Adipocytes are central players in energy metabolism and in the obesity epidemic, yet their protein composition remains largely unexplored. We report the most complete and informative adipocyte proteome by combining high accuracy, high sensitivity protein identification technology with subcellular fractionation of nuclei, mitochondria, membrane and cytosol of 3T3-L1 adipocyte. A total of 3,287 proteins were identified while essentially eliminating false positives, mng this one of the largest high-confidence proteomes reported to date.

Comprehensive bioinformatics analysis revealed that the adipocyte proteome, despite its specialized role, is very complex and provides a wealth of information in addition to a simple parts list. Comparison to microarray data shows that the mRNA abundance of detected vs. non-detected proteins is less than two-fold and that proteomics covered as large a proportion of the insulin signaling pathway. We use the Endeavour gene prioritization algorithms to associate a number of factors with vesicle transport in response to insulin stimulation - a key function of adipocytes. Our data and analysis can serve as a model for cellular proteomics and illustrates that proteomics is becoming as general and useful as microarray analysis for systems biology.
This database accompanies the article:
Adachi J., Kumar C., Zhang Y., Mann M., In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics, Mol Cell Proteomics. Apr 5 (2007)