{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T00:09:20Z","timestamp":1784592560406,"version":"3.55.0"},"reference-count":71,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,4,1]],"date-time":"2025-04-01T00:00:00Z","timestamp":1743465600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,3,3]],"date-time":"2025-03-03T00:00:00Z","timestamp":1740960000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013322","name":"European Federation of Pharmaceutical Industries and Associations","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015570","name":"Blood Cancer UK","doi-asserted-by":"publisher","award":["22009"],"award-info":[{"award-number":["22009"]}],"id":[{"id":"10.13039\/501100015570","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003246","name":"Dutch Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020580","name":"Center for Ocean Leadership","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020580","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018173","name":"International Max Planck Research School for Environmental, Cellular and Molecular Microbiology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018173","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["C67500\/A29686"],"award-info":[{"award-number":["C67500\/A29686"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["CANCTA-2023\/100002"],"award-info":[{"award-number":["CANCTA-2023\/100002"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["CTRQQR-2021\/100004"],"award-info":[{"award-number":["CTRQQR-2021\/100004"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010665","name":"H2020 Marie Sk\u0142odowska-Curie Actions","doi-asserted-by":"publisher","award":["101065466"],"award-info":[{"award-number":["101065466"]}],"id":[{"id":"10.13039\/100010665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["812915"],"award-info":[{"award-number":["812915"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["945528"],"award-info":[{"award-number":["945528"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["mcponline.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular &amp; Cellular Proteomics"],"published-print":{"date-parts":[[2025,4]]},"DOI":"10.1016\/j.mcpro.2025.100937","type":"journal-article","created":{"date-parts":[[2025,3,3]],"date-time":"2025-03-03T19:51:29Z","timestamp":1741031489000},"page":"100937","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":9,"title":["PEPSeek-Mediated Identification of Novel Epitopes From Viral and Bacterial Pathogens and the Impact on Host Cell Immunopeptidomes"],"prefix":"10.1016","volume":"24","author":[{"given":"John A.","family":"Cormican","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lobna","family":"Medfai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena","family":"Wawrzyniuk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0652-1574","authenticated-orcid":false,"given":"Martin","family":"Pa\u0161en","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hassnae","family":"Afrache","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Constance","family":"Fourny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-3408-5695","authenticated-orcid":false,"given":"Sahil","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0094-9892","authenticated-orcid":false,"given":"Pascal","family":"Gnei\u00dfe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wai Tuck","family":"Soh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8374-9438","authenticated-orcid":false,"given":"Arianna","family":"Timelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanuele","family":"Nolfi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne","family":"Pannekoek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Cope","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henning","family":"Urlaub","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3815-4788","authenticated-orcid":false,"given":"Alice J.A.M.","family":"Sijts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3042-2792","authenticated-orcid":false,"given":"Michele","family":"Mishto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2515-9707","authenticated-orcid":false,"given":"Juliane","family":"Liepe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.mcpro.2025.100937_bib1","doi-asserted-by":"crossref","first-page":"2434","DOI":"10.1016\/j.cell.2022.05.022","article-title":"Humoral and cellular immune memory to four COVID-19 vaccines","volume":"185","author":"Zhang","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2025.100937_bib2","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1111\/cei.13589","article-title":"Spliced HLA bound peptides; a Black-Swan event in Immunology","volume":"204","author":"Faridi","year":"2021","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib3","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.3389\/fimmu.2017.01441","article-title":"An unexpected major role for proteasome-catalyzed peptide splicing in generation of T cell epitopes: is there relevance for vaccine development?","volume":"8","author":"Platteel","year":"2017","journal-title":"Front. