Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA)

Phytochemistry

Volumn 72, Issue 10, 2011, Pages 1028-1039

  Guo, Guangyu ^a   Li, Ning ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Arabidopsis; In vivo 15N metabolic labeling; Mass spectrometry; Quantitative and differential proteomics; SILIA; Stable isotope

Indexed keywords

NITROGEN; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; CHEMISTRY; ISOTOPE LABELING; MASS SPECTROMETRY; PROTEOMICS;

ARABIDOPSIS; ISOTOPE LABELING; MASS SPECTROMETRY; NITROGEN ISOTOPES; PLANT PROTEINS; PROTEOMICS;

ARABIDOPSIS;

EID: 79958150765     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2011.01.007     Document Type: Article

References (48)

1. M. Anderle, S. Roy, H. Lin, C. Becker, and K. Joho Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum Bioinformatics 20 2004 3575 3582 (Pubitemid 40136793)
2. K. Baggerly, J. Morris, J. Wang, D. Gold, L. Xiao, and K. Coombes A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples Proteomics 3 2003 1667 1672 (Pubitemid 37129810)
3. J. Benschop, S. Mohammed, M. O'Flaherty, A. Heck, M. Slijper, and F. Menke Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis Molecular and Cellular Proteomics 6 2007 1198 1214 (Pubitemid 47099230)
4. R. Beynon, and J. Pratt Metabolic labeling of proteins for proteomics Molecular and Cellular Proteomics 4 2005 857 872 (Pubitemid 41309145)
5. S. Cullen, and B. Schwartz An improved method for isolation of H-2 and Ia alloantigens with immunoprecipitation induced by protein A-bearing staphylococci The Journal of Immunology 117 1976 136
6. B. Domon, and R. Aebersold Challenges and opportunities in proteomics data analysis Molecular and Cellular Proteomics 5 2006 1921 1926 (Pubitemid 44688200)
7. T. Dunkley, R. Watson, J. Griffin, P. Dupree, and K. Lilley Localization of organelle proteins by isotope tagging (LOPIT) Molecular and Cellular Proteomics 3 2004 1128 1134 (Pubitemid 40012105)
8. N. Dyson Chromatographic Integration Methods 1998 Royal Society of Chemistry
9. 3 as a tool for quantitative analysis of proteins and metabolites Plant Methods 2 2006 14
10. P. Everley, J. Krijgsveld, B. Zetter, and S. Gygi Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research Molecular and Cellular Proteomics 3 2004 729 735 (Pubitemid 39077003)
11. S. Güsewell N: P ratios in terrestrial plants: variation and functional significance New Phytologist 164 2004 243 266 (Pubitemid 39393907)
12. M. Gehrmann, Y. Hathout, and C. Fenselau Evaluation of metabolic labeling for comparative proteomics in breast cancer cells Journal of Proteome Research 3 2004 1063 1068 (Pubitemid 39425664)
13. M. Goshe, J. Blonder, and R. Smith Affinity labeling of highly hydrophobic integral membrane proteins for proteome-wide analysis Journal of Proteome Research 2 2003 153 161 (Pubitemid 37099051)
14. J. Gouw, J. Krijgsveld, and A. Heck Quantitative proteomics by metabolic labeling of model organisms Molecular and Cellular Proteomics 9 2010 11 24
15. S. Gygi, B. Rist, S. Gerber, F. Turecek, M. Gelb, and R. Aebersold Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nature Biotechnology 17 1999 994 999 (Pubitemid 29474856)
16. R. Hebeler, S. Oeljeklaus, K. Reidegeld, M. Eisenacher, C. Stephan, B. Sitek, K. Stöhler, H. Meyer, M. Sturre, and P. Dijkwel Study of early leaf senescence in Arabidopsis thaliana by quantitative proteomics using reciprocal 14N/15N labeling and difference gel electrophoresis Molecular and Cellular Proteomics 7 2008 108 120 (Pubitemid 351248237)
17. E. Huttlin, A. Hegeman, A. Harms, and M. Sussman Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana Molecular and Cellular Proteomics 6 2007 860 881 (Pubitemid 46831937)
18. A. Jones, M. Bennett, J. Mansfield, and M. Grant Analysis of the defence phosphoproteome of Arabidopsis thaliana using differential mass tagging Proteomics 6 2006 4155 4165
19. J. Kast, M. Gentzel, M. Wilm, and K. Richardson Noise filtering techniques for electrospray quadrupole time of flight mass spectra Journal of the American Society for Mass Spectrometry 14 2003 766 776 (Pubitemid 36870960)
20. A. Kolkman, M. Olsthoorn, C. Heeremans, A. Heck, and M. Slijper Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol Molecular and Cellular Proteomics 4 2005 1 11 (Pubitemid 40309321)
21. J. Krijgsveld, R. Ketting, T. Mahmoudi, J. Johansen, M. Artal-Sanz, C. Verrijzer, R. Plasterk, and A. Heck Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics Nature Biotechnology 21 2003 927 931 (Pubitemid 36936200)
22. H. Li, W. Wong, L. Zhu, H. Guo, J. Ecker, and N. Li Phosphoproteomic analysis of ethylene-regulated protein phosphorylation in etiolated seedlings of Arabidopsis mutant ein2 using two-dimensional separations coupled with a hybrid quadrupole time-of-flight mass spectrometer Proteomics 9 2009 1646 1661
23. L. Li, J. Kresh, N. Karabacak, J. Cobb, J. Agar, and P. Hong A hierarchical algorithm for calculating the isotopic fine structures of molecules Journal of the American Society for Mass Spectrometry 19 2008 1867 1874
