Table 1.
Strategies used for selection of candidate neoantigens.
| Strategy | Advantages | Disadvantages |
|---|---|---|
| In silico peptide prediction and prioritization | Narrows down the number of candidate neoantigens Identifies minimal epitopes |
Depends on accuracy of prediction algorithms Not optimal for HLA-II-presented peptides Less accurate predictions for low frequent HLA clonotypes |
| LC-MS/MS based immunopeptidomics | Direct identification of naturally presented HLA binding peptides Narrows down the number of candidate neoantigens Allows the identification of post-translational modified peptides and non-canonical neoantigens Identifies minimal epitopes |
Limited sensitivity of mass spectrometry Biased toward detecting the more abundant peptides Relies on efficient peptide ionization and fragmentation Depends on HLA expression of tumor cells High amount of tumor tissue needed |
| List of all candidate neoantigens based on whole-exome sequencing data | Identification of all candidate neoantigens | Minimal epitope is not defined Limited feasibility in tumors with high mutation burden |
HLA, human leukocyte antigen.