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib4","doi-asserted-by":"crossref","first-page":"4187","DOI":"10.1042\/BCJ20200910","article-title":"Mechanistic diversity in MHC class I antigen recognition","volume":"478","author":"Barbosa","year":"2021","journal-title":"Biochem. J."},{"key":"10.1016\/j.mcpro.2025.100937_bib5","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1038\/nmeth1113","article-title":"Semi-supervised learning for peptide identification from shotgun proteomics datasets","volume":"4","author":"Kall","year":"2007","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mcpro.2025.100937_bib6","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2021.100076","article-title":"Spectral prediction features as a solution for the search space size problem in proteogenomics","volume":"20","author":"Verbruggen","year":"2021","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.100937_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2022.100266","article-title":"MS(2)Rescore: data-driven rescoring dramatically boosts immunopeptide identification rates","volume":"21","author":"Declercq","year":"2022","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.100937_bib8","doi-asserted-by":"crossref","first-page":"3346","DOI":"10.1038\/s41467-021-23713-9","article-title":"Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics","volume":"12","author":"Wilhelm","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.100937_bib9","doi-asserted-by":"crossref","DOI":"10.1002\/pmic.202300112","article-title":"Oktoberfest: open-source spectral library generation and rescoring pipeline based on Prosit","volume":"24","author":"Picciani","year":"2024","journal-title":"Proteomics"},{"key":"10.1016\/j.mcpro.2025.100937_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2022.100432","article-title":"inSPIRE: an open-source tool for increased mass spectrometry identification rates using Prosit spectral prediction","volume":"21","author":"Cormican","year":"2022","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.100937_bib11","doi-asserted-by":"crossref","first-page":"4539","DOI":"10.1038\/s41467-023-40129-9","article-title":"MSBooster: improving peptide identification rates using deep learning-based features","volume":"14","author":"Yang","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.100937_bib12","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","article-title":"Coronavirus biology and replication: implications for SARS-CoV-2","volume":"19","author":"V'Kovski","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib13","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.abd2071","article-title":"Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome","volume":"5","author":"Weiskopf","year":"2020","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib14","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.abf7517","article-title":"T\u00a0cell and antibody kinetics delineate SARS-CoV-2 peptides mediating long-term immune responses in COVID-19 convalescent individuals","volume":"13","author":"Bilich","year":"2021","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.mcpro.2025.100937_bib15","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41590-020-00808-x","article-title":"SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition","volume":"22","author":"Nelde","year":"2021","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib16","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1038\/nri1461","article-title":"Immune responses to Listeria monocytogenes","volume":"4","author":"Pamer","year":"2004","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib17","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1002\/eji.201545989","article-title":"CD8(+) T cells of Listeria monocytogenes-infected mice recognize both linear and spliced proteasome products","volume":"46","author":"Platteel","year":"2016","journal-title":"Eur. J. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib18","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1016\/j.celrep.2017.07.026","article-title":"Multi-level strategy for identifying proteasome-catalyzed spliced epitopes targeted by CD8+ T cells during bacterial infection","volume":"20","author":"Platteel","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.mcpro.2025.100937_bib19","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.4049\/jimmunol.166.3.1877","article-title":"A\u00a0novel approach of direct ex\u00a0vivo epitope mapping identifies dominant and subdominant CD4 and CD8 T cell epitopes from Listeria monocytogenes","volume":"166","author":"Geginat","year":"2001","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib20","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/B978-0-12-394590-7.00005-1","article-title":"Probing CD8 T cell responses with Listeria monocytogenes infection","volume":"113","author":"Condotta","year":"2012","journal-title":"Adv. