HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: M700460-MCP200v1 7/4/672    most recent Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Glossary Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Graumann, J. Articles by Mann, M. Search for Related Content PubMed PubMed Citation Articles by Graumann, J. Articles by Mann, M. Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 7:672-683, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Special Issue: 8th International Symposium On Mass Spectrometry In The Life Sciences

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins^*,S

Johannes Graumann^,,¶, Nina C. Hubner^,, Jeong Beom Kim^||,**, Kinarm Ko^||, Markus Moser, Chanchal Kumar, Jürgen Cox, Hans Schöler^|| and Matthias Mann^,

From the Departments of Proteomics and Signal Transduction and Molecular Medicine, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany and ^|| Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Roentgenstr. 20, 48149 Münster, Germany

Embryonic stem (ES) cells are pluripotent cells isolated from mammalian preimplantation embryos. They are capable of differentiating into all cell types and therefore hold great promise in regenerative medicine. Here we show that murine ES cells can be fully SILAC (stable isotope labeling by amino acids in cell culture)-labeled when grown feeder-free during the last phase of cell culture. We fractionated the SILAC-labeled ES cell proteome by one-dimensional gel electrophoresis and by isoelectric focusing of peptides. High resolution analysis on a linear ion trap-orbitrap instrument (LTQ-Orbitrap) at sub-ppm mass accuracy resulted in confident identification and quantitation of more than 5,000 distinct proteins. This is the largest quantified proteome reported to date and contains prominent stem cell markers such as OCT4, NANOG, SOX2, and UTF1 along with the embryonic form of RAS (ERAS). We also quantified the proportion of the ES cell proteome present in cytosolic, nucleoplasmic, and membrane/chromatin fractions. We compared two different preparation approaches, cell fractionation followed by one-dimensional gel separation and in-solution digestion of total cell lysate combined with isoelectric focusing, and found comparable proteome coverage with no apparent bias for any functional protein classes for either approach. Bioinformatics analysis of the ES cell proteome revealed a broad distribution of cellular functions with overrepresentation of proteins involved in proliferation. We compared the proteome with a recently published map of chromatin states of promoters in ES cells and found excellent correlation between protein expression and the presence of active and repressive chromatin marks.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				N. Ozlu, F. Monigatti, B. Y. Renard, C. M. Field, H. Steen, T. J. Mitchison, and J. J. Steen Binding Partner Switching on Microtubules and Aurora-B in the Mitosis to Cytokinesis Transition Mol. Cell. Proteomics, February 1, 2010; 9(2): 336 - 350. [Abstract] [Full Text] [PDF]

				J. V. Olsen, M. Vermeulen, A. Santamaria, C. Kumar, M. L. Miller, L. J. Jensen, F. Gnad, J. Cox, T. S. Jensen, E. A. Nigg, et al. Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis Sci. Signal., January 12, 2010; 3(104): ra3 - ra3. [Abstract] [Full Text] [PDF]

				C. Pan, J. V. Olsen, H. Daub, and M. Mann Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics Mol. Cell. Proteomics, December 1, 2009; 8(12): 2796 - 2808. [Abstract] [Full Text] [PDF]

				L. F. Waanders, K. Chwalek, M. Monetti, C. Kumar, E. Lammert, and M. Mann Quantitative proteomic analysis of single pancreatic islets PNAS, November 10, 2009; 106(45): 18902 - 18907. [Abstract] [Full Text] [PDF]

				D. Kobayashi, J. Kumagai, T. Morikawa, M. Wilson-Morifuji, A. Wilson, A. Irie, and N. Araki An Integrated Approach of Differential Mass Spectrometry and Gene Ontology Analysis Identified Novel Proteins Regulating Neuronal Differentiation and Survival Mol. Cell. Proteomics, October 1, 2009; 8(10): 2350 - 2367. [Abstract] [Full Text] [PDF]

				S. T. Bakker, H. J. van de Vrugt, M. A. Rooimans, A. B. Oostra, J. Steltenpool, E. Delzenne-Goette, A. van der Wal, M. van der Valk, H. Joenje, H. te Riele, et al. Fancm-deficient mice reveal unique features of Fanconi anemia complementation group M Hum. Mol. Genet., September 15, 2009; 18(18): 3484 - 3495. [Abstract] [Full Text] [PDF]

				M. Hilger, T. Bonaldi, F. Gnad, and M. Mann Systems-wide Analysis of a Phosphatase Knock-down by Quantitative Proteomics and Phosphoproteomics Mol. Cell. Proteomics, August 1, 2009; 8(8): 1908 - 1920. [Abstract] [Full Text] [PDF]

				F. Butter, M. Scheibe, M. Morl, and M. Mann Unbiased RNA-protein interaction screen by quantitative proteomics PNAS, June 30, 2009; 106(26): 10626 - 10631. [Abstract] [Full Text] [PDF]

				T. A. Prokhorova, K. T. G. Rigbolt, P. T. Johansen, J. Henningsen, I. Kratchmarova, M. Kassem, and B. Blagoev Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells Mol. Cell. Proteomics, May 1, 2009; 8(5): 959 - 970. [Abstract] [Full Text] [PDF]

				I. Jorge, P. Navarro, P. Martinez-Acedo, E. Nunez, H. Serrano, A. Alfranca, J. M. Redondo, and J. Vazquez Statistical Model to Analyze Quantitative Proteomics Data Obtained by 18O/16O Labeling and Linear Ion Trap Mass Spectrometry: Application to the Study of Vascular Endothelial Growth Factor-induced Angiogenesis in Endothelial Cells Mol. Cell. Proteomics, May 1, 2009; 8(5): 1130 - 1149. [Abstract] [Full Text] [PDF]

				Y. Wang, C. Mulligan, G. Denyer, F. Delom, F. Dagna-Bricarelli, V. L. J. Tybulewicz, E. M. C. Fisher, W. J. Griffiths, D. Nizetic, and J. Groet Quantitative Proteomics Characterization of a Mouse Embryonic Stem Cell Model of Down Syndrome Mol. Cell. Proteomics, April 1, 2009; 8(4): 585 - 595. [Abstract] [Full Text] [PDF]

				C. Pan, C. Kumar, S. Bohl, U. Klingmueller, and M. Mann Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions Mol. Cell. Proteomics, March 1, 2009; 8(3): 443 - 450. [Abstract] [Full Text] [PDF]

				M. Mann and N. L. Kelleher Mass Spectrometry Special Feature: Precision proteomics: The case for high resolution and high mass accuracy PNAS, November 25, 2008; 105(47): 18132 - 18138. [Abstract] [Full Text] [PDF]

				J. Schimmel, K. M. Larsen, I. Matic, M. van Hagen, J. Cox, M. Mann, J. S. Andersen, and A. C. O. Vertegaal The Ubiquitin-Proteasome System Is a Key Component of the SUMO-2/3 Cycle Mol. Cell. Proteomics, November 1, 2008; 7(11): 2107 - 2122. [Abstract] [Full Text] [PDF]

				T. F. Wu and D. S. Chu Sperm Chromatin: Fertile Grounds for Proteomic Discovery of Clinical Tools Mol. Cell. Proteomics, October 1, 2008; 7(10): 1876 - 1886. [Abstract] [Full Text] [PDF]

				U. Kruse, M. Bantscheff, G. Drewes, and C. Hopf Chemical and Pathway Proteomics: Powerful Tools for Oncology Drug Discovery and Personalized Health Care Mol. Cell. Proteomics, October 1, 2008; 7(10): 1887 - 1901. [Abstract] [Full Text] [PDF]