Ligand.MHC Atlas

Ligand.MHC Atlas provides a comprehensive repository of HLA-presented ligands and annotations derived from large-scale immunopeptidomics data across human cancers.

Key Features:

• Large-scale immunopeptidomics data integration: The atlas aggregates data from 5821 immunopeptidomic samples comprising 305.7 million MS2 spectra.
• Peptide-spectrum match identification: The resource contains 24,380,595 peptide-spectrum matches leading to 1,017,731 unique MHC immune ligands.
• HLA allele deconvolution: Ligands are deconvolved and classified to specific HLA alleles, including 582,852 HLA-I peptides and 434,879 HLA-II peptides binding to 292 HLA alleles.
• Post-translational modification annotation: The atlas includes 372,720 tumor-associated post-translational modification (PTM) peptides revealing the landscape of PTM antigens.
• Cancer subtype coverage: The repository spans 26 major human cancers with 54 subtypes.

Scientific Applications:

• Cancer vaccine development: The resource accelerates advancement of cancer vaccines by providing comprehensive tumor-derived HLA-presented ligand data.
• Immunotherapy research: The atlas supports immunotherapy development through insights into tumor epitopes detectable by T cells.
• Tumor immunology investigation: The resource enables analysis of molecular dialog between tumor and T cells through MHC presented ligand profiling.
• PTM antigen discovery: The comprehensive landscape of tumor-associated post-translational modification peptides supports investigation of modified antigens.

Methodology:

The pipeline incorporates batch-effect correction and leverages optimized software with a novel deconvolution approach for immunopeptidomics analysis and ligand identification from liquid chromatography-tandem mass spectrometry data.