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib21","doi-asserted-by":"crossref","first-page":"51","DOI":"10.3389\/fcimb.2014.00051","article-title":"Attenuated Listeria monocytogenes: a powerful and versatile vector for the future of tumor immunotherapy","volume":"4","author":"Wood","year":"2014","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib22","doi-asserted-by":"crossref","first-page":"5132","DOI":"10.1016\/j.vaccine.2016.08.039","article-title":"Strategies to enhance immunogenicity of cDNA vaccine encoded antigens by modulation of antigen processing","volume":"34","author":"Platteel","year":"2016","journal-title":"Vaccine"},{"key":"10.1016\/j.mcpro.2025.100937_bib23","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nrmicro.2016.30","article-title":"Chlamydia cell biology and pathogenesis","volume":"14","author":"Elwell","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib24","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2023.1281823","article-title":"Molecular pathogenesis of Chlamydia trachomatis","volume":"13","author":"Jury","year":"2023","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib25","doi-asserted-by":"crossref","DOI":"10.1128\/mmbr.00034-23","article-title":"Type III secretion in Chlamydia","volume":"87","author":"Rucks","year":"2023","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.mcpro.2025.100937_bib26","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1080\/14760584.2022.2117694","article-title":"Chlamydia trachomatis vaccine development - a view on the current challenges and how to move forward","volume":"21","author":"Borges","year":"2022","journal-title":"Expert Rev. Vaccin."},{"key":"10.1016\/j.mcpro.2025.100937_bib27","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/nri1551","article-title":"Immunology of Chlamydia infection: implications for a Chlamydia trachomatis vaccine","volume":"5","author":"Brunham","year":"2005","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib28","doi-asserted-by":"crossref","DOI":"10.1093\/femspd\/ftab014","article-title":"T\u00a0cell responses to Chlamydia","volume":"79","author":"Helble","year":"2021","journal-title":"Pathog. Dis."},{"key":"10.1016\/j.mcpro.2025.100937_bib29","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1073\/pnas.98.3.1160","article-title":"CD8+ T cells recognize an inclusion membrane-associated protein from the vacuolar pathogen Chlamydia trachomatis","volume":"98","author":"Fling","year":"2001","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2025.100937_bib30","doi-asserted-by":"crossref","first-page":"3831","DOI":"10.1073\/pnas.0711504105","article-title":"Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers","volume":"105","author":"Grotenbreg","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2025.100937_bib31","doi-asserted-by":"crossref","first-page":"5195","DOI":"10.1128\/iai.62.11.5195-5197.1994","article-title":"Role for CD8+ T cells in antichlamydial immunity defined by Chlamydia-specific T-lymphocyte clones","volume":"62","author":"Igietseme","year":"1994","journal-title":"Infect. Immun."},{"key":"10.1016\/j.mcpro.2025.100937_bib32","doi-asserted-by":"crossref","first-page":"4742","DOI":"10.4049\/jimmunol.171.9.4742","article-title":"An inclusion membrane protein from Chlamydia trachomatis enters the MHC class I pathway and stimulates a CD8+ T cell response","volume":"171","author":"Starnbach","year":"2003","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib33","article-title":"Comparative analysis of data-driven rescoring platforms for improved peptide identification in HeLa digest\u00a0samples","author":"Castano","year":"2025","journal-title":"Proteomics"},{"key":"10.1016\/j.mcpro.2025.100937_bib34","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1038\/s41467-024-45339-3","article-title":"Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing","volume":"15","author":"Soh","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.100937_bib35","doi-asserted-by":"crossref","first-page":"6075","DOI":"10.1038\/s41467-022-33721-y","article-title":"Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes","volume":"13","author":"Mayer","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.100937_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109305","article-title":"Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics","volume":"35","author":"Nagler","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.mcpro.2025.100937_bib37","doi-asserted-by":"crossref","first-page":"3962","DOI":"10.1016\/j.cell.2021.05.046","article-title":"Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs","volume":"184","author":"Weingarten-Gabbay","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2025.100937_bib38","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2025.100937_bib39","doi-asserted-by":"crossref","first-page":"7181","DOI":"10.1021\/acs.analchem.1c05435","article-title":"Prosit-TMT: deep learning boosts identification of TMT-labeled