We are using progressive stable isotope labeling in plant systems to provide a bird's-eye view of the activity of the translation machinery and the proteolysis network as they maintain and sculpt the proteome1. Using peptide mass spectrometry, the progressive labeling of new peptides and the decrease in the abundance of peptides with natural isotope profiles enable the degradation and synthesis rate of specific root, leaf and seed proteins to be separated and quantified2. This allows new insights in selective proteolysis of proteins in vivo for different applications in fundamental and applied plant science. New evidence of changes in turnover rate of specific leaf and root proteins in autophagy mutants will be presented. This shows the selective effect of pathways in autophagy on the fate of organelle types and on biochemical functions in leaves and roots. New data on differential protein synthesis and degradation rates amongst cytosolic 80S ribosome subunits in the model plant Arabidopsis and between storage proteins and enzymes during grain filling in wheat will also be presented. These datasets are revealing the maintenance of protein complexes, the selectivity of autophagy, and allowing the cost of synthesis and degradation of particular cellular structures and processes in plants to be calculated.