We validated the identified immunopeptides based on known HLA motifs, as well as predicted binding affinity using NetMHCpan.
In conclusion, our timsTOF fragment ion intensity prediction model can be used for PSM rescoring to highly accurately and sensitively identify immunopeptides. This has several important implications for the discovery of (neo-)epitopes and development of #immunotherapies.
For more detailed information, check out the preprint! https://www.biorxiv.org/content/10.1101/2023.07.17.549401v1