GenomeProt: User friendly proteogenomics for canonical and non-canonical proteoform characterisation

Quantifying the diversity of RNAs and proteins produced by cells is fundamental to the biological and clinical sciences. However, many RNAs and proteins remain uncharacterised, especially proteins translated from alternate RNA isoforms; untranslated regions of mRNAs and non-coding RNAs, as well as the effects of DNA variation on protein sequences. Proteogenomics aims to characterise the complete proteome by integrating genomics and/or transcriptomics with proteomics, but current tools have limitations in useability, analysis features and visualisation of resulting data. To address these gaps, we developed GenomeProt, a user-friendly GUI-based tool for integrative proteogenomic analysis. We demonstrate its utility by integrating long-read RNA sequencing with mass-spectrometry-based proteomics to pinpoint proteoform expression generated by alternative splicing; discover novel, unannotated proteins in human brain samples; and quantify variant-containing peptides associated with treatment resistance in a melanoma xenograft model. GenomeProt brings the discovery power of proteogenomics to biologists, illuminating the hidden proteome.