{"id":"https://openalex.org/W4408227164","doi":"https://doi.org/10.1093/bib/bbaf087","title":"Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey","display_name":"Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408227164","doi":"https://doi.org/10.1093/bib/bbaf087","pmid":"https://pubmed.ncbi.nlm.nih.gov/40052441"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf087","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf087/62310237/bbaf087.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf087/62310237/bbaf087.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Shifu Luo","orcid":"https://orcid.org/0000-0001-9735-4670"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN","MO"],"is_corresponding":true,"raw_author_name":"Shifu Luo","raw_affiliation_strings":["Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","Faculty of Health Sciences, University of Macau , Taipa, Macao SAR 999078 ,","Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I204512498"]},{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035414166","display_name":"Hui Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210118524","display_name":"Universit\u00e9 Bourgogne Franche-Comt\u00e9","ror":"https://ror.org/02dn7x778","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210118524"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN","FR","SG"],"is_corresponding":false,"raw_author_name":"Hui Peng","raw_affiliation_strings":["Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive ,","School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore","Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive ,","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore","institution_ids":["https://openalex.org/I172675005","https://openalex.org/I4210118524"]},{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101787464","display_name":"Ying Shi","orcid":"https://orcid.org/0000-0003-1443-1912"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I181877577","display_name":"Shanxi University","ror":"https://ror.org/03y3e3s17","country_code":"CN","type":"education","lineage":["https://openalex.org/I181877577"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Shi","raw_affiliation_strings":["Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","School of Computer and Information Technology, Shanxi University , Taiyuan, 030006, Shanxi ,","Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","School of Computer and Information Technology, Shanxi University, Taiyuan, 030006, Shanxi, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"School of Computer and Information Technology, Shanxi University , Taiyuan, 030006, Shanxi ,","institution_ids":["https://openalex.org/I181877577"]},{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"School of Computer and Information Technology, Shanxi University, Taiyuan, 030006, Shanxi, China","institution_ids":["https://openalex.org/I181877577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088949458","display_name":"Jiaxin Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxin Cai","raw_affiliation_strings":["Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079985557","display_name":"Songming Zhang","orcid":"https://orcid.org/0000-0001-7695-5880"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Songming Zhang","raw_affiliation_strings":["Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014846775","display_name":"Ning\u2010Yi Shao","orcid":"https://orcid.org/0000-0003-4231-828X"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Ningyi Shao","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau , Taipa, Macao SAR 999078 ,","Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau , Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I204512498"]},{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017861049","display_name":"Jinyan Li","orcid":"https://orcid.org/0000-0003-1833-7413"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinyan Li","raw_affiliation_strings":["Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology , Shenzhen, 518107, Guangdong ,","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]},{"raw_affiliation_string":"Faculty of Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China","institution_ids":["https://openalex.org/I4210152380","https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I180726961","https://openalex.org/I204512498","https://openalex.org/I4210152380"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03760917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.7840349674224854},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.5475207567214966},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5325433611869812},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.46135544776916504},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.454863965511322},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4386332631111145},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2995684742927551},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19137844443321228},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08430597186088562},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07612749934196472},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06611847877502441}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7840349674224854},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5475207567214966},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5325433611869812},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.46135544776916504},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.454863965511322},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4386332631111145},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2995684742927551},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19137844443321228},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08430597186088562},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07612749934196472},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06611847877502441}],"mesh":[{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056945","descriptor_name":"Hep G2 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf087","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf087/62310237/bbaf087.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40052441","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40052441","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11886573","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11886573","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf087","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf087/62310237/bbaf087.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408227164.pdf"},"referenced_works_count":157,"referenced_works":["https://openalex.org/W1418224","https://openalex.org/W752259472","https://openalex.org/W1525575010","https://openalex.org/W1791584368","https://openalex.org/W1875025089","https://openalex.org/W1970696723","https://openalex.org/W1971887998","https://openalex.org/W1975450451","https://openalex.org/W1995478292","https://openalex.org/W2002665761","https://openalex.org/W2006759360","https://openalex.org/W2008117982","https://openalex.org/W2011920499","https://openalex.org/W2023010129","https://openalex.org/W2026465178","https://openalex.org/W2028673251","https://openalex.org/W2029979788","https://openalex.org/W2036321220","https://openalex.org/W2038615001","https://openalex.org/W2043398720","https://openalex.org/W2047006637","https://openalex.org/W2052912081","https://openalex.org/W2057282070","https://openalex.org/W2064675550","https://openalex.org/W2073619906","https://openalex.org/W2074643144","https://openalex.org/W2076948707","https://openalex.org/W2080752012","https://openalex.org/W2083782746","https://openalex.org/W2084323507","https://openalex.org/W2087872380","https://openalex.org/W2089273345","https://openalex.org/W2095650214","https://openalex.org/W2105009956","https://openalex.org/W2112796928","https://openalex.org/W2127325419","https://openalex.org/W2129718327","https://openalex.org/W2130374917","https://openalex.org/W2130706354","https://openalex.org/W2135078307","https://openalex.org/W2135581618","https://openalex.org/W2138924321","https://openalex.org/W2149441684","https://openalex.org/W2150056019","https://openalex.org/W2160515792","https://openalex.org/W2166810745","https://openalex.org/W2214699570","https://openalex.org/W2242659647","https://openalex.org/W2258573009","https://openalex.org/W2270152626","https://openalex.org/W2290266703","https://openalex.org/W2291298003","https://openalex.org/W2336315810","https://openalex.org/W2346680365","https://openalex.org/W2398637015","https://openalex.org/W2523343093","https://openalex.org/W2544360569","https://openalex.org/W2557260411","https://openalex.org/W2571606850","https://openalex.org/W2590497374","https://openalex.org/W2603081759","https://openalex.org/W2605808699","https://openalex.org/W2607310450","https://openalex.org/W2626631226","https://openalex.org/W2736859409","https://openalex.org/W2745376284","https://openalex.org/W2748343486","https://openalex.org/W2749499006","https://openalex.org/W2750771238","https://openalex.org/W2765357310","https://openalex.org/W2783769451","https://openalex.org/W2792595511","https://openalex.org/W2793742921","https://openalex.org/W2806959873","https://openalex.org/W2811035881","https://openalex.org/W2898789672","https://openalex.org/W2908241150","https://openalex.org/W2918023653","https://openalex.org/W2918815995","https://openalex.org/W2919115771","https://openalex.org/W2934533499","https://openalex.org/W2952108587","https://openalex.org/W2952994284","https://openalex.org