Upon starvation cells undergo autophagy, a cellular degradation pathway important in the turn-over of whole organelles and long-lived proteins. Starvation-induced protein degradation has been regarded as an unspecific bulk degradation process. We studied global protein dynamics during amino acid starvation-induced autophagy by quantitative mass spectrometry and were able to record near 1500 protein profiles during 36 hours of starvation. Cluster analysis of the recorded protein profiles revealed that cytosolic proteins were degraded rapidly, whereas proteins annotated to various complexes and organelles were degraded later at different time periods. Inhibition of protein degradation pathways identified the lysosomal/autophagosomal system as the main degradative route. Thus, starvation induces degradation via autophagy which appears to be selective and to degrade proteins in an ordered fashion and not completely arbitrary, as anticipated so far.