{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T15:16:24Z","timestamp":1777648584142,"version":"3.51.4"},"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2012,5,17]],"date-time":"2012-05-17T00:00:00Z","timestamp":1337212800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002517","type":"journal-article","created":{"date-parts":[[2012,5,17]],"date-time":"2012-05-17T16:57:56Z","timestamp":1337273876000},"page":"e1002517","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":33,"title":["Proteome Sampling by the HLA Class I Antigen Processing Pathway"],"prefix":"10.1371","volume":"8","author":[{"given":"Ilka","family":"Hoof","sequence":"first","affiliation":[]},{"given":"Debbie","family":"van Baarle","sequence":"additional","affiliation":[]},{"given":"William H.","family":"Hildebrand","sequence":"additional","affiliation":[]},{"given":"Can","family":"Ke\u015fmir","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2012,5,17]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1146\/annurev.immunol.21.120601.141107","article-title":"Positive and negative selection of T cells.","volume":"21","author":"TK Starr","year":"2003","journal-title":"Annu Rev Immunol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.cell.2005.05.013","article-title":"How the T cell repertoire becomes peptide and MHC specific.","volume":"122","author":"ES Huseby","year":"2005","journal-title":"Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1084\/jem.20082553","article-title":"Self-class I MHC molecules support survival of naive CD8 T cells, but depress their functional sensitivity through regulation of CD8 expression levels.","volume":"206","author":"K Takada","year":"2009","journal-title":"J Exp Med"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1146\/annurev.immunol.22.012703.104554","article-title":"Control of T cell viability.","volume":"22","author":"P Marrack","year":"2004","journal-title":"Annu Rev Immunol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1146\/annurev.immunol.20.092501.134942","article-title":"KIR: diverse, rapidly evolving receptors of innate and adaptive immunity.","volume":"20","author":"C Vilches","year":"2002","journal-title":"Annu Rev Immunol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1038\/ni.2107","article-title":"The carboxypeptidase ACE shapes the MHC class I peptide repertoire.","volume":"12","author":"XZ Shen","year":"2011","journal-title":"Nat Immunol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1038\/ni1089","article-title":"Post-proteasomal antigen processing for major histocompatibility complex class I presentation.","volume":"5","author":"KL Rock","year":"2004","journal-title":"Nat Immunol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2944","DOI":"10.4049\/jimmunol.172.5.2944","article-title":"Toward a definition of self: proteomic evaluation of the class I peptide repertoire.","volume":"172","author":"HD Hickman","year":"2004","journal-title":"J Immunol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1016\/j.humimm.2006.08.294","article-title":"Sampling of major histocompatibility complex class I-associated peptidome suggests relatively looser global association of HLA-B*5101 with peptides.","volume":"67","author":"D Gebreselassie","year":"2006","journal-title":"Hum Immunol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1074\/mcp.M500241-MCP200","article-title":"The turnover kinetics of major histocompatibility complex peptides of human cancer cells.","volume":"5","author":"E Milner","year":"2006","journal-title":"Mol Cell Proteomics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1074\/mcp.M600310-MCP200","article-title":"Distorted relation between mRNA copy number and corresponding major histocompatibility complex ligand density on the cell surface.","volume":"6","author":"AO Weinzierl","year":"2007","journal-title":"Mol Cell Proteomics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1084\/jem.20071985","article-title":"The MHC class I peptide repertoire is molded by the transcriptome.","volume":"205","author":"MH Fortier","year":"2008","journal-title":"J Exp Med"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.vaccine.2009.09.126","article-title":"Discovery of naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass spectrometry for vaccine development.","volume":"28","author":"KL Johnson","year":"2009","journal-title":"Vaccine"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1002\/art.27257","article-title":"The HLA-B*2705 peptidome.","volume":"62","author":"L Ben Dror","year":"2010","journal-title":"Arthritis Rheum"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"W509","DOI":"10.1093\/nar\/gkn202","article-title":"NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8\u201311.","volume":"36","author":"C Lundegaard","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1093\/bioinformatics\/btn128","article-title":"Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.","volume":"24","author":"C Lundegaard","year":"2008","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1093\/protein\/15.4.287","article-title":"Prediction of proteasome cleavage motifs by neural networks.","volume":"15","author":"C Kesmir","year":"2002","journal-title":"Protein Eng"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1007\/s00251-003-0585-6","article-title":"Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome.","volume":"55","author":"C Kesmir","year":"2003","journal-title":"Immunogenetics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.4049\/jimmunol.171.4.1741","article-title":"Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors.","volume":"171","author":"B