Fig. 1.

High-resolution proteomics analysis of the S. elongatus proteome. A, S. elongatus cells were synchronized and cultured in light/dark (12:12 h) conditions. Samples were collected across a 48-h period at 20 independent time points with 1-h to 3-h intervals. Peptides were labeled with TMT 6-plex isobaric tags, with the sixth channel used to label a mixture of all the time points. Before LC-MS/MS analysis with an Orbitrap Velos, the four resulting sample mixtures were fractionated via SCX. B, logarithmic protein copy numbers of all 2179 proteins identified, as calculated using spectral counts (described in “Experimental Procedures”). Their abundances cover a dynamic range of 5 orders of magnitude. The most abundant proteins belong to the photosynthetic pathway (highlighted in green), and some proteins relevant to the circadian rhythm mechanism had medium to high abundances (central clock mechanism proteins—KaiA, KaiB, and KaiC—are highlighted in red, and the transcriptional regulator PadR family (Pex) is highlighted in purple).