This SNSF project aims to largely improve genome annotations by discovering unannotated small ORF encoded proteins (SEPs) by mass spectrometry-based proteomics. Such SEPs are often missed in genome annotations but can carry out key biological functions, including roles in cell-cell communication, multi-drug resistance as enzymes or antimicrobial peptides. Our first, basic proteogenomics solution allowed us to identify novel differentially regulated proteins, membrane-associated proteins and metabolic enzymes for each bacterium tested. Yet, feedback from experimental collaborators revealed a few limitations that prevented a more widespread use. We will thus extend and iteratively improve the functionality of our solution relying on functional genomics data from relevant systems, e.g. on plant growth promotion, targeted bacterial cell killing and synthetic bacterial communities.
Later, we will release software tools that enable any researcher to identify such missed proteins using proteogenomics, allowing them to obtain a more accurate genome annotation of their favorite model organism(s), from beneficals to pathogens, improving the basis for further discoveries.