{"doi":"10.1101/2022.12.05.519200","title":"HLA-Glyco: A large-scale interrogation of the glycosylated immunopeptidome","abstract":"Abstract MHC-associated peptides (MAPs) bearing post-translational modifications (PTMs) have raised intriguing questions regarding their attractiveness for targeted therapies. Here, we developed a novel computational glyco-immunopeptidomics workflow that integrates the ultrafast glycopeptide search of MSFragger with a glycopeptide-focused false discovery rate (FDR) control. We performed a harmonized analysis of 8 large-scale publicly available studies and found that glycosylated MAPs are predominantly presented by the MHC class II. We created HLA-Glyco, a resource containing over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. Our comprehensive resource reveals high levels of truncated glycans, conserved HLA-binding cores, and differences in glycosylation positional specificity between classical HLA class II allele groups. To support the nascent field of glyco-immunopeptidomics, we include the optimized workflow in the FragPipe suite and provide HLA-Glyco as a free web resource.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":305076,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9261,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":230156,"name":"Daniel A. Polasky","orcid":"0000-0002-0515-1735","position":1,"is_corresponding":false},{"id":842280,"name":"Yi Hsiao","orcid":"0000-0002-9435-0305","position":2,"is_corresponding":false},{"id":230152,"name":"Fengchao Yu","orcid":"0000-0002-7695-3698","position":3,"is_corresponding":false},{"id":51779,"name":"Felipe da Veiga Leprevost","orcid":"0000-0002-8228-5374","position":4,"is_corresponding":false},{"id":618033,"name":"Javier A. Alfaro","orcid":"0000-0002-5553-6991","position":5,"is_corresponding":false},{"id":108226,"name":"Marcin Cieślik","orcid":"0000-0002-5467-1040","position":6,"is_corresponding":false},{"id":51780,"name":"Alexey I. Nesvizhskii","orcid":"0000-0002-2806-7819","position":7,"is_corresponding":false},{"id":618039,"name":"Georges Bedran","orcid":"0000-0002-3086-3742","position":0,"is_corresponding":true}],"reference_count":54,"raw_metadata":null,"created_at":"2026-07-19T00:32:37.185846Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}