Proteomic and phosphoproteomic comparison of human ES and iPS cells

Douglas H. Phanstiel; Justin Brumbaugh; Craig D. Wenger; Shulan Tian; Mitchell D. Probasco; Derek J. Bailey; Danielle L. Swaney; Mark A. Tervo; Jennifer M. Bolin; Victor Ruotti; Ron Stewart; James A. Thomson; Joshua J. Coon

doi:10.1038/nmeth.1699

Proteomic and phosphoproteomic comparison of human ES and iPS cells

Douglas H. Phanstiel, Justin Brumbaugh, Craig D. Wenger, Shulan Tian, Mitchell D. Probasco, Derek J. Bailey, Danielle L. Swaney, Mark A. Tervo, Jennifer M. Bolin, Victor Ruotti, Ron Stewart, James A. Thomson, Joshua J. Coon

Quantitative Health Sciences

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Pages (from-to)	821-827
Number of pages	7
Journal	Nature Methods
Volume	8
Issue number	10
DOIs	https://doi.org/10.1038/nmeth.1699
State	Published - Oct 2011

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.1699

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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.",

author = "Phanstiel, {Douglas H.} and Justin Brumbaugh and Wenger, {Craig D.} and Shulan Tian and Probasco, {Mitchell D.} and Bailey, {Derek J.} and Swaney, {Danielle L.} and Tervo, {Mark A.} and Bolin, {Jennifer M.} and Victor Ruotti and Ron Stewart and Thomson, {James A.} and Coon, {Joshua J.}",

note = "Funding Information: We acknowledge A.J. Bureta for helping with and providing illustrations, A. Williams and K. Eastman for editing the text, G.McAlister for assistance with instrumentation, J. Yu for providing transcriptomic data before publication and Thomson lab members for critical reading and discussion of this manuscript. This work was supported by the University of Wisconsin, the Beckman Foundation and US National Institutes of Health (NIH) grants R01GM080148 (to J.J.C.) and P01GM081629 (to J.A.T. and J.J.C.). D.H.P. acknowledges support from a NIH predoctoral traineeship, the Genomic Sciences Training Program, NIH grant 5T32HG002760.",

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doi = "10.1038/nmeth.1699",

language = "English (US)",

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AU - Phanstiel, Douglas H.

AU - Brumbaugh, Justin

AU - Wenger, Craig D.

AU - Tian, Shulan

AU - Probasco, Mitchell D.

AU - Bailey, Derek J.

AU - Swaney, Danielle L.

AU - Tervo, Mark A.

AU - Bolin, Jennifer M.

AU - Ruotti, Victor

AU - Stewart, Ron

AU - Thomson, James A.

AU - Coon, Joshua J.

N1 - Funding Information: We acknowledge A.J. Bureta for helping with and providing illustrations, A. Williams and K. Eastman for editing the text, G.McAlister for assistance with instrumentation, J. Yu for providing transcriptomic data before publication and Thomson lab members for critical reading and discussion of this manuscript. This work was supported by the University of Wisconsin, the Beckman Foundation and US National Institutes of Health (NIH) grants R01GM080148 (to J.J.C.) and P01GM081629 (to J.A.T. and J.J.C.). D.H.P. acknowledges support from a NIH predoctoral traineeship, the Genomic Sciences Training Program, NIH grant 5T32HG002760.

PY - 2011/10

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N2 - 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.

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Proteomic and phosphoproteomic comparison of human ES and iPS cells

Abstract

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