title: Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD).
abstract: The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification of HLA class I-associated peptides. However, the HLA class I peptide repertoire remains largely unexplored because the variable nature of endogenous peptides represents difficulties in conventional peptide fragmentation technology. Here, we substantially enhanced (about threefold) the identification success rate of peptides presented by HLA class I using combined electron-transfer/higher-energy collision dissociation (EThcD), reporting over 12,000 high-confident (false discovery rate <1%) peptides from a single human B-cell line. The direct importance of such an unprecedented large dataset is highlighted by the discovery of unique features in antigen presentation. The observation that a substantial part of proteins is sampled across different HLA alleles, and the common occurrence of HLA class I nested sets, suggest that the constraints of HLA class I to comprehensively present the health states of cells are not as tight as previously thought. Our dataset contains a substantial set of peptides bearing a variety of posttranslational modifications presented with marked allele-specific differences. We propose that EThcD should become the method of choice in analyzing HLA class I-presented peptides.
authors.affiliation: Formulation and Analytical Research, Institute for Translational Vaccinology, 3721 MA, Bilthoven, The Netherlands.
authors.forename: Geert P M
authors.initials: GP
authors.lastname: Mommen
authors.forename: Christian K
authors.initials: CK
authors.lastname: Frese
authors.forename: Hugo D
authors.initials: HD
authors.lastname: Meiring
authors.forename: Jacqueline
authors.initials: J
authors.lastname: van Gaans-van den Brink
authors.forename: Ad P J M
authors.initials: AP
authors.lastname: de Jong
authors.forename: Cécile A C M
authors.initials: CA
authors.lastname: van Els
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
mesh_terms: D000483:Alleles; D001402:B-Lymphocytes / Q000276:immunology; D002460:Cell Line; D002853:Chromatography, Liquid; D004579:Electron Transport; D006680:HLA Antigens / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D006801:Humans; D010455:Peptides / Q000737:chemistry* / Q000276:immunology; D053719:Tandem Mass Spectrometry
chemical_list: D006680:HLA Antigens; D010455:Peptides
keywords: binding motif; electron-transfer dissociation; human leukocyte antigen class I; major histocompatibility complex; phosphorylation