CONCLUSION
To date, detailed analyses of plant functions during a 24 h diurnal cycle have mostly focused on genome-wide changes in gene expression. Transcript-level changes can serve as a proxy for protein-level changes, but in plants transcript levels often do not correlate with protein abundance. While proteomes have a narrower dynamic range than transcriptomes, they nevertheless complement transcriptome studies because they provide direct insights into protein-level changes. Our quantitative analysis of the proteome over a 12 h light : 12 h dark 24 h photoperiod and the phosphoproteome at the L-D and D-L transitions during the diurnal cycle in a single experimental workflow has generated new information on diurnal abundance fluctuations and/or phosphorylation changes for Arabidopsis proteins involved in different cellular and biological processes (Figure 6). The identified proteins and phosphoproteins provide a useful basis for further experimental studies. In particular, it will be interesting to understand the specific functions of diurnally fluctuating ribosomal proteins and other proteins involved in translation considering that hundreds of ribosomal protein isoforms are encoded by plant genomes with little information of what dictates their combinatorial assembly. The regulation of protein translation in plants at the protein complex level remains poorly understood, but specific time-of-day abundance peaks for these proteins suggests that temporal differences in the ribosome complex exists that likely correlated with the specific time-of-day requirements of the plant cell. Further elucidation of ribosome and protein translation regulation will be instrumental in filling the current knowledge gap between the transcriptome and proteome. Lastly, our phosphoproteome analysis during the transitions from D-L and L-D provides new information about candidate protein kinase sub-families catalyzing the phosphorylation events, providing new opportunities for future systems-level and targeted studies.