The proBAM and proBed formats are relatively straightforward adaptations for proteomics of the tab-delimited BAM/SAM and BED formats widely used in genomics. Existing columns were defined to be applicable to peptide-based MS proteomics, and a few additional columns were added for peptide-specific contexts. Peptide data thus written in proBAM and proBed are compatible with transcript alignment viewers and other similar software already widely used in transcriptomics. No further changes are planned. Unfortunately, the formats have not been widely adopted so far. Most people use their own variation of the original BED format for representing peptide coordinates in a genome context, by using a small number of columns. Additionally, there is not a perceived need yet to use the more verbose proBAM format. In our view, by using these formats, proteogenomics studies would benefit from a greater standardization in data representation. The added advantage is that most genomics viewers developed would be able to visualize these files.