Proteomic and phosphoproteomic comparison of human ES and iPS cells

Nature Methods

Volumn 8, Issue 10, 2011, Pages 821-827

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

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^c MORGRIDGE INSTITUTE FOR RESEARCH   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; EMBRYONIC STEM CELL; HUMAN; HUMAN CELL; MASS SPECTROMETRY; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; RNA SEQUENCE; STATISTICAL ANALYSIS;

EMBRYONIC STEM CELLS; HUMANS; INDUCED PLURIPOTENT STEM CELLS; PROTEOME; PROTEOMICS;

IPS;

EID: 80053374337     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1699     Document Type: Article

References (47)

1. Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).
2. Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872 (2007). (Pubitemid 350138099)
3. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917-1920 (2007).
4. Chin, M.H. et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 5, 111-123 (2009).
5. Guenther, M.G. et al. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 7, 249-257 (2010).
6. Chin, M.H., Pellegrini, M., Plath, K. & Lowry, W.E. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell 7, 263-269 (2010).
7. Bock, C. et al. Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144, 439-452 (2011).
8. Stadtfeld, M. et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 465, 175-181 (2010).
9. Doi, A. et al. Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet. 41, 1350-1353 (2009).
10. Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73 (2011).
11. Olsen, J.V. et al. Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4, 709-712 (2007). (Pubitemid 47338163)
12. McAlister, G.C., Phanstiel, D., Wenger, C.D., Lee, M.V. & Coon, J.J. Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal. Chem. 82, 316-322 (2010).
13. Olsen, J.V. et al. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol. Cell. Proteomics 8, 2759-2769 (2009).
14. Nagaraj, N., D'Souza, R.C.J., Cox, J., Olsen, J.V. & Mann, M. Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J. Proteome Res. 9, 6786-6794 (2010).
15. Thompson, A. et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 75, 1895-1904 (2003). (Pubitemid 36438013)
16. Ross, P.L. et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169 (2004).
17. Choe, L. et al. 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics 7, 3651-3660 (2007). (Pubitemid 350022271)
18. Ow, S.Y. et al. iTRAQ underestimation in simple and complex mixtures: the good, the bad and the ugly. J. Proteome Res. 8, 5347-5355 (2009).
19. Wenger, C.D., Phanstiel, D.H., Lee, M.V., Bailey, D.J. & Coon, J.J. COMPASS: a suite of pre-and post-search proteomics software tools for OMSSA. Proteomics 6, 1064-1074 (2011).
20. Shadforth, I.P., Dunkley, T.P.J., Lilley, K.S. & Bessant, C. i-Tracker: for quantitative proteomics using iTRAQ (TM). BMC Genomics 6, 145 (2005).
21. Griffin, T.J. et al. iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J. Proteome Res. 6, 4200-4209 (2007). (Pubitemid 350158498)
22. Becker, K.A., Stein, J.L., Lian, J.B., van Wijnen, A.J. & Stein, G.S. Establishment of histone gene regulation and cell cycle checkpoint control in human embryonic stem cells. J. Cell. Physiol. 210, 517-526 (2007). (Pubitemid 44956897)
23. Xue, Y. et al. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol. Cell. Proteomics 7, 1598-1608 (2008).
24. Manning, G., Whyte, D.B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912-1934 (2002). (Pubitemid 35425239)
25. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57, 289-300 (1995).
26. Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25-29 (2000). (Pubitemid 30257031)
27. Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). (Pubitemid 30047706)
28. Frye, M. & Watt, F.M. The RNA methyltransferase Misu (NSun2) mediates Myc-induced proliferation and is upregulated in tumors. Curr. Biol. 16, 971-981 (2006). (Pubitemid 43728217)
29. Singh, M.K. et al. The T-box transcription factor Tbx15 is required for skeletal development. Mech. Dev. 122, 131-144 (2005). (Pubitemid 40126674)
30. Dong, F. et al. Pitx2 promotes development of splanchnic mesoderm-derived branchiomeric muscle. Development 133, 4891-4899 (2006). (Pubitemid 46085055)
31. Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285-290 (2010).
32. Polo, J.M. et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat. Biotechnol. 28, 848-855 (2010).
33. Hu, B.Y. et al. Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc. Natl. Acad. Sci. USA 107, 4335-4340 (2010).
34. Siu, I.M. et al. Coexpression of neuronatin splice forms promotes medulloblastoma growth. Neuro-oncol. 10, 716-724 (2008).
35. Hargrave, M. et al. Expression of the Sox11 gene in mouse embryos suggests roles in neuronal maturation and epithelio-mesenchymal induction. Dev. Dyn. 210, 79-86 (1997). (Pubitemid 27424253)
36. Kawano, Y. et al. CRMP-2 is involved in kinesin-1-dependent transport of the Sra-1/WAVE1 complex and axon formation. Mol. Cell. Biol. 25, 9920-9935 (2005). (Pubitemid 41572740)
37. Zhu, H., Coppinger, J.A., Jang, C.Y., Yates, J.R. III & Fang, G. FAM29A promotes microtubule amplification via recruitment of the NEDD1-gamma-tubulin complex to the mitotic spindle. J. Cell Biol. 183, 835-848 (2008).
38. Bourke, E., Brown, J.A.L., Takeda, S., Hochegger, H. & Morrison, C.G. DNA damage induces Chk1-dependent threonine-160 phosphorylation and activation of Cdk2. Oncogene 29, 616-624 (2010).
39. Ludwig, T.E. et al. Derivation of human embryonic stem cells in defined conditions. Nat. Biotechnol. 24, 185-187 (2006). (Pubitemid 43221701)
40. Sengupta, S. et al. Highly consistent, fully representative mRNA-Seq libraries from ten nanograms of total RNA. Biotechniques 49, 898-904 (2010).
41. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10 R25 (2009).
42. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008). (Pubitemid 351911867)
43. Good, D.M. et al. Post-acquisition ETD spectral processing for increased peptide identifications. J. Am. Soc. Mass Spectrom. 20, 1435-1440 (2009).
44. Geer, L.Y. et al. Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964 (2004). (Pubitemid 39425651)
45. Kersey, P.J. et al. The International Protein Index: An integrated database for proteomics experiments. Proteomics 4, 1985-1988 (2004). (Pubitemid 38880363)
46. Nesvizhskii, A.I. & Aebersold, R. Interpretation of shotgun proteomic data-The protein inference problem. Mol. Cell. Proteomics 4, 1419-1440 (2005). (Pubitemid 41555469)
47. Swaney, D.L., Wenger, C.D., Thomson, J.A. & Coon, J.J. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 106, 995-1000 (2009).