Proteogenomics: Splice-Junction Peptide Mapper (2D)

Proteogenomics links genomic variation to the proteins a cell actually makes: a sample-specific database is built from RNA-seq (capturing each patient's splice variants and coding SNVs), and mass spectrometry then searches that custom database instead of a generic reference proteome. This 2D track-view simulator renders a small four-exon gene — exons and introns on top, the spliced mature mRNA in the middle, the translated peptide chain at the bottom — and lets you toggle exon 3 in or out and introduce a single-nucleotide variant in exon 2, panning and zooming the tracks to inspect individual bases. Because exon 3 is 8 nucleotides long (not a multiple of three), skipping it shifts the downstream reading frame entirely, producing a peptide that spans a novel exon-exon junction and would never appear in a standard reference database. Live readouts track the peptide's monoisotopic mass and whether a simulated mass-spectrometry search — subject to an adjustable ppm tolerance — would accept it as a match.