Updated project metadata. Chlamydomonas reinhardtii PSI-Cyt b6f complexes from sucrose density gradient fractions were identified by western blot and SMF spectroscopy, but showed high heterogeneity, as evident from the multiple bands present in the Coomassie stained SDS gel and original EM micrographs. Therefore potential PSI-Cyt b6f supercomplexes were enriched by a subsequent PsaA HisTag purification step. Only this additional enrichment enabled the identification of novel PSI supercomplexes, although the sample remained far from being homogeneous. This dataset describes the quantitative mass spectrometric analysis of the enriched PSI supercomplex fraction in comparison to unpurified samples using metabolic 15N labeling.