Schematic workflow of proteogenomic analysis. Mass spectrometry derived data was searched against protein database and six-frame translated genome database of C. neoformans var. grubii. Peptides mapping to the protein database confirmed annotated proteins and annotated splice junctions. C represents the number of peptides identified mapping to exons excluding A and B. Peptides unique to six-frame translated genome database were categorized based on their mapping to intergenic regions and regions within the annotated genes. These peptides were used to refine the annotation of genome.