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# Appendix Table 2. Predicted Features
| Field | Definition | Tool / Source |
|--------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------|
| netmhcpan_rank | Percentile rank of peptide–MHC binding predicted by NetMHCpan | NetMHCpan v4.1 |
| netmhcstabpan_stability | Predicted stability of peptide–MHC complex | NetMHCstabpan v1.0 |
| prime_rank | Predicted probability rank of TCR recognition | PRIME v1.0.1 |
| bigmhc_im_score | Predicted immunogenicity probability of the peptide–MHC complex, as output by BigMHC (IM module). Continuous value between 0 and 1; higher scores indicate higher likelihood of immunogenicity. | BigMHC-IM (latest version, 2024 release) |
| tap_score | Predicted TAP transport efficiency score | NetCTLpan v1.1 |
| netchop_score | Predicted proteasomal cleavage score | NetChop v3.1 |
| dai_netmhcpan | Differential agretopicity index (mutant vs wild-type, NetMHCpan). Calculation: log(rank(neo-pep)/rank(wt-pep)) if rank(neo-pep)>0 and rank(wt-pep)>0. 0 otherwise. Negative values indicate a large difference between neo-pep and wt-pep. | NetMHCpan v4.1 |
| anchor_mutation | Whether mutation occurs at HLA anchor position | MixMHCpred v3.0 |
| eluted_ligand_match | Whether peptide is observed in MHC ligand elution/MS experiments | IEDB (MHC ligand elution, 2025 export) |
| tcga_cancer_expression_tpm_median | Median log2(TPM+0.001) across TCGA primary tumor samples for the matching cancer type | TCGA (Data Release 43.0 – May 07, 2025) |
| driver_status | Gene-level driver status annotation | IntOGen 2024 |
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