Prophane enables the automatic annotation of metaproteomes on both taxonomic and functional level. The highly flexible protein-centric workflow integrates results from different algorithms (e.g. Diamantblastp, hmmer) and databases (e.g. NCBI nr, eggNOG, FOAM, ResFams). Furthermore, protein frequencies are estimated on the basis of normalized spectral counts. Prophane provides tabular outputs and interactive plots of taxonomic/functional sample composition, thus facilitating the exploratory analysis of complex metaproteomic data.