Proteomic and phosphoproteomic comparison of human ES and iPS cells

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Abstract
A comparison of the proteomes and phosphoproteomes of four human embryonic stem cell lines and four induced pluripotent stem cell lines is reported, revealing subtle differences in these cell types at the protein level. Also introduced is the Stem Cell-Omics Repository (SCOR), a database of quantitative information for transcripts, proteins and post-translational modifications. Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very large set of identified proteins and phosphorylation sites in pluripotent cells. The statistical analysis afforded by our approach revealed subtle but reproducible differences in protein expression and protein phosphorylation between embryonic stem cells and induced pluripotent cells. Merging these results with RNA-seq analysis data, we found functionally related differences across each tier of regulation. We also introduce the Stem Cell–Omics Repository (SCOR), a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications.