Journal
JOURNAL OF PROTEOME RESEARCH
Volume 7, Issue 1, Pages 266-275Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr700580m
Keywords
cenSus; MudPIT; Snf4; AMP-activated kinase; 15N; mass spectrometry; proteomics
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Funding
- NATIONAL CENTER FOR RESEARCH RESOURCES [P41RR011823] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF MENTAL HEALTH [R01MH067880] Funding Source: NIH RePORTER
- NCRR NIH HHS [P41 RR11823, P41 RR011823, P41 RR011823-09] Funding Source: Medline
- NIMH NIH HHS [R01 MH067880-05, R01 MH067880, 5R01 MH067880] Funding Source: Medline
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The quantitative proteomic analysis of complex protein mixtures is emerging as a technically challenging but viable systems-level approach for studying cellular function. This study presents a large-scale comparative analysis of protein abundances from yeast protein lysates derived from both wild-type yeast and yeast strains lacking key components of the Snf1 kinase complex. Four different strains were grown under well-controlled chemostat conditions. Multidimensional protein identification technology followed by quantitation using either spectral counting or stable isotope labeling approaches was used to identify relative changes in the protein expression levels between the strains. A total of 2388 proteins were relatively quantified, and more than 350 proteins were found to have significantly different expression levels between the two strains of comparison when using the stable isotope labeling strategy. The stable isotope labeling based quantitative approach was found to be highly reproducible among biological replicates when complex protein mixtures containing small expression changes were analyzed. Where poor correlation between stable isotope labeling and spectral counting was found, the major reason behind the discrepancy was the lack of reproducible sampling for proteins with low spectral counts. The functional categorization of the relative protein expression differences that occur in Snf1-deficient strains uncovers a wide range of biological processes regulated by this important. cellular kinase.
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