Photosystem II of higher plants and cyanobacteria is composed of more than 20 polypeptide subunits. The pronounced hydrophobicity of these proteins hinders their purification and subsequent analysis by mass spectrometry. This paper reports the results obtained by application of matrix-assisted laser desorption/ionization mass spectrometry directly to isolated complexes and thylakoid membranes prepared from cyanobacteria and spinach. Changes in protein contents following physiopathological stimuli are also described. Good correlations between expected and measured molecular masses allowed the identification of the main, as well as most of the minor, low molecular weight components of photosystem II. These results open up new perspectives for clarifying the functional role of the various polypeptide components of photosystems and other supramolecular integral membrane complexes.Photosystem II is a pigment-protein complex of the thylakoid membrane of higher plants, eukaryotic algae, and cyanobacteria. It catalyzes light-induced electron transfer from water to plastoquinone, with associated production of molecular oxygen. PSII 1 consists of a large complex with a number of polypeptide components, most of which are integral membrane proteins. A number of extrinsic proteins are also associated with it at the membrane surface. The entire set of electron transfer cofactors, including chlorophyll a, pheophytin a, plastoquinones, and non-heme iron, is associated with the D1/D2 heterodimer. These two proteins, together with the ␣ and  subunits of cytochrome b 559 and the PsbI protein, constitute the so-called reaction center II (RCII), which is the smallest PSII subparticle still able to perform light-induced charge separation (1). Two large integral membrane proteins, CP43 and CP47, each coordinating a number (12-15) of chlorophyll a molecules, and several low molecular mass (Ͻ10 kDa) polypeptides are constituents of the PSII core complex, which is very similar in higher plants and prokaryotic cyanobacteria.During the last decade, considerable progress has been made in our understanding of the organization of polypeptides constituting the reaction center of PSII, but the topology and functional role of the small protein subunits are still largely unknown. Some of them are universal, whereas others are present only in cyanobacteria (PsbU and PsbV) or only in higher plants (e.g. PsbP, PsbQ, PsbS) (2).Investigation of the structural and functional roles of the various PSII subunits requires, as a preliminary step, a suitable method to detect them in the thylakoid membrane or purified subparticle preparations. The detection and study of stimuli-induced modifications of several PSII components have mainly been based on the use of polyclonal antibodies. However, these are often not available and, when available, are time-consuming to use.A different technique, capable of accurately detecting even small amounts of the various PSII subunits in an integrated system, could be of great help in studying the function of these protein...