Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression Saccharomyces cerevisiae strains: The comparison of two quantitative methods

Journal of Proteome Research

Volumn 7, Issue 1, 2008, Pages 266-275

  Usaite, Renata ^a,b   Wohlschlegel, James ^b   Venable, John D ^b   Park, Sung K ^b   Nielsen, Jens ^a   Olsson, Lisbeth ^a   Yates III, John R ^b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

15N; AMP activated kinase; CenSus; Mass spectrometry; MudPIT; Proteomics; Snf4

Indexed keywords

CELL ENZYME; GLUCOSE; PROTEOME; TRANSCRIPTION FACTOR SNF; TRANSCRIPTION FACTOR SNF1; UNCLASSIFIED DRUG;

ARTICLE; BIOTECHNOLOGY; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; FUNGAL STRAIN; FUNGUS CULTURE; FUNGUS GROWTH; INTERMETHOD COMPARISON; ISOTOPE LABELING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEOMICS; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SAMPLING; SPECTRUM; STATISTICAL SIGNIFICANCE; WILD TYPE; YEAST;

COMPLEX MIXTURES; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; METHODS; MUTATION; PROTEIN-SERINE-THREONINE KINASES; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE PROTEINS; YEASTS;

SACCHAROMYCES CEREVISIAE;

EID: 38649098761     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr700580m     Document Type: Article

References (34)

1. Humphery-Smith, I. A human proteome project with a beginning and an end. Proteomics 2004, 4, 2519-2521.
2. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422 (13), 198-207.
3. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19 (3), 242-7.
4. Delahunty, C.; Yates, J. R., III. Protein identifcation using 2D-LC-MS/MS. Methods 2005, 35, 248-255.
5. Washburn, M. P.; Ulaszek, R.; Deciu, C.; Schieltz, D. M.; Yates, J. R., III. Analysis of Quantitative Proteomic Data Generated via Multidimensional Protein Identification Technology. Anal. Chem. 2002, 74, 1650-1657.
6. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17 (10), 994-999.
7. Patterson, S. D.; Aebersold, R. H. Proteomics: the first decade and beyond. Nat. Genet. 2003, 33 (Suppl), 311-323.
8. Pang, J. X.; Ginanni, N.; Dongre, A. R.; Hefta, S. A.; Opitek, G. J. Biomarker discovery in urine by proteomics. J. Proteome Res. 2002, 1 (2), 161-169.
9. Venable, J. D.; Wohlschlegel, J.; McClatchy, D. B.; Park, S. K.; Yates, J. R., III. Relative quantification of stable isotope labeled peptides using a linear ion trap-orbitrap hybrid mass spectrometer. Anal. Chem. 2007, 79 (8), 3056-3064.
10. Saito, A.; Nagasaki, M.; Oyama, M.; Kozuka-Hata, H.; Semba, K.; Sugano, S.; Yamamoto, T.; Miyano, S. AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics 2007, 8, 15.
11. Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4 (10), 1487-1502.
12. Kolkman, A.; Dirksen, E. H.; Slijper, M.; Heck, A. J. Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling. Mol. Cell. Proteomics 2005, 4 (3), 255-266.
13. Zybailov, B.; Coleman, M. K.; Florens, L.; Washburn, M. P. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal. Chem. 2005, 77 (19), 6218-6224.
14. Carlson, M. Glucose repression in yeast. Curr. Opin. Microbiol. 1999, 2 (2), 202-207.
15. Shirra, M. K.; Patton-Vogt, J.; Ulrich, A.; Liuta-Tehlivets, O.; Kohlwein, S. D.; Henry, S. A.; Arndt, K. M. Inhibition of acetyl coenzyme A carboxylase activity restores expression of the INO1gene in a snf1mutant strain of Saccharomyces cerevisiae. Mol. Cell. Biol. 2001, 21 (17), 5710-5722.
16. Lo, W. S.; Duggan, L.; Emre, N. C.; Belotserkovskya, R.; Lane, W. S.; Shiekhattar, R.; Berger, S. L. Snf1 - a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription. Science 2001, 293 (553), 1142-1146.
17. Carling, D. AMP-activated protein kinase: balancing the scales. Biochimie 2005, 87 (1), 87-91.
18. Usaite, R.; Patil, K. R.; Grotkjær, T.; Nielsen, J.; Regenberg, B. Global Transcriptional and Physiological Responses of Saccharomyces cerevisiae to Ammonium, L-Alanine, or L-Glutamine Limitation. Appl. Microbiol. Biotechnol. 2006, 72 (9), 6194-6203.
19. Usaite, R.; Nielsen, J.; Olsson, L. Physiological characterization of glucose repression in the strains with SNF1and SNF4genes deleted. J. Biotechnol. 2008, 133, 73-81.
20. Yates, J. R., III; Cociorva, D.; Liao, L.; Zabrouskov, V. Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Anal. Chem. 2006, 78 (2), 493-500.
21. Ferea, T. L.; Botstein, D.; Brown, P. O.; Rosenzweig, R. F. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U.S.A 1999, 96 (17), 9721-9726.
22. Verduyn, C.; Postma, E.; Scheffers, W. A.; Van Dijken, J. P. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 1992, 8 (7), 501-517.
23. Eng, J.; McCormack, A.; Yates, J. An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
24. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2003, 2 (1), 43-50.
25. Tabb, D. L.; McDonald, W. H.; Yates, J. R., 3rd. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 2002, 1 (1), 21-26.
26. Liu, H.; Sadygoy, R. G.; Yates, J. R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76 (14), 4193-4201.
27. de Godoy, L. M.; Olsen, J. V.; de Souza, G. A.; Li, G.; Mortensen, P.; Mann, M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 2006, 7 (6), R50.
28. Wei, J.; Sun, J.; Yu, W.; Jones, A.; Oeller, P.; Keller, M.; Woodnutt, G.; Short, J. M. Global proteome discovery using an online three-dimensional LC-MS/MS. J. Proteome Res. 2005, 4 (3), 801-808.
29. Ghaemmaghami, S.; Huh, W. K.; Bower, K.; Howson, R. W.; Belle, A.; Dephoure, N.; O'Shea, E. K.; Weissman, J. S. Global analysis of protein expression in yeast. Nature 2003, 425 (6959), 737-741.
30. McDonald, W. H.; Yates, J. R., III. Shotgun proteomics and biomarker discovery. Dis. Markers 2002, 18 (2), 99-105.
31. Schuller, H. J. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr.Genet. 2003, 43, 139-160.
32. Verdone, L.; Wu, J.; van Riper, K.; Kacherovsky, N.; Vogelauer, M.; Young, E. T.; Grunstein, M.; Di Mauro, E.; Caserta, M. Hyperacetylation of chromatin at the ADH2promoter allows Adr1 to bind in repressed condition. EMBO J. 2002, 21 (5), 1101-1111.
33. Polge, C.; Thomas, M. SNF1/AMPK/SnRK1 kinases, global regulators at the heart of energy control. Trends Plant Sci. 2007, 12 (1), 20-28.
34. Van Dijken, J. P.; Bauer, J.; Brambilla, L.; Duboc, P.; Francois, J. M.; Gancedo, C.; Giuseppin, M. L.; Heijnen, J. J.; Hoare, M.; Lange, H. C.; Madden, E. A.; Niederberger, P.; Nielsen, J.; Parrou, J. L.; Petit, T.; Porro, D.; Reuss, M.; van, R. N.; Rizzi, M.; Steensma, H. Y.; Verrips, C. T.; Vindelov, J.; Pronk, J. T. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb.Technol. 2000, 26 (9-10), 706-714.