Mass spectrometric-based quantitative proteomics using SILAC

Methods in Enzymology

Volumn 500, Issue , 2011, Pages 133-150

  Lanucara, Francesco ^a   Eyers, Claire E ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Amino acids; Mass Spectrometry; Peptides; Proteome; quantification; SILAC; stable isotope labelling

Indexed keywords

AMINO ACID; CELL EXTRACT; CELL PROTEIN; STABLE ISOTOPE;

ARTICLE; CELL CULTURE; CELL POPULATION; HUMAN; ISOTOPE LABELING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN METABOLISM; PROTEIN PROCESSING; PROTEOMICS;

EID: 80053081195     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385118-5.00008-6     Document Type: Chapter

References (32)

1. C.C. Bicho A genetic engineering solution to the "arginine conversion problem" in stable isotope labeling by amino acids in cell culture (SILAC) Mol. Cell. Proteomics 9 7 2010 1567 1577
2. D. Bonenfant Analysis of dynamic changes in post-translational modifications of human histones during cell cycle by mass spectrometry Mol. Cell. Proteomics 6 11 2007 1917 1932 (Pubitemid 350201868)
3. T.P. Conrads Utility of accurate mass tags for proteome-wide protein identification Anal. Chem. 72 14 2000 3349 3354 (Pubitemid 30482514)
4. J. Cox, and M. Mann MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 26 12 2008 1367 1372
5. J. Cox A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics Nat. Protoc. 4 5 2009 698 705
6. A. Cuomo SILAC-based proteomic analysis to dissect the "histone modification signature" of human breast cancer cells Amino Acids 41 5 2011 387 399
7. M.K. Doherty Turnover of the human proteome: Determination of protein intracellular stability by dynamic SILAC J. Proteome Res. 8 1 2009 104 112
8. H.Y. Gao Two-dimensional electrophoretic/chromatographic separations combined with electrospray ionization FTICR mass spectrometry for high throughput proteome analysis J. Microcolumn Sep. 12 7 2000 383 390
9. T. Geiger Super-SILAC mix for quantitative proteomics of human tumor tissue Nat. Methods 7 5 2010 383 385
10. A. Gruhler Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway Mol. Cell. Proteomics 4 3 2005 310 327 (Pubitemid 40439774)
11. A. Gruhler Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry Mol. Cell. Proteomics 4 11 2005 1697 1709 (Pubitemid 41749263)
12. A. Iliuk Playing tag with quantitative proteomics Anal. Bioanal. Chem. 393 2 2009 503 513 (Pubitemid 50296309)
13. H. Jiang, and A.M. English Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine J. Proteome Res. 1 4 2002 345 350 (Pubitemid 36395875)
14. M.J. Kerner Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli Cell 122 2 2005 209 220 (Pubitemid 41032985)
15. R. Lund Efficient isolation and quantitative proteomic analysis of cancer cell plasma membrane proteins for identification of metastasis-associated cell surface markers J. Proteome Res. 8 6 2009 3078 3090
16. P. Mortensen MSQuant, an open source platform for mass spectrometry-based quantitative proteomics J. Proteome Res. 9 1 2010 393 403
17. L. Nilse SILACAnalyzer - A tool for differential quantitaion of stable isotope derived data Lect. Notes Comput. Sci. 6160 1 2010 45 55
18. Y. Oda Accurate quantitation of protein expression and site-specific phosphorylation Proc. Natl. Acad. Sci. USA 96 12 1999 6591 6596 (Pubitemid 29274927)
19. S.E. Ong, and M. Mann Mass spectrometry-based proteomics turns quantitative Nat. Chem. Biol. 1 5 2005 252 262
20. S.E. Ong, and M. Mann A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC) Nat. Protoc. 1 6 2006 2650 2660
21. S.E. Ong Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 1 5 2002 376 386
22. S.E. Ong Properties of C-13-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC) J. Proteome Res. 2 2 2003 173 181
23. S.E. Ong Identifying and quantifying in vivo methylation sites by heavy methyl SILAC Nat. Methods 1 2 2004 119 126
24. J.M. Pratt Dynamics of protein turnover, a missing dimension in proteomics Mol. Cell. Proteomics 1 8 2002 579 591
25. J.M. Pratt Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting Proteomics 2 2 2002 157 163 (Pubitemid 34273085)
26. F. Ren Comparative serum proteomic analysis of patients with acute-on-chronic liver failure: Alpha-1-acid glycoprotein maybe a candidate marker for prognosis of hepatitis B virus infection J. Viral Hepat. 17 11 2010 816 824
27. W.X. Schulze, and B. Usadel Quantitation in mass-spectrometry-based proteomics Annu. Rev. Plant Biol. 61 2010 491 516
28. H. Steen, and M. Mann The ABC's (and XYZ's) of peptide sequencing Nat. Rev. Mol. Cell Biol. 5 9 2004 699 711 (Pubitemid 39208180)
29. Y.H. Xu Application of the SILAC (stable isotope labelling with amino acids in cell culture) technique in quantitative comparisons for tissue proteome expression Biotechnol. Appl. Biochem. 54 2009 11 20
30. A. Zamo, and D. Cecconi Proteomic analysis of lymphoid and haematopoietic neoplasms: There's More than biomarker discovery J. Proteomics 73 3 2010 508 520
31. R.J. Zhang Controlling deuterium isotope effects in comparative proteomics Anal. Chem. 74 15 2002 3662 3669
32. H.N. Zhu Amino acid residue specific stable isotope labeling for quantitative proteomics Rapid Commun. Mass Spectrom. 16 22 2002 2115 2123