{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Nanaware PP"],"funding":["National Institute of Allergy and Infectious Diseases","NIAID NIH HHS"],"pagination":["658601"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8116589"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["12"],"pubmed_abstract":["Antigen presentation by MHC-II proteins in the thymus is central to selection of CD4 T cells, but analysis of the full repertoire of presented peptides responsible for positive and negative selection is complicated by the low abundance of antigen presenting cells. A key challenge in analysis of limiting abundance immunopeptidomes by mass spectrometry is distinguishing true MHC-binding peptides from co-eluting non-specifically bound peptides present in the mixture eluted from immunoaffinity-purified MHC molecules. Herein we tested several approaches to minimize the impact of non-specific background peptides, including analyzing eluates from isotype-control antibody-conjugated beads, considering only peptides present in nested sets, and using predicted binding motif analysis to identify core"],"journal":["Frontiers in immunology"],"pubmed_title":["Distinguishing Signal From Noise in Immunopeptidome Studies of Limiting-Abundance Biological Samples: Peptides Presented by I-A<sup>b</sup> in C57BL/6 Mouse Thymus."],"pmcid":["PMC8116589"],"funding_grant_id":["AI146189, AI127869","R01 AI137198"],"pubmed_authors":["Jurewicz MM","Nanaware PP","Lu L","Santambrogio L","Clement CC","Stern LJ"],"additional_accession":[]},"is_claimable":false,"name":"Distinguishing Signal From Noise in Immunopeptidome Studies of Limiting-Abundance Biological Samples: Peptides Presented by I-A<sup>b</sup> in C57BL/6 Mouse Thymus.","description":"Antigen presentation by MHC-II proteins in the thymus is central to selection of CD4 T cells, but analysis of the full repertoire of presented peptides responsible for positive and negative selection is complicated by the low abundance of antigen presenting cells. A key challenge in analysis of limiting abundance immunopeptidomes by mass spectrometry is distinguishing true MHC-binding peptides from co-eluting non-specifically bound peptides present in the mixture eluted from immunoaffinity-purified MHC molecules. Herein we tested several approaches to minimize the impact of non-specific background peptides, including analyzing eluates from isotype-control antibody-conjugated beads, considering only peptides present in nested sets, and using predicted binding motif analysis to identify core","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021","modification":"2025-04-04T12:33:52.799Z","creation":"2022-02-10T10:35:52.91Z"},"accession":"S-EPMC8116589","cross_references":{"pubmed":["33995376"],"doi":["10.3389/fimmu.2021.658601"]}}