The subcellular proteome of mouse pluripotent embryonic stem cells

Our understanding of the biology of embryonic stem (ES) cells is deeply rooted in characterization of their transcriptomes, epigenetics and underlying gene regulatory networks. There is evidence that post-transcriptional processes such as signaling, adhesion, protein turnover and post translational modifications make a significant contribution to regulating the balance between self-renewal and differentiation, and it is therefore necessary to also characterize ES cells at the protein level. In this experiment, we used a workflow termed hyperLOPIT (hyperplexed localization of organelle proteins by isotope tagging) to characterize the subcellular distribution of proteins in a population of self-renewing E14TG2a mouse ES cells. Over 5,000 protein groups were quantified in both of the two replicates, enabling characterization of protein localization to organelles (including sub-nuclear resolution), cell surface, cytoskeleton and cytosol. The steady-state localization of transitory proteins, protein complex constituents, and signaling cascades could also be mapped.