Table 1. Immunopeptidome databases for human cancer.
| Database | Cancer and normal tissue types | Data type | Peptides (MHC I / II) | Access | Citation |
|---|---|---|---|---|---|
| SysteMHC Atlas (V.2.0) | Multiple published datasets covering various cancer types, cell lines, and some normal tissues; 303 HLA allotypes | Mass spectrometry-identified HLA class I and II ligands including post-translational modifications | ~1.0 million (class I)/~1.1 million (class II) unique peptides | Public | Huang et al119 |
| HLA Ligand Atlas | 29 healthy tissue types from 227 samples (from 21 donors) | Mass spectrometry-identified HLA class I and II ligandomes from benign tissues | 90 428 (class I)/142 625 (class II) unique peptides | Public | Marcu et al122 |
| cancer antigen atlas (caAtlas) | 9 cancer types (311 tumor samples) + 29 normal tissue types (707 non-cancer samples) | Re-analyzed MS immunopeptidomics from published studies; includes modified peptides, cancer/testis, and tumor-associated antigens | 252 974 unique HLA class I peptides and 266 057 unique HLA class II peptides | Public | Yi et al120 |
| IEAtlas | 15 cancer types+30 non-cancerous tissues | Re-analysis of MS HLA peptidomes focusing on non-coding region-derived peptides; includes immunogenicity metrics | 245 870 non-canonical peptides (total across class I/II) | Public | Cai et al121 |
| PCI-DB | 45 cancer types and 32 benign tissue types | 10 000 raw mass spectrometry files from over 3000 tissue samples | >6.6 million HLA class I and >3.4 million HLA class II peptides | Public | Lemke et al112 https://pci-db.org/ |
HLA, human leukocyte antigen; MHC, major histocompatability complex; PCI-DB, Peptides for Cancer Immunotherapy Database.