This study was designed to yield data on the supramolecular organization of the phycobilisome apparatus from Synechocystis, and the possible effects of environmental stress on this arrangement. Phycobilisomes were dissociated in a low ionic strength solution and a quantitative estimation of the protein components present in each subcomplex was obtained using liquid chromatography coupled on-line with a mass spectrometer equipped with an electrospray ion source (ESI-MS). An advantage of this approach is that information can be collected on the initial events, which take place as this organism adapts to environmental changes. Ultracentrifugation of whole phycobilisomes revealed five subcomplexes; the lightest contained four linker proteins plus free phycocyanin, the second the core complex, while the last three bands contained the rod complexes. Four linkers were found in band 1 with higher molecular masses than those expected from the DNA sequence, indicating that they also contain linked chemical groups. UV-B irradiation specifically destroyed the beta-phycocyanin and one rod linker, which resulted in the disintegration of the rod complexes. The two bilins present in beta-phycocyanin give a greater contribution to the UV absorption than the single bilin of the other bilinproteins and probably react with atmospheric oxygen forming toxic radicals. The protein backbone is, in fact, protected from damage in anaerobic conditions and in the presence of radical scavengers. Cells grown in sulfur- and nitrogen-deficient medium contained significantly reduced levels of beta-phycocyanin and one rod linker.