ArticleBriefings in bioinformatics2025
Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.
Article in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Post‑translational modification‑governed immune states in cancer immunity: Biomarker implications for checkpoint competence, tumor visibility and immunotherapy resistance (Review).International journal of oncology · 2026Review
- Discovery of Post-Translationally Modified Epitopes in Autoimmunity: Someone Has to Fish so Everyone Can Eat.Immunological reviews · 2026Review
- Normal-immunopeptidome denominator: a safety atlas for immunotherapies targeting non-canonical and aberrantly expressed tumor antigens.Journal for immunotherapy of cancer · 2026Article
- Mature tertiary lymphoid structures tumor microenvironment-based risk model to assess patients with pancreatic ductal adenocarcinoma.Translational cancer research · 2026Article
- Rewiring tumor visibility: The immunopeptidome as a dynamic interface between antigen processing, microenvironmental stress, and immune recognition.Frontiers in oncology · 2025Review
- Bispecific immunotherapy based on antibodies, T-cell receptors, and aptamers: mechanisms of action, adverse effects, and future perspectives.Frontiers in immunology · 2025Review
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Authors and funding
10 authors.
Funding
Abstract
A fundamental principle of immunotherapy is that T cells are capable of detecting tumor epitopes presented on cancer cell surfaces. Immunopeptidomic strategies empowered by liquid chromatography-tandem mass spectrometry have transformed tumor epitopes identification and provided novel insights into tumor immunology. It enables in-depth profiling of major histocompatibility complex (MHC) presented ligands, thereby offering valuable perspectives on the molecular dialog among tumor and T cells. Here, we developed an immune-ligand identification and analysis pipeline from large-scale immunopeptidomics data. Through an extensive collection and processing of 5821 immunopeptidomic samples, which amounted to 305.7 million MS2 spectra, we identified 24 380 595 peptide-spectrum matches from these samples and further detected a total of 1 017 731 unique MHC immune ligands. These ligands were deconvolved and classified to specific HLA alleles. In total, we detected 582 852 HLA-I peptides and 434 879 HLA-II peptides that can bind to 292 HLA alleles, thereby greatly expanding the cancer immunopeptidome. Additionally, we identified and annotated 372 720 tumor-associated post-translational modification (PTM) peptides, revealing the comprehensive landscape of PTM antigens. All ligands and annotations were aggregated into Ligand.MHC Atlas, a comprehensive repository dedicated to tumor-derived HLA-presented ligands across 26 major human cancers (54 subtypes). Overall, our study uniquely integrates batch-effect correction, leverages the optimized software with novel deconvolution approach for immunopeptidomics analysis and ligand identification, and provides a public web portal with a comprehensive HLA ligand repository. Ligand.MHC Atlas functions as an invaluable resource, offering crucial understandings into immunology investigations. It will accelerate the advancement of cancer vaccines and immunotherapies. Ligand.MHC Atlas is available at http://modinfor.com/Ligand.MHC-Atlas/.
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