HLA-C and cancer: To make the proteogenomics-based neoantigen prioritization method directly available to the cancer research community, we have implemented it in NeoFlow, which includes four modules as shown in Fig. 7d: (1) variant annotation and customized database construction; (2) variant peptide identification including MS/MS searching, FDR estimation, PepQuery validation, and optional RT-based validation; (3) human leukocyte antigen (HLA) typing; and (4) MHC-binding prediction and neoantigen prioritization.