title: The nature of self for T cells-a systems-level perspective.
abstract: T-cell development and function are regulated by MHC-associated self peptides, collectively referred to as the immunopeptidome. Large-scale mass spectrometry studies have highlighted three key features of the immunopeptidome. First, it is not a mirror of the proteome or the transcriptome, and its content cannot be predicted with currently available bioinformatic tools. Second, the immunopeptidome is more plastic than previously anticipated, and is molded by several cell-intrinsic and cell-extrinsic factors. Finally, the complexity of the immunopeptidome goes beyond the 20-amino acids alphabet encoded in the germline, and is not restricted to canonical reading frames. The large amounts of 'dark matter' in the immunopeptidome, such as polymorphic, cryptic and mutant peptides, can now be explored using novel proteogenomic approaches that combine mass spectrometry and next-generation sequencing.
authors.affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7; Department of Medicine, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7.
authors.forename: Diana P
authors.initials: DP
authors.lastname: Granados
authors.affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7; Department of Medicine, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7.
authors.forename: Céline M
authors.initials: CM
authors.lastname: Laumont
authors.affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7; Department of Chemistry, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7.
authors.forename: Pierre
authors.initials: P
authors.lastname: Thibault
authors.affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7; Department of Medicine, Université de Montréal, P.O. Box 6128, Downtown Station, Montreal, QC, Canada H3C 3J7. Electronic address: claude.perreault@umontreal.ca.
authors.forename: Claude
authors.initials: C
authors.lastname: Perreault
mesh_terms: D000818:Animals; D017951:Antigen Presentation; D001324:Autoantigens / Q000032:analysis / Q000276:immunology; D006801:Humans; D007239:Infections / Q000276:immunology; D007249:Inflammation / Q000276:immunology; D040901:Proteomics; D017634:Self Tolerance; D013601:T-Lymphocytes / Q000276:immunology*
chemical_list: D001324:Autoantigens