Discovery of tumor-specific and neoantigenic peptides in cancer tissue samples using mass spectrometry-based immunopeptidomics

Therapeutic peptide-based vaccination is a promising strategy for cancer immunotherapies. The identification of tumor-specific antigens is key to developing such therapies. Mass spectrometry has emerged as the primary technique for identifying peptides presented on human leukocyte antigen (HLA), i.e., immunopeptides.
While tremendous progress has been made, the analysis of immunopeptides remains challenging, especially when working with scarce clinical tissue samples below 20 mg. Here, we present a robust and scalable workflow utilizing the BeatBox tissue homogenizer that enables deep immunopeptidomics profiling of clinically relevant samples, facilitating the discovery of tumor-specific and neoantigenic peptides for therapeutic development.