Peptides are small molecules that play important roles in numerous biological processes. We used mass spectrometry to comprehensively analyze the endogenous peptide pools generated from functionally active proteins inside the cell from the model plant Physcomitrella patens. The secretomeand cellular peptidomes did not show a significant overlap, and the respective protein precursors had different protein degradation patterns. Furthermore, treatment with the plant stress hormones methyl jasmonate and salicylic acid induced significant differential changes in the two peptide pools.