Proteomic and phosphoproteomic comparison of human ES and iPS cells
Douglas H. Phanstiel,Justin Brumbaugh,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,James A. Thomson,James A. Thomson,Joshua J. Coon +15 more
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TLDR
Deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate is reported and the Stem Cell–Omics Repository is introduced, a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications.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.read more
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Coral: Clear and Customizable Visualization of Human Kinome Data
Kathleen S. Metz,Erika M. Deoudes,Matthew E. Berginski,Ivan Jimenez-Ruiz,Bulent Arman Aksoy,Jeff Hammerbacher,Shawn M. Gomez,Douglas H. Phanstiel +7 more
TL;DR: Coral is a user-friendly interactive web application for visualizing both quantitative and qualitative data that can encode data in three features, allows three modes of kinome visualization, and generates high-resolution scalable vector graphics files suitable for publication without the need for refinement using graphics editing software.
Journal ArticleDOI
Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers.
Anja M. Billing,Hisham Ben Hamidane,Shaima S. Dib,Richard Cotton,Aditya M. Bhagwat,Pankaj Kumar,Shahina Hayat,Noha A. Yousri,Neha Goswami,Karsten Suhre,Arash Rafii,Johannes Graumann +11 more
TL;DR: An in depth characterization of human ESC-MSC is performed, comparing them to human bone marrow-derived MSC (BM- MSC) as well as human embryonic stem cells (hESC) by transcriptomics (RNA-seq) and quantitative proteomics (nanoLC-MS/MS using SILAC) and an unprecedented coverage of MSC CD markers.
Journal ArticleDOI
Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells.
Yu Lu,Yu Lu,Yuin-Han Loh,Yuin-Han Loh,Yuin-Han Loh,Hu Li,Hu Li,Hu Li,Marcella Cesana,Marcella Cesana,Scott B. Ficarro,Jignesh R. Parikh,Jignesh R. Parikh,Nathan Salomonis,Cheng Xu Delon Toh,Stelios T. Andreadis,C. John Luckey,James J. Collins,James J. Collins,George Q. Daley,George Q. Daley,Jarrod A. Marto +21 more
TL;DR: A molecular signature suggesting a central role for AS in maintaining human pluripotent stem cell (hPSC) self-renewal and reprogramming is identified and data suggest that OCT4, SFRS2, and MBD2 participate in a positive feedback loop, regulating proteome diversity in support of hPSC self-reprogramming.
Journal ArticleDOI
Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development.
Liangliang Sun,Michelle M. Bertke,Matthew M. Champion,Guijie Zhu,Paul W. Huber,Norman J. Dovichi +5 more
TL;DR: It is observed decline in the expression of ten DNA replication factors after the midblastula transition (MBT), including a marked decline of the licensing factor XCdc6, which leads to apoptosis; temporal changes in this protein are critical for proper development.
Journal ArticleDOI
Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics
Dominic Helm,Johannes P. C. Vissers,Chris Hughes,Hannes Hahne,Benjamin Ruprecht,Fiona Pachl,Arkadiusz Grzyb,Keith Richardson,Jason Wildgoose,Stefan Maier,Harald Marx,Mathias Wilhelm,Isabelle Becher,Simone Lemeer,Marcus Bantscheff,James I. Langridge,Bernhard Kuster,Bernhard Kuster +17 more
TL;DR: A method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments is described.
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Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors
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