Global mapping of short-lived proteins in human cells

Rapid protein degradation enables cells to quickly modulate protein abundance in response to stimuli. Previous studies have generally sought to delineate basic features of proteome turnover. A focused map of short-lived proteins, however, remains a missing piece of the human proteome. To begin to address this, we combined cycloheximide chase assays with advanced high-throughput quantitative proteomics to map short-lived proteins in four genetically distinct human cell lines. Apparent half-lives of ≤ 8 hr were measured for 1,017 proteins. Systematic analyses revealed general properties of short-lived proteins (e.g., enriched in substrate recognition subunits of E3 ubiquitin ligase complexes, thermally instable, evolutionarily younger). We further quantified 103 proteins with widely different stabilities among cell lines. Of these, we show that truncated forms of ATRX and GMDS were expressed in U2OS and HCT116 cells, respectively, which had shorter half-lives than their full-length counterparts. This study provides a large-scale resource of human short-lived proteins in cultured cells, leading to untapped avenues of protein regulation for therapeutic intervention.