Initial characterization of the human central proteome

We experimentally identify a central proteome comprising 1,124 proteins that are ubiquitously and abundantly expressed in human cells using state of the art mass spectrometry and protein identification bioinformatics. The main represented functions are proteostasis, primary metabolism and proliferation. We further characterize the central proteome considering gene structures, conservation, interaction networks, pathways, drug targets, and coordination of biological processes. Among other new findings, we show that the central proteome is encoded by exon-rich genes, indicating an increased regulatory flexibility through alternative splicing to adapt to multiple environments, and that the protein interaction network linking the central proteome is very efficient for synchronizing translation with other biological processes. Surprisingly, at least 10% of the central proteome has no or very limited functional annotation.Our data and analysis provide a new and deeper description of the human central proteome compared to previous results thereby extending and complementing our knowledge of commonly expressed human proteins. All the data are made publicly available to help other researchers who, for instance, need to compare or link focused datasets to a common background.The understanding of living cells at a systemic level is being recognized more and more as an important component of biology and medicine research [1-9]. Biological pathways and networks of protein interactions are key paradigms to link molecules to biological functions and by so doing bridging the genotype-to-phenotype gap as well as understanding properties of the organization of biological matter [10-13]. In this work we aim at answering three simple but fundamental questions: i) What is the complement of human proteins expressed ubiquitously and abundantly in different cell types? ii) Does this central proteome (C.Prot) [14] display properties that are distinct from the rest? iii) Can one identify glo