/W2954615294","https://openalex.org/W2971041153","https://openalex.org/W2972257613","https://openalex.org/W2977528366","https://openalex.org/W2979770225","https://openalex.org/W2980949872","https://openalex.org/W2998313390","https://openalex.org/W3005641657","https://openalex.org/W3009889677","https://openalex.org/W3009999407","https://openalex.org/W3024570138","https://openalex.org/W3044880600","https://openalex.org/W3090166847","https://openalex.org/W3091991776","https://openalex.org/W3102843928","https://openalex.org/W3124720941","https://openalex.org/W3125092523","https://openalex.org/W3127841695","https://openalex.org/W3132887062","https://openalex.org/W3132948359","https://openalex.org/W3134443156","https://openalex.org/W3136021864","https://openalex.org/W3136924813","https://openalex.org/W3146944767","https://openalex.org/W3179726909","https://openalex.org/W3185907431","https://openalex.org/W3194049481","https://openalex.org/W3194810341","https://openalex.org/W3201305288","https://openalex.org/W3203588026","https://openalex.org/W3208861989","https://openalex.org/W3210982033","https://openalex.org/W3211239537","https://openalex.org/W4206384730","https://openalex.org/W4210348552","https://openalex.org/W4214929667","https://openalex.org/W4221071191","https://openalex.org/W4283796993","https://openalex.org/W4285097347","https://openalex.org/W4292846877","https://openalex.org/W4293043553","https://openalex.org/W4296071823","https://openalex.org/W4297102201","https://openalex.org/W4303699434","https://openalex.org/W4308452317","https://openalex.org/W4308834807","https://openalex.org/W4309506674","https://openalex.org/W4309573581","https://openalex.org/W4310593400","https://openalex.org/W4311029059","https://openalex.org/W4313547267","https://openalex.org/W4313830530","https://openalex.org/W4323652437","https://openalex.org/W4324061310","https://openalex.org/W4360999048","https://openalex.org/W4365513261","https://openalex.org/W4375864036","https://openalex.org/W4383500090","https://openalex.org/W4384028715","https://openalex.org/W4384341779","https://openalex.org/W4385245566","https://openalex.org/W4387773470","https://openalex.org/W4389639889","https://openalex.org/W4390498794","https://openalex.org/W4392519792","https://openalex.org/W4393969605","https://openalex.org/W4394063358","https://openalex.org/W4401107218","https://openalex.org/W4402454718","https://openalex.org/W4402482829","https://openalex.org/W4407504556","https://openalex.org/W4407660965","https://openalex.org/W6639604430","https://openalex.org/W6645882359"],"related_works":["https://openalex.org/W1488408180","https://openalex.org/W2161444195","https://openalex.org/W2360290178","https://openalex.org/W2035260723","https://openalex.org/W2985540061","https://openalex.org/W2088324202","https://openalex.org/W2126703991","https://openalex.org/W2610897791","https://openalex.org/W4366463707","https://openalex.org/W4402024459"],"abstract_inverted_index":{"Cancer":[0],"neoantigens":[1,127],"are":[2],"peptides":[3,15],"that":[4,93],"originate":[5],"from":[6],"alterations":[7],"in":[8,57,87],"the":[9,84,105,118,123,132],"genome,":[10],"transcriptome,":[11],"or":[12],"proteome.":[13],"These":[14],"can":[16],"elicit":[17],"cancer-specific":[18],"T-cell":[19],"recognition,":[20],"making":[21],"them":[22],"potential":[23,36,119],"candidates":[24],"for":[25,37,70,122,147],"cancer":[26,126],"vaccines.":[27],"The":[28],"rapid":[29],"advancement":[30],"of":[31,104,120,125,131],"proteomics":[32,114,121],"technology":[33],"holds":[34],"tremendous":[35],"identifying":[38],"these":[39,63,140],"neoantigens.":[40],"Here,":[41],"we":[42,60,116,142],"provided":[43],"an":[44],"up-to-date":[45],"survey":[46,82],"about":[47],"database-based":[48],"search":[49],"methods":[50,64,134],"and":[51,59,109,128],"de":[52,88],"novo":[53,89],"peptide":[54,90],"sequencing":[55,91],"approaches":[56,92],"proteomics,":[58],"also":[61],"compared":[62],"to":[65,135],"recommend":[66],"reliable":[67],"analytical":[68],"tools":[69],"neoantigen":[71,79,148],"identification.":[72],"Unlike":[73],"previous":[74],"surveys":[75],"on":[76,101],"mass":[77],"spectrometry-based":[78],"discovery,":[80],"this":[81],"summarizes":[83],"key":[85],"advancements":[86],"utilize":[94],"artificial":[95],"intelligence.":[96],"From":[97],"a":[98,102,144],"comparative":[99],"study":[100],"dataset":[103],"HepG2":[106],"cell":[107],"line":[108],"nine":[110],"mixed":[111],"hepatocellular":[112],"carcinoma":[113],"samples,":[115],"demonstrated":[117],"identification":[124],"conducted":[129],"comparisons":[130],"existing":[133],"illustrate":[136],"their":[137],"limits.":[138],"Understanding":[139],"limits,":[141],"suggested":[143],"novel":[145],"workflow":[146],"discovery":[149],"as":[150],"perspectives.":[151]},"counts_by_year":[],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}