24. C. Lincoln, J.H. Britton, and M. Estelle Growth and development of the axr1 mutants of Arabidopsis Plant Cell 2 1990 1071 1080 (Pubitemid 120015459)
25. H. Liu, Y. Zhang, L. Meng, P. Qin, J. Wei, W. Jia, X. Li, Y. Cai, and X. Qian Non-gel-based dual 18O labeling quantitative proteomics strategy Analytical Chemistry 79 2007 7700 7707 (Pubitemid 47622398)
26. B. Lu, L. Pei, W. Chan, H. Zhang, G. Zhu, J. Li, and N. Li The dual effects of ethylene on the negative gravicurvature of arabidopsis inflorescence, an intriguing action model for the plant hormone ethylene Chinese Science Bulletin 46 2001 279 283
27. K. Mackey, T. Rivlin, A. Grossman, A. Post, and A. Paytan Picophytoplankton responses to changing nutrient and light regimes during a bloom Marine Biology 156 2009 1531 1546
28. D. McClatchy, M. Dong, C. Wu, J. Venable, and J. Yates III 15N metabolic labeling of mammalian tissue with slow protein turnover Journal of Proteome Research 6 2007 2005 2010 (Pubitemid 46814521)
29. C. Nelson, E. Huttlin, A. Hegeman, A. Harms, and M. Sussman Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana Proteomics 7 2007 1279 1292 (Pubitemid 46722452)
30. W. Old, K. Meyer-Arendt, L. Aveline-Wolf, K. Pierce, A. Mendoza, J. Sevinsky, K. Resing, and N. Ahn Comparison of label-free methods for quantifying human proteins by shotgun proteomics Molecular and Cellular Proteomics 4 2005 1487 1498
31. S. Ong, B. Blagoev, I. Kratchmarova, D. Kristensen, H. Steen, A. Pandey, and M. Mann Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Molecular and Cellular Proteomics 1 2002 376 386
32. S. Ong, I. Kratchmarova, and M. Mann Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC) Journal of Proteome Research 2 2003 173 181 (Pubitemid 37099053)
33. M. Ono, M. Shitashige, K. Honda, T. Isobe, H. Kuwabara, H. Matsuzuki, S. Hirohashi, and T. Yamada Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry Molecular and Cellular Proteomics 5 2006 1338 1347 (Pubitemid 44103403)
34. R. Rios-Estepa, and B. Lange Experimental and mathematical approaches to modeling plant metabolic networks Phytochemistry 68 2007 2351 2374 (Pubitemid 47214579)
35. P. Ross, Y. Huang, J. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, and S. Daniels Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Molecular and Cellular Proteomics 3 2004 1154 1169
36. A. Rudella, G. Friso, J. Alonso, J. Ecker, and K. Van Wijk Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis The Plant Cell Online 18 2006 1704 1721 (Pubitemid 44025554)
37. J. Schaff, F. Mbeunkui, K. Blackburn, D. Bird, and M. Goshe SILIP: a novel stable isotope labeling method for in planta quantitative proteomic analysis The Plant Journal 56 2008 840 854
38. B. Sefton Labeling cultured cells with 32Pi and preparing cell lysates for immunoprecipitation Current Protocols in Molecular Biology 2005 1 8
39. Senko, M., IsoPro 3.0. MS/MS Software, Sunnyvale, CA 94086.
40. J. Sevinsky, K. Brown, B. Cargile, J. Bundy, and J. Stephenson Jr. Minimizing back exchange in 18O/16O quantitative proteomics experiments by incorporation of immobilized trypsin into the initial digestion step Analytical Chemistry 79 2007 2158 2162 (Pubitemid 46355252)
41. A. Snijders, M. de Vos, and P. Wright Novel approach for peptide quantitation and sequencing based on 15N and 13C metabolic labeling Journal of Proteome Research 4 2005 578 585 (Pubitemid 40548166)
42. A. Staes, H. Demol, J. Van Damme, L. Martens, J. Vandekerckhove, and K. Gevaert Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18 Journal of Proteome Research 3 2004 786 791 (Pubitemid 39166239)
43. T. Tabata, T. Sato, J. Kuromitsu, and Y. Oda Pseudo internal standard approach for label-free quantitative proteomics Analytical Chemistry 79 2007 8440 8445 (Pubitemid 350171350)
44. M. Washburn, R. Ulaszek, C. Deciu, D. Schieltz, and J. Yates III Analysis of quantitative proteomic data generated via multidimensional protein identification technology Analytical Chemistry 74 2002 1650 1657 (Pubitemid 34297605)
45. J. Whitelegge, J. Katz, K. Pihakari, R. Hale, R. Aguilera, S. Gömez, K. Faull, D. Vavilin, and W. Vermaas Subtle modification of isotope ratio proteomics; an integrated strategy for expression proteomics Phytochemistry 65 2004 1507 1515 (Pubitemid 38969933)
46. X. Yao, C. Afonso, and C. Fenselau Dissection of proteolytic 18O labeling: endoprotease-catalyzed 16O-to-18O exchange of truncated peptide substrates Journal of Proteome Research 2 2003 147 152 (Pubitemid 37099050)
47. X. Yao, A. Freas, J. Ramirez, P. Demirev, and C. Fenselau Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus Analytical Chemistry 73 2001 2836 2842 (Pubitemid 32868136)
48. B. Zybailov, M. Coleman, L. Florens, and M. Washburn Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling Analytical Chemistrty 77 2005 6218 6224 (Pubitemid 41436955)