MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. An established method to identify acquired MS/MS spectra is the comparison of each spectrum with peptides in a reference database. The PeptideDB tool helps to create peptide databases by in silico digestion given proteome information in the FASTA format and a set of parameters that allow the user to mimic conditions of their specific experiment. The created database stores peptide protein relationships in a SQLite database which can then be supplied to other ProteomIQon tools.