Screenshot of the Bacterial Proteogenomic Pipeline GUI. The GUI of the Bacterial Proteogenomic Pipeline leads the user through all steps required for a proteogenomic analysis. Shown is the final step, the analysis of the combined search results. After opening a file created in the "Combine Identifications" step, the identified peptide sequences are shown in a table with information about the sequence, the originating genomic sequence (usually the chromosome or a plasmid), corresponding protein accessions, whether or not the peptide occurs only in a pseudo protein, in an elongation of an annotated protein or is a standalone pseudo protein. Additionally the numbers of distinct identifications in all files and the (normalized) numbers of identifications per condition of the searched samples are given and represented in the bar charts in the lower half of the screen. For a selected peptide, the protein sequences containing the peptide are depicted, with the identified sequences highlighted in bold. The result table can be filtered and additional spectrum identification files can be added, for which the condition groups may be freely chosen.