Fig. 1

The workflow of ProGeo-neo: neoantigen prediction and selection with proteogenomic strategy. It includes three functional blocks: (1) RNA-seq data analysis, leading to variant peptides, which was used to create a customized database (highlighted in blue above); (2) HLA alleles were inferred from RNA-seq data (highlighted in red above). To increase the flexibility of ProGeo-neo, users have the option to upload their own HLA alleles; (3) Neoantigen prediction based on genomic data. Neoantigen screening by proteomics data (LC-MS/MS). Neoantigen filtration by RNA expression and by T cell receptor recognition (epitope). (highlighted in green above)