Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

Nature Protocols

Volumn 6, Issue 2, 2011, Pages 147-157

  Geiger, Tamar ^a   Wisniewski, Jacek R ^a   Cox, Juergen ^a   Zanivan, Sara ^a   Kruger, Marcus ^b   Ishihama, Yasushi ^c   Mann, Matthias ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b MAX PLANCK INSTITUTE FOR HEART AND LUNG RESEARCH   (Germany)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

AMINO ACID SUBSTITUTION; AMINO ACID SYNTHESIS; ARTICLE; CELL LABELING; CELL LINE; CYTOLYSIS; GENETIC ENGINEERING; ISOTOPE LABELING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEOMICS; QUANTITATIVE ANALYSIS; STABLE ISOTOPE LABELING BY AMINO ACID IN CELL CULTURE;

AMINO ACIDS; CELL CULTURE TECHNIQUES; ISOTOPE LABELING; MASS SPECTROMETRY; PROTEINS; PROTEOMICS;

EID: 79551663189     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2010.192     Document Type: Article

References (44)

1. Wolters, D.A., Washburn, M.P. & Yates, J.R. III. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690 (2001).
2. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
3. Steen, H. & Mann, M. The ABCs (and XYZs) of peptide sequencing. Nat. Rev. Mol. Cell. Biol. 5, 699-711 (2004).
4. Ong, S.E. & Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262 (2005).
5. Bachi, A. & Bonaldi, T. Quantitative proteomics as a new piece of the systems biology puzzle. J. Proteomics 71, 357-367 (2008).
6. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J. & Kuster, B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389, 1017-1031 (2007).
7. Gruhler, A. et al. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 4, 310-327 (2005).
8. Kohlbacher, O. et al. TOPP-the OpenMS proteomics pipeline. Bioinformatics 23, e191-e197 (2007).
9. Mueller, L.N. et al. SuperHirn-a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470-3480 (2007).
10. Luber, C.A. et al. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 32, 279-289 (2010).
11. Leitner, A. & Lindner, W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics 6, 5418-5434 (2006).
12. Beynon, R.J. & Pratt, J.M. Metabolic labeling of proteins for proteomics. Mol. Cell. Proteomics 4, 857-872 (2005).
13. Gouw, J.W., Krijgsveld, J. & Heck, A.J. Quantitative proteomics by metabolic labeling of model organisms. Mol. Cell. Proteomics 9, 11-24 (2010).
14. Oda, Y., Huang, K., Cross, F.R., Cowburn, D. & Chait, B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 96, 6591-6596 (1999).
15. Ong, S.E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386 (2002).
16. Mann, M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell. Biol. 7, 952-958 (2006).
17. Hanke, S., Besir, H., Oesterhelt, D. & Mann, M. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J. Proteome Res. 7, 1118-1130 (2008).
18. Soufi, B. et al. Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis. J. Proteome Res. 9, 3638-3646 (2010).
19. de Godoy, L.M. et al. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 7, R50 (2006).
20. Sury, M.D., Chen, J.X. & Selbach, M. The SILAC fly allows for accurate protein quantification in vivo. Mol. Cell. Proteomics 9, 2173-2183 (2010).
21. Kruger, M. et al. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134, 353-364 (2008).
22. Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J.R. & Mann, M. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat. Methods 7, 383-385 (2010).
23. Ishihama, Y. et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 23, 617-621 (2005).
24. Ong, S.E. & Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 1, 2650-2660 (2006).
25. Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W. & Gygi, S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100, 6940-6945 (2003).
26. Beynon, R.J., Doherty, M.K., Pratt, J.M. & Gaskell, S.J. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2, 587-589 (2005).
27. Pratt, J.M. et al. Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 1, 1029-1043 (2006).
28. Singh, S., Springer, M., Steen, J., Kirschner, M.W. & Steen, H. FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J. Proteome Res. 8, 2201-2210 (2009).
29. Brun, V. et al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell. Proteomics 6, 2139-2149 (2007).
30. de Godoy, L.M. et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008).
31. Bicho, C.C., de Lima Alves, F., Chen, Z.A., Rappsilber, J. & Sawin, K.E. A genetic engineering solution to the Arginine Conversion Problem in stable isotope labeling by amino acids in cell culture (SILAC). Mol. Cell. Proteomics 9, 1567-1577 (2010).
32. Walther, D.M. & Mann, M. Accurate quantification of more than 4,000 mouse tissue proteins reveals minimal proteome changes during aging. Mol. Cell. Proteomics 9 published online, doi: 10.1074/mcp.M110.004523 (3 November 2010).
33. Scigelova, M. & Makarov, A. Orbitrap mass analyzer-overview and applications in proteomics. Proteomics 6 (Suppl 2): 16-21 (2006).
34. Makarov, A. et al. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78, 2113-2120 (2006).
35. 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).
36. Shevchenko, A., Tomas, H., Havlis, J., Olsen, J.V. & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856-2860 (2006).
37. Masuda, T., Saito, N., Tomita, M. & Ishihama, Y. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol. Cell. Proteomics 8, 2770-2777 (2009).
38. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372 (2008).
39. Cox, J. et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protoc. 4, 698-705 (2009).
40. Cox, J. & Mann, M. Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap. J. Am. Soc. Mass. Spectrom. 20, 1477-1485 (2009).
41. Wisniewski, J.R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362 (2009).
42. Wisniewski, J.R., Zougman, A. & Mann, M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 8, 5674-5678 (2009).
43. Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896-1906 (2007).
44. Bendall, S.C. et al. Prevention of amino acid conversion in SILAC experiments with embryonic stem cells. Mol. Cell. Proteomics 7, 1587-1597 (2008).