The Fenna-Matthews-Olson: FMO) bacteriochlorophyll a protein has served as a model antenna system for understanding pigment-protein interaction and the energy transfer mechanism. The FMO protein has been extensively studied by a wide range of spectroscopic and theoretical techniques due to its stability, spectral resolution of pigments, water-soluble nature and availability of high-resolution structural information. A new 1.3 Å FMO structure: PDB: 3EOJ) revealed an 8th pigment at the monomer connection region with partial occupancy. To understand the nature and stoichiometry of this new pigment, the molecular weight of the whole FMO complex was measured by the recently developed mass spectrometry: MS) technique called native spray MS. The first non-natural FMO complex was generated by replacing the phytol tail of BChl a with geranylgeraniol. The recently discovered sixth phylum of photosynthetic species - the Candidatus Chloracidobacterium thermophilum: Cab), also contains the FMO protein, which is significantly divergent from the FMO found in green sulfur bacteria: GSB). This FMO has two distinct structural regions different from the FMOs from GSB and also shows distinct spectral properties. The collection of these different FMO complexes has greatly facilitated our understanding of this protein. The FMO connects the chlorosome to the reaction center in the cytoplasmic membrane and functionally forms a bridge to transfer the excitation energy. The orientation of the FMO protein on the membrane in vivo was revealed by chemical labeling and MS5. The orientational information places the newly discovered 8th pigment near the chlorosome, and it is proposed to serve as an energy transfer intermediate between the chlorosome and the rest of the FMO protein. The detailed interaction between the FMO protein and the baseplate: CsmA) protein was studied by hydrogen/deuterium exchange coupled with MS. The identified binding region first confirms the FMO orientation on the membrane; secondly this region is located at one of the two structurally different regions on the Cab-FMO protein, and the highly conserved region in the baseplate of GSB is not conserved in that of Cab
