Neoantigen-7-HLA-Binding-Novel-Peptides

Neoantigens are peptides derived from tumor-specific mutations, which are recognized by the immune system as foreign and can stimulate an immune response against cancer cells. Identifying these neoantigens is a crucial step in the development of personalized cancer immunotherapies, as they serve as targets for T-cell mediated immune responses. However, predicting which peptides from the tumor genome will bind effectively to major histocompatibility complex (MHC) molecules—key proteins that present antigens to immune cells—remains a significant challenge.

This tutorial outlines a comprehensive workflow for the identification, prediction, and validation of potential neoantigens. We begin by using the Immune Epitope Database (IEDB) to predict the binding affinity of peptide sequences to MHC molecules. IEDB provides powerful tools to model how peptides interact with different MHC alleles, helping to prioritize peptides that are most likely to be presented by the immune system. Next, we validate these peptides using PepQuery, a tool that allows for the comparison of predicted neoantigens with experimental proteomics data, providing an additional layer of confidence in their relevance. Finally, we categorize the peptides into strong and weak binders, based on their predicted affinity, which helps in identifying the most promising candidates for cancer immunotherapy.