Our study is focused on the characterization of the Arabidopsis flower peptidome, using the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous in comparison to the wild type. For peptide identification by LC-MS/MS, an extensive database of hypothetical novel Arabidopsis peptides was created. It comprised putative sORF-encoded peptides (SEPs) from intergenic regions, UTRs, ‘non-coding’ RNAs and other transcripts.