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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Comet: An open-source MS/MS sequence database search tool
TL;DR: The Comet search engine is introduced, open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years.
Journal ArticleDOI
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
Ning Leng,John A. Dawson,James A. Thomson,Victor Ruotti,Anna I. Rissman,Bart M. G. Smits,Jill D. Haag,Michael N. Gould,Ron Stewart,Christina Kendziorski +9 more
TL;DR: EBSeq is developed, using the merits of empirical Bayesian methods, for identifying DE isoforms in an RNA-seq experiment comparing two or more biological conditions and proves to be a robust approach for identifying De genes.
Journal ArticleDOI
PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity
Lesley A. Kane,Michael Lazarou,Adam I. Fogel,Yan Li,Koji Yamano,Shireen A. Sarraf,Soojay Banerjee,Richard J. Youle +7 more
TL;DR: PINK1 phosphorylates ubiquitin, which then binds to Parkin and activates its E3 ligase activity, leading to induction of selective autophagy of damaged mitochondria.
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Next-generation proteomics: towards an integrative view of proteome dynamics
TL;DR: MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis, and to highlight recent applications.
References
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Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
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The Protein Kinase Complement of the Human Genome
TL;DR: The protein kinase complement of the human genome is catalogued using public and proprietary genomic, complementary DNA, and expressed sequence tag sequences to provide a starting point for comprehensive analysis of protein phosphorylation in normal and disease states and a detailed view of the current state of human genome analysis through a focus on one large gene family.
Journal ArticleDOI
Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents
Philip L. Ross,Yulin N. Huang,Jason Marchese,Brian L. Williamson,Kenneth C. Parker,Stephen J. Hattan,Nikita Khainovski,Sasi Pillai,Subhakar Dey,Scott Daniels,Subhasish Purkayastha,Peter Juhasz,Stephen A. Martin,Michael Bartlet-Jones,Feng He,Allan Jacobson,Darryl J. Pappin,Darryl J. Pappin +17 more
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Supporting Online Material for Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells
Junying Yu,Maxim A. Vodyanik,Kim Smuga-Otto,Jessica Antosiewicz-Bourget,Jennifer L. Frane,Shulan Tian,Jeff Nie,Gudrun A. Jonsdottir,Victor Ruotti,Ron M. Stewart,Igor I. Slukvin,James A. Thomson +11 more
TL;DR: Yu et al. as discussed by the authors proposed online material for induced pluripotent stem cell lines derived from human Somatic Cells, which can be used for transplanting human stem cells to humans.