Self peptides from MS-based immunopeptidomics are available for 4 of 18 patients: Mel-15, Mel-0D5P, Mel-51, and iSPC2_IFN.
They can be found in the folder "self peptides".

For the remaining 14 patients, their HLA-I alleles (Table 1) are used to search the file "mhc_ligand_full.csv.hla_1.host_human.csv" for MHC-I eluted peptides.

The self peptides or allele-matched MHC-I eluted peptides of each individual patient are used as negative training data.

For positive training data, the HLA-I alleles of each patient are used to search the file "tcell_table_export_1665561938.csv" for T cell epitopes.
Other search filters include positive Assay Qualitative Measure (Positive, Positive-High, Positive-Intermedia, Positive-Low), 
and length from 8 1o 14 amino acids. 
