Virus infection expands a biased subset of T cells that bind tetrameric class I peptide complexes. Specificity and detection of insulin-reactive CD4 + T cells in type 1 diabetes in the nonobese diabetic (NOD) mouse. The potential and challenges of exploiting the vast but dynamic neoepitope landscape for immunotherapy. Neoepitopes as cancer immunotherapy targets: key challenges and opportunities. More than one reason to rethink the use of peptides in vaccine design. A totally synthetic polyoxime malaria vaccine containing Plasmodium falciparum B cell and universal T cell epitopes elicits immune responses in volunteers of diverse HLA types. Major histocompatibility complex and T cell interactions of a universal T cell epitope from Plasmodium falciparum circumsporozoite protein. Immunomic analysis of the repertoire of T-cell specificities for influenza A virus in humans. Towards identification of immune and genetic correlates of severe influenza disease in indigenous Australians. Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Generation of peptide-MHC class I complexes through UV-mediated ligand exchange. Enumeration and characterization of memory cells in the TH compartment. Phenotypic analysis of antigen-specific T lymphocytes. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction. Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Elife 4, e07661 (2015).īassani-Sternberg, M., Pletscher-Frankild, S., Jensen, L. An open-source computational and data resource to analyze digital maps of immunopeptidomes. A comprehensive analysis of peptides presented by HLA-A1. Revisiting the arthritogenic peptide theory: quantitative not qualitative changes in the peptide repertoire of HLA-B27 allotypes. Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD). Sampling from the proteome to the human leukocyte antigen-DR (HLA-DR) ligandome proceeds via high specificity. Early kinetics of the HLA class I-associated peptidome of MVA.HIVconsv-infected cells. A systems approach to understand antigen presentation and the immune response. With this protocol, several thousand peptides can be identified from a wide variety of cell types, including cancerous and infected cells and those from tissues, with a turnaround time of 2–3 d.ĭudek, N. This peptide cargo is then extracted and separated into fractions by HPLC, and the peptides in these fractions are identified using nUPLC–MS/MS. The peptides dissociate from the class I human leukocyte antigens (HLAs) upon acid denaturation. The protocol starts with the immunoaffinity capture of naturally processed MHC-peptide complexes. Here, we describe a robust protocol for the identification of MHC-bound peptides from cell lines and tissues, using nano-ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (nUPLC–MS/MS) and recent improvements in methods for isolation and characterization of these peptides. Methods to identify these peptide antigens are critical to the development of new vaccines, for which the goal is the generation of effective adaptive immune responses and long-lasting immune memory. This critical arm of the adaptive immune system facilitates the eradication of pathogen-infected and cancerous cells, as well as the production of antibodies. Peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface form the targets of T lymphocytes.
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