peptides","volume":"94","author":"Gabriel","year":"2022","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2025.100937_bib40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005725","article-title":"Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity","volume":"13","author":"Bassani-Sternberg","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.mcpro.2025.100937_bib41","doi-asserted-by":"crossref","first-page":"W458","DOI":"10.1093\/nar\/gkx248","article-title":"GibbsCluster: unsupervised clustering and alignment of peptide sequences","volume":"45","author":"Andreatta","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2025.100937_bib42","doi-asserted-by":"crossref","first-page":"2492","DOI":"10.4049\/jimmunol.1600808","article-title":"Unsupervised HLA peptidome deconvolution improves ligand prediction accuracy and predicts cooperative effects in peptide-HLA interactions","volume":"197","author":"Bassani-Sternberg","year":"2016","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib43","doi-asserted-by":"crossref","first-page":"23771","DOI":"10.1021\/acsomega.2c02425","article-title":"Predicting the success of Fmoc-based peptide synthesis","volume":"7","author":"Gutman","year":"2022","journal-title":"ACS Omega"},{"key":"10.1016\/j.mcpro.2025.100937_bib44","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1021\/acs.jproteome.9b00328","article-title":"ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion","volume":"19","author":"Hulstaert","year":"2020","journal-title":"J.\u00a0Proteome Res."},{"key":"10.1016\/j.mcpro.2025.100937_bib45","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1007\/s13361-016-1460-7","article-title":"Fast and accurate protein false discovery rates on large-scale proteomics data sets with percolator 3.0","volume":"27","author":"The","year":"2016","journal-title":"J.\u00a0Am. Soc. Mass Spectrom."},{"key":"10.1016\/j.mcpro.2025.100937_bib46","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1086\/508203","article-title":"Identification of CT521 as a frequent target of Th1 cells in patients with urogenital Chlamydia trachomatis infection","volume":"194","author":"Olsen","year":"2006","journal-title":"J.\u00a0Infect. Dis."},{"key":"10.1016\/j.mcpro.2025.100937_bib47","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mcpro.2025.100937_bib48","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating and analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.mcpro.2025.100937_bib49","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mcpro.2025.100937_bib50","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M111.010587","article-title":"PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification","volume":"11","author":"Zhang","year":"2012","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.100937_bib51","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41587-019-0322-9","article-title":"A\u00a0large peptidome dataset improves HLA class I epitope prediction across most of the human population","volume":"38","author":"Sarkizova","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.mcpro.2025.100937_bib52","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1021\/pr700739d","article-title":"Posterior error probabilities and false discovery rates: two sides of the same coin","volume":"7","author":"Kall","year":"2008","journal-title":"J.\u00a0Proteome Res."},{"key":"10.1016\/j.mcpro.2025.100937_bib53","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1126\/science.282.5389.754","article-title":"Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis","volume":"282","author":"Stephens","year":"1998","journal-title":"Science"},{"key":"10.1016\/j.mcpro.2025.100937_bib54","doi-asserted-by":"crossref","first-page":"6905","DOI":"10.4049\/jimmunol.173.11.6905","article-title":"Human CD8+ T cells recognize the 60-kDa cysteine-rich outer membrane protein from Chlamydia trachomatis","volume":"173","author":"Gervassi","year":"2004","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib55","doi-asserted-by":"crossref","first-page":"2217","DOI":"10.1084\/jem.20111266","article-title":"A\u00a0live-attenuated chlamydial vaccine protects against trachoma in nonhuman primates","volume":"208","author":"Kari","year":"2011","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.mcpro.2025.100937_bib56","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/infdis\/jiz522","article-title":"Discordance in the epithelial cell-dendritic cell major histocompatibility complex class II immunoproteome: implications for Chlamydia vaccine development","volume":"221","author":"Karunakaran","year":"2020","journal-title":"J.\u00a0Infect. Dis."},{"key":"10.1016\/j.mcpro.2025.100937_bib57","doi-asserted-by":"crossref","first-page":"363","DOI":"10.3184\/003685017X15063357842574","article-title":"Moonlighting proteins - nature's Swiss army knives","volume":"100","author":"Jeffery","year":"2017","journal-title":"Sci. Prog."