal-article","created":{"date-parts":[[2020,1,12]],"date-time":"2020-01-12T12:07:33Z","timestamp":1578830853000},"source":"Crossref","is-referenced-by-count":66,"title":["dbPepNeo: a manually curated database for human tumor neoantigen peptides"],"prefix":"10.1093","volume":"2020","author":[{"given":"Xiaoxiu","family":"Tan","sequence":"first","affiliation":[{"name":"School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China"},{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daixi","family":"Li","sequence":"first","affiliation":[{"name":"School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengjie","family":"Huang","sequence":"first","affiliation":[{"name":"School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China"},{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingxing","family":"Jian","sequence":"first","affiliation":[{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"},{"name":"Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education; Key Laboratory of Carcinogenesis, National Health and Family Planning Commission, Xiangya Hospital, Central South University, Central South University, No. 932, South Lushan Road, Yuelu District, Changsha 410083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huihui","family":"Wan","sequence":"first","affiliation":[{"name":"School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China"},{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangzhi","family":"Wang","sequence":"first","affiliation":[{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"},{"name":"College of Food Science and Technology, Shanghai Ocean University, No. 999, Hucheng Ring Road, Pudong New District, Shanghai 201306, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuyu","family":"Li","sequence":"first","affiliation":[{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"},{"name":"College of Food Science and Technology, Shanghai Ocean University, No. 999, Hucheng Ring Road, Pudong New District, Shanghai 201306, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Ouyang","sequence":"first","affiliation":[{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Lin","sequence":"first","affiliation":[{"name":"School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516, Jungong Road, Yangpu District, Shanghai 200093, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lu","family":"Xie","sequence":"first","affiliation":[{"name":"Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, No. 1278, Keyuan Road, Pudong New District, Shanghai 201203, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,2,22]]},"reference":[{"key":"2020022321294292300_ref1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"},{"key":"2020022321294292300_ref2","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.oraloncology.2016.09.010","article-title":"Neoantigens in immunotherapy and personalized vaccines: implications for head and neck squamous cell carcinoma","volume":"71","author":"Zolkind","year":"2017","journal-title":"Oral Oncol"},{"key":"2020022321294292300_ref3","doi-asserted-by":"crossref","first-page":"xii11","DOI":"10.1093\/annonc\/mdx681","article-title":"Preclinical and clinical development of neoantigen vaccines","volume":"28","author":"Li","year":"2017","journal-title":"Ann Oncol"},{"key":"2020022321294292300_ref4","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/nrc3670","article-title":"Tumour antigens recognized by T lymphocytes: at the core of cancer immunotherapy","volume":"14","author":"Coulie","year":"2014","journal-title":"Nat. Rev. Cancer"},{"key":"2020022321294292300_ref5","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/nature13988","article-title":"Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens","volume":"515","author":"Gubin","year":"2014","journal-title":"Nature"},{"key":"2020022321294292300_ref6","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nri.2017.131","article-title":"Towards personalized, tumour-specific, therapeutic vaccines for cancer","volume":"18","author":"Hu","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"2020022321294292300_ref7","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1038\/nri1250","article-title":"Making sense of mass destruction: quantitating MHC class I antigen presentation","volume":"3","author":"Yewdell","year":"2003","journal-title":"Nat. Rev. Immunol."},{"key":"2020022321294292300_ref8","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/j.immuni.2007.04.003","article-title":"The final touches make perfect the peptide-MHC class I repertoire","volume":"26","author":"Hammer","year":"2007","journal-title":"Immunity"},{"key":"2020022321294292300_ref9","doi-asserted-by":"crossref","first-page":"4690","DOI":"10.1172\/JCI88590","article-title":"MHC class I-associated peptides derive from selective regions of the human genome","volume":"126","author":"Pearson","year":"2016","journal-title":"J. Clin. 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Res."},{"key":"2020022321294292300_ref15","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature22991","article-title":"An immunogenic personal neoantigen vaccine for patients with melanoma","volume":"547","author":"Ott","year":"2017","journal-title":"Nature"},{"key":"2020022321294292300_ref16","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature23003","article-title":"Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer","volume":"547","author":"Sahin","year":"2017","journal-title":"Nature"},{"key":"2020022321294292300_ref17","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1038\/s41586-018-0792-9","article-title":"Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial","volume":"565","author":"Keskin","year":"2019","journal-title":"Nature"},{"key":"2020022321294292300_ref18","doi-asserted-by":"crossref","first-page":"e1700259","DOI":"10.1002\/pmic.201700259","article-title":"The role of mass spectrometry and proteogenomics in the advancement of HLA epitope prediction","volume":"18","author":"Creech","year":"2018","journal-title":"Proteomics"},{"key":"2020022321294292300_ref19","doi-asserted-by":"crossref","first-page":"5110","DOI":"10.18632\/oncotarget.6960","article-title":"Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens","volume":"7","author":"Kalaora","year":"2016","journal-title":"Oncotarget"},{"key":"2020022321294292300_ref20","doi-asserted-by":"crossref","first-page":"13404","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. 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