title: Proteomic and phosphoproteomic comparison of human ES and iPS cells.
abstract: 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.
authors: Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
authors: Douglas H
authors: DH
authors: Phanstiel
authors: Justin
authors: J
authors: Brumbaugh
authors: Craig D
authors: CD
authors: Wenger
authors: Shulan
authors: S
authors: Tian
authors: Mitchell D
authors: MD
authors: Probasco
authors: Derek J
authors: DJ
authors: Bailey
authors: Danielle L
authors: DL
authors: Swaney
authors: Mark A
authors: MA
authors: Tervo
authors: Jennifer M
authors: JM
authors: Bolin
authors: Victor
authors: V
authors: Ruotti
authors: Ron
authors: R
authors: Stewart
authors: James A
authors: JA
authors: Thomson
authors: Joshua J
authors: JJ
authors: Coon
mesh_terms: D053595:Embryonic Stem Cells / Q000378:metabolism*; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics
chemical_list: D020543:Proteome