We developed and validated a proteogenomics pipeline for neoantigen discovery from patient tumor samples. By integrating genomic data analysis with advanced proteomic technologies, this pipeline enables the identification of unique neoantigens resulting from tumor-specific mutations.

Through our comprehensive approach, we analyze tumor samples to detect patient-specific protein-coding variants and validate the presence of these neoantigens on the protein level. This ensures the right selection of variants to be included in cancer vaccines and thereby the effectiveness of immunotherapy treatments, providing a powerful tool in the fight against cancer and paving the way for highly personalized treatment strategies.