We describe how searching chimeric spectra with post-processing including MS²PIP-derived features aids the identification of hypothetical and unannotated proteins. We apply our workflow to the well-characterized human bacterial pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and validate novel protein-coding regions with by ribo-seq translation evidence. We further elaborate how riboproteogenomics is instrumental for reannotating ORFs and the discovery of novel ORFs across bacteria.