Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry

Nature Protocols

Volumn 1, Issue 1, 2006, Pages 139-145

  Shiio, Yuzuru ^a   Aebersold, Ruedi ^b,c  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; DEUTERIUM; PROTEIN;

AFFINITY LABELING; ARTICLE; CHEMISTRY; FRACTIONATION; ISOTOPE LABELING; METHODOLOGY; PROTEOMICS; TANDEM MASS SPECTROMETRY;

AFFINITY LABELS; CARBON ISOTOPES; CHEMICAL FRACTIONATION; DEUTERIUM; ISOTOPE LABELING; PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 34250657012     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.22     Document Type: Article

References (30)

1. Tian, Q. et al. Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol. Cell. Proteomics 3, 960-969 (2004).
2. Baliga, N.S. et al. Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. USA 99, 14913-14918 (2002).
3. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
4. Gygi, S.P., Rochon, Y., Franza, B.R. & Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730 (1999).
5. Gygi, S.P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 994-999 (1999).
6. Han, D.K., Eng, J., Zhou, H. & Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951 (2001).
7. Zhang, H., Yan, W. & Aebersold, R. Chemical probes and tandem mass spectrometry: A strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 8, 66-75 (2004).
8. Pandey, A. & Mann, M. Proteomics to study genes and genomes. Nature 405, 837-846 (2000).
9. Shiio, Y. et al. Quantitative proteomic analysis of Myc oncoprotein function. EMBO J. 21, 5088-5096 (2002).
10. Shiio, Y. et al. Quantitative proteomic analysis of chromatin-associated factors. J. Am. Soc. Mass Spectrom. 14, 696-703 (2003).
11. Jin, J. et al. Quantitative proteomic analysis of mitochondrial proteins: Relevance to Lewy body formation and Parkinson's disease. Brain Res. Mol. Brain Res. 134, 119-138 (2005).
12. Shiio, Y. et al. Quantitative proteomic analysis of Myc-induced apoptosis: A direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4. J. Biol. Chem. 281, 2750-2756 (2006).
13. Von Haller, P.D. et al. The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry: II. Evaluation of Tandem Mass Spectrometry Methodologies for Large-Scale Protein Analysis, and the Application of Statistical Tools for Data Analysis and Interpretation. Mol. Cell. Proteomics 2, 428-442 (2003).
14. Ranish, J.A. et al. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349-355 (2003).
15. Ranish, J.A. et al. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat. Genet. 36 707-713 (2004).
16. Brand, M. et al. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat. Struct. Mol. Biol. 11, 73-80 (2004).
17. Himeda, C.L. et al. Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol. Cell. Biol. 24, 2132-2143 (2004).
18. Shiio, Y. et al. Identification and Characterization of SAP25, a Novel Component of the mSin3 Corepressor Complex. Mol. Cell. Biol. 26, 1386-1397 (2006).
19. Kubota, K., Wakabayashi, K. & Matsuoka, T. Proteome analysis of secreted proteins during osteoclast differentiation using two different methods: two-dimensional electrophoresis and isotope-coded affinity tags analysis with two-dimensional chromatography. Proteomics 3, 616-626 (2003).
20. Martin, D.B. et al. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res. 64, 347-355 (2004).
21. Tam, E.M., Morrison, C.J., Wu, Y.I., Stack, M.S. & Overall, C.M. Membrane protease proteomics: Isotope-coded affinity tag MS identification of undescribed MT1-matrix metalloproteinase substrates. Proc. Natl. Acad. Sci. USA 101, 6917-6922 (2004).
22. Zhang, J. et al. Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol. Aging 26, 207-227 (2005).
23. Zhang, J. et al. Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J. Alzheimers Dis. 7, 125-133 (2005).
24. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
25. Tao, W.A. & Aebersold, R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 14, 110-118 (2003).
26. 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).
27. Eng, J., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994).
28. Keller, A., Nesvizhskii, A.I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392 (2002).
29. Nesvizhskii, A.I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 (2003).
30. Li, X.J., Zhang, H., Ranish, J.A. & Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem. 75, 6648-6657 (2003).