Criteria for an ideal approach were a), quantitative extraction and solubilization of all S. Our problems with the quantification of release factor levels prompted an attempt to develop an improved, more quantitative protein extraction procedure. Although the poor consistency between genome-wide protein abundance studies is likely to arise from many different sources, these observations suggest that varying extraction efficiencies could be one factor contributing to high data variance. cerevisiae, we found that apparent abundance values for both factors varied widely depending on the exact protein preparation procedures used. During attempts to quantify intracellular levels of the polypeptide release factors eRF1 (Sup45p) and eRF3 (Sup35p) in S. Importantly, none of these studies evaluated the efficiencies of the respective extraction procedures they employed. With the exception of one study, all of the work cited above analyzed protein abundance following the extraction of these molecules from cells. Importantly, this spread of reported abundance values is representative for the data set as a whole, since the weighted standard deviation for reported eEF2 abundance equals the median of weighted standard deviations for data sets of all individual proteins (TvdH, unpublished). A good illustration of the variability of published abundance data is given by the example of translation elongation factor eEF2, for which values during logarithmic growth in YPD at 30☌ are given as 78,100 321,782 and 8,764 proteins per cell –. However, a detailed comparison showed that correlations between data sets generated by different groups are generally poor (see the supplementary data in Lu et al., ref. These studies provide an important data source for the emerging fields of systems biology and control analysis, where macromolecular abundance data are required for the construction of meaningful models. ![]() The recent literature has seen a significant increase in the number of publications that attempt the determination of protein abundances in yeast cells on a large scale –.
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