ArticleNucleic acids research2024
The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 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
- Computational identification of antigen-specific T cell groups through generative epitope modeling.iScience · 2026Article
- TIPs: a deep learning-guided proteogenomic framework to expand the landscape of transposable element-derived antigens with immunopeptidomics.Genome biology · 2026Article
- The critical role of artificial intelligence and bioinformatics in accelerating peptide-based vaccine discovery for tackling global infectious diseases.Briefings in bioinformatics · 2026Review
- Deciphering small sequence differences in T cell receptor-antigen pairing.Nature communications · 2026Article
- AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity.bioRxiv : the preprint server for biology · 2026Article
- TransBindpMHCI: a transformer-based model for pan-specific MHC-I peptide binding prediction.BMC bioinformatics · 2026Article
- Clinical peptidomics for respiratory diseases: matrices, workflows, and translation towards treatable traits, with a focus on COPD.Clinical proteomics · 2026Review
- Bright side of the dark genome: antigens for next-gen cancer vaccines.Journal for immunotherapy of cancer · 2026Review
- The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer.iScience · 2026Article
- Review
- Unlocking the Next Decade of Proteomics with Standardized, Structured Metadata.Journal of proteome research · 2026Review
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- Utilizing Protein Bioinformatics to Delve Deeper into Immunopeptidomic Datasets with AIMS: An Automated Immune Molecule Separator.Methods in molecular biology (Clifton, N.J.) · 2026Article
- An Interpretable Multi-instance Learner Decodes Cellular Recruitment from Spatially Resolved Transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Review
- MHCquant2 refines immunopeptidomics tumor antigen discovery.Genome biology · 2025Article
- HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry.Journal for immunotherapy of cancer · 2025Article
- SCAN-ACT: adoptive T cell therapy target discovery through single-cell transcriptomics.Genome medicine · 2025Article
- Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.Briefings in bioinformatics · 2025Article
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7 authors.
Funding
Abstract
The SysteMHC Atlas v1.0 was the first public repository dedicated to mass spectrometry-based immunopeptidomics. Here we introduce a newly released version of the SysteMHC Atlas v2.0 (https://systemhc.sjtu.edu.cn), a comprehensive collection of 7190 MS files from 303 allotypes. We extended and optimized a computational pipeline that allows the identification of MHC-bound peptides carrying on unexpected post-translational modifications (PTMs), thereby resulting in 471K modified peptides identified over 60 distinct PTM types. In total, we identified approximately 1.0 million and 1.1 million unique peptides for MHC class I and class II immunopeptidomes, respectively, indicating a 6.8-fold increase and a 28-fold increase to those in v1.0. The SysteMHC Atlas v2.0 introduces several new features, including the inclusion of non-UniProt peptides, and the incorporation of several novel computational tools for FDR estimation, binding affinity prediction and motif deconvolution. Additionally, we enhanced the user interface, upgraded website framework, and provided external links to other resources related. Finally, we built and provided various spectral libraries as community resources for data mining and future immunopeptidomic and proteomic analysis. We believe that the SysteMHC Atlas v2.0 is a unique resource to provide key insights to the immunology and proteomics community and will accelerate the development of vaccines and immunotherapies.
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Registered trials
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