},{"key":"10.1016\/j.mcpro.2025.100937_bib58","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1016\/j.molcel.2008.12.010","article-title":"Transcription by moonlight: structural basis of an extraribosomal activity of ribosomal protein S10","volume":"32","author":"Weisberg","year":"2008","journal-title":"Mol. Cell"},{"key":"10.1016\/j.mcpro.2025.100937_bib59","article-title":"The ribosome as a switchboard for bacterial stress response","volume":"11","author":"Cheng-Guang","year":"2020","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib60","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.molcel.2008.09.019","article-title":"DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression","volume":"32","author":"Mukhopadhyay","year":"2008","journal-title":"Mol. Cell"},{"key":"10.1016\/j.mcpro.2025.100937_bib61","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1016\/j.cell.2007.10.009","article-title":"Ribosomal protein S3: a KH domain subunit in NF-kappaB complexes that mediates selective gene regulation","volume":"131","author":"Wan","year":"2007","journal-title":"Cell"},{"key":"10.1016\/j.mcpro.2025.100937_bib62","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/ni.2007","article-title":"IKKbeta phosphorylation regulates RPS3 nuclear translocation and NF-kappaB function during infection with Escherichia coli strain O157:H7","volume":"12","author":"Wan","year":"2011","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib63","doi-asserted-by":"crossref","first-page":"7804","DOI":"10.4049\/jimmunol.180.12.7804","article-title":"A\u00a0novel trafficking signal within the HLA-C cytoplasmic tail allows regulated expression upon differentiation of macrophages","volume":"180","author":"Schaefer","year":"2008","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib64","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1111\/cmi.12455","article-title":"Chlamydiae interaction with the endoplasmic reticulum: contact, function and consequences","volume":"17","author":"Derre","year":"2015","journal-title":"Cell Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib65","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.22311","article-title":"Structural basis for the hijacking of endosomal sorting nexin proteins by Chlamydia trachomatis","volume":"6","author":"Paul","year":"2017","journal-title":"Elife"},{"key":"10.1016\/j.mcpro.2025.100937_bib66","doi-asserted-by":"crossref","first-page":"2791","DOI":"10.4049\/jimmunol.1202741","article-title":"Amphisomal route of MHC class I cross-presentation in bacteria-infected dendritic cells","volume":"190","author":"Fiegl","year":"2013","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.mcpro.2025.100937_bib67","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.902492","article-title":"Chlamydia trachomatis requires functional host-cell mitochondria and NADPH oxidase 4\/p38MAPK signaling for growth in normoxia","volume":"12","author":"Thapa","year":"2022","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib68","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-021-89921-x","article-title":"Dual RNA-seq analysis of in\u00a0vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells","volume":"11","author":"Hayward","year":"2021","journal-title":"Sci. Rep."},{"key":"10.1016\/j.mcpro.2025.100937_bib69","doi-asserted-by":"crossref","first-page":"392","DOI":"10.3389\/fcimb.2019.00392","article-title":"Early transcriptional landscapes of Chlamydia trachomatis-infected epithelial cells at single cell resolution","volume":"9","author":"Hayward","year":"2019","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10.1016\/j.mcpro.2025.100937_bib70","doi-asserted-by":"crossref","first-page":"D442","DOI":"10.1093\/nar\/gky1106","article-title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","volume":"47","author":"Perez-Riverol","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.mcpro.2025.100937_bib71","doi-asserted-by":"crossref","first-page":"2272","DOI":"10.1093\/bioinformatics\/btz921","article-title":"Logomaker: beautiful sequence logos in Python","volume":"36","author":"Tareen","year":"2020","journal-title":"Bioinformatics"}],"container-title":["Molecular &amp; Cellular Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947625000350?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947625000350?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T20:25:25Z","timestamp":1778617525000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535947625000350"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4]]},"references-count":71,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,4]]}},"alternative-id":["S1535947625000350"],"URL":"https:\/\/doi.org\/10.1016\/j.mcpro.2025.100937","relation":{},"ISSN":["1535-9476"],"issn-type":[{"value":"1535-9476","type":"print"}],"subject":[],"published":{"date-parts":[[2025,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"PEPSeek-Mediated Identification of Novel Epitopes From Viral and Bacterial Pathogens and the Impact on Host Cell Immunopeptidomes","name":"articletitle","label":"Article Title"},{"value":"Molecular & Cellular Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mcpro.2025.100937","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology\u00e9","name":"copyright","label":"Copyright"}],"article-number":"100937"}}