Experimental elucidation of the structural genome annotation. (A) Determination of new open reading frames, ORFs, (orange arrows) by proteogenomics compared with current annotation (gray arrows). Peptide reads (brown bars) were mapped onto the genome sequence. Strand-specific transcription data (green), binding of RNA polymerase (RNAP) (red), and single-base pair resolution TSS data were used for confirmation. (B) New ORFs (orange arrow) determined by transcriptomic data (green), RNAP binding (red), sigma D binding (blue), and TSS reads. (C) Examples of sRNAs (orange arrows) determined by transcription profiling (green), RNAP (red) and sigma D binding profiles (blue), and TSS reads. Secondary structures confirmed sRNA models (TPP and T-Box) predicted by computational methods (brown).