Peters","year":"2003","journal-title":"J Immunol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1007\/s00018-005-4528-2","article-title":"Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding.","volume":"62","author":"S Tenzer","year":"2005","journal-title":"Cell Mol Life Sci"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1002\/eji.201040339","article-title":"MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation.","volume":"40","author":"JJ Calis","year":"2011","journal-title":"Eur J Immunol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.4049\/jimmunol.182.3.1526","article-title":"A comparative study of HLA binding affinity and ligand diversity: implications for generating immunodominant CD8+ T cell responses.","volume":"182","author":"X Rao","year":"2009","journal-title":"J Immunol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e7448","DOI":"10.1371\/journal.pone.0007448","article-title":"Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands.","volume":"4","author":"AS Juncker","year":"2009","journal-title":"PLoS One"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2140","DOI":"10.1073\/pnas.0711573105","article-title":"Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes.","volume":"105","author":"E Assarsson","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1126\/science.3287615","article-title":"Measuring the accuracy of diagnostic systems.","volume":"240","author":"JA Swets","year":"1988","journal-title":"Science"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"5586","DOI":"10.4049\/jimmunol.153.12.5586","article-title":"The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes.","volume":"153","author":"A Sette","year":"1994","journal-title":"J Immunol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1002\/eji.200939342","article-title":"Tapasin edits peptides on MHC class I molecules by accelerating peptide exchange.","volume":"40","author":"PV Praveen","year":"2010","journal-title":"Eur J Immunol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/S1074-7613(02)00304-7","article-title":"Optimization of the MHC class I peptide cargo is dependent on tapasin.","volume":"16","author":"AP Williams","year":"2002","journal-title":"Immunity"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.4049\/jimmunol.180.5.3210","article-title":"Characterizing the N-terminal processing motif of MHC class I ligands.","volume":"180","author":"MM Schatz","year":"2008","journal-title":"J Immunol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"4725","DOI":"10.4049\/jimmunol.0903125","article-title":"Characterizing the specificity and cooperation of aminopeptidases in the cytosol and endoplasmic reticulum during MHC class I antigen presentation.","volume":"184","author":"A Hearn","year":"2010","journal-title":"J Immunol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"11572","DOI":"10.1073\/pnas.1104104108","article-title":"Major source of antigenic peptides for the MHC class I pathway is produced during the pioneer round of mRNA translation.","volume":"108","author":"S Apcher","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.4049\/jimmunol.157.5.1823","article-title":"Defective ribosomal products (DRiPs): a major source of antigenic peptides for MHC class I molecules?","volume":"157","author":"JW Yewdell","year":"1996","journal-title":"J Immunol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/j.it.2011.08.001","article-title":"DRiPs solidify: progress in understanding endogenous MHC class I antigen processing.","volume":"32","author":"JW Yewdell","year":"2011","journal-title":"Trends Immunol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1002\/pmic.200900414","article-title":"Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.","volume":"10","author":"M Weiss","year":"2010","journal-title":"Proteomics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.0400782101","article-title":"A gene atlas of the mouse and human protein-encoding transcriptomes.","volume":"101","author":"AI Su","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00251-008-0341-z","article-title":"NetMHCpan, a method for MHC class I binding prediction beyond humans.","volume":"61","author":"I Hoof","year":"2009","journal-title":"Immunogenetics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1007\/s00251-005-0781-7","article-title":"The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage.","volume":"57","author":"M Nielsen","year":"2005","journal-title":"Immunogenetics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"W585","DOI":"10.1093\/nar\/gkm259","article-title":"WoLF PSORT: protein localization predictor.","volume":"35","author":"P Horton","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks.","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3448","DOI":"10.1093\/bioinformatics\/bti551","article-title":"BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.","volume":"21","author":"S Maere","year":"2005","journal-title":"Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002517","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T13:02:35Z","timestamp":1713963755000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002517"}},"subtitle":[],"editor":[{"given":"Bjoern","family":"Peters","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2012,5,17]]},"references-count":40,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2012,5,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002517","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.716597906.793469748","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,5,17]]}}}