With the recent development of techniques for analyzing transmembrane thylakoid proteins by two-dimensional gel electrophoresis, systematic approaches for proteomic analyses of membrane proteins became feasible. In this study, we established detailed two-dimensional protein maps of Chlamydomonas reinhardtii light-harvesting proteins (Lhca and Lhcb) by extensive tandem mass spectrometric analysis. We predicted eight distinct Lhcb proteins. Although the major Lhcb proteins were highly similar, we identified peptides which were unique for specific lhcbm gene products. Interestingly, lhcbm6 gene products were resolved as multiple spots with different masses and isoelectric points. Gene tagging experiments confirmed the presence of differentially N-terminally processed Lhcbm6 proteins. The mass spectrometric data also revealed differentially N-terminally processed forms of Lhcbm3 and phosphorylation of a threonine residue in the N terminus. The N-terminal processing of Lhcbm3 leads to the removal of the phosphorylation site, indicating a potential novel regulatory mechanism. At least nine different lhca-related gene products were predicted by comparison of the mass spectrometric data against Chlamydomonas expressed sequence tag and genomic databases, demonstrating the extensive variability of the C. reinhardtii Lhca antenna system. Out of these nine, three were identified for the first time at the protein level. This proteomic study demonstrates the complexity of the light-harvesting proteins at the protein level in C. reinhardtii and will be an important basis of future functional studies addressing this diversity.In all eukaryotic oxygenic photosynthetic organisms, lightharvesting chlorophyll a-or b-binding proteins (LHC proteins) function in the collection and transfer of light energy to the reaction centers of photosystem II (PSII) (Lhcb proteins) and photosystem I (PSI) (Lhca proteins). Additionally these proteins are also involved in light dissipation and energy quenching. Therefore, light-harvesting proteins are important components of the photosynthetic machinery that optimize photosynthetic function and minimize photooxidative damage in response to light quantity and quality. It has been known for several years that light-harvesting proteins are products of many genes. This concept is illustrated by a recent analysis of the Arabidopsis genome which revealed that the lhc gene family is composed of more than 20 genes (24). Besides the large number of lhc gene products, posttranslational modifications, such as phophorylation, contribute to even more complexity at the protein level (31, 45). Phosphorylation of the major Lhcb proteins of PSII is important in the process of state transitions. This process leads to a redistribution of excitation energy between PSII and PSI by reorganization of the antennae and thereby regulates energy flow between the photosystems. The importance of phosphorylation for state transitions is shown by the phenotype of the Chlamydomonas reinhardtii Stt7 mutant. This mutant is markedly ...