Selecting thresholds (cut-offs) for MHC class I and II binding predictions

The predicted binding affinities and ranks that result from the IEDB prediction tools should be treated as ranking metrics as a way to prioritize peptides for experimental testing.  There are many ways to rank the peptides.  Here, we list only the latest recommendations.

MHC class I

For MHC class I T cell epitope predictions, the latest research from our group¹ shows that setting a common threshold for eluted ligand (EL) rank of ~1.1 in NetMHCPan 4.0 across all alleles results in 80% sensitivity for capturing immunogenic peptides.  Allele-specific thresholds have also been established and are contained within the supplemental data of the paper.  However, the increase in sensitivity and specificity is marginal unless there are relatively few alleles being considered with very divergent thresholds.

MHC class II

For MHC class II T cell epitope predictions, selection of predicted binders can be done based on the percentile rank or MHC binding affinity.  The IEDB currently recommends making selections based on a consensus percentile rank of the top 20%², which captures 50% of the immune response.   Alternatively, selecting peptides predicted to bind at 1,000nM is also supported by experimental data³. 

1. Reardon et al., 2021 Mol. Cell. Proteomics (PMID 34303001)
2. Paul eg al., 2015 J. Imm. Methods (PMID 25862607)
3. Southwood et al., 1998, J. Immunology (PMID 9531296)