| Comments |
P.5 left column top paragraph: "Conversion of GFP measurements to molecules per cell resulted in a unified dataset covering 97% of the yeast proteome (Table S3). Of the 5858 protein proteome, only 156 proteins were not detected in any study (Table S4). The 156 proteins are enriched for uncharacterized ORFs (hypergeometric p = 6.9×10^-81) and for genes involved in proton transport and glucose import (p = 5.9×10^-5 and p =0.0080, respectively). 353 proteins were detected in only a single study. In general, there is agreement in the molecules per cell for each protein among the data sets analyzed in [investigators'] study, with protein abundances ranging from 5 to 1.3×10^6 molecules per cell (Figure 2A and Table S3)." P.7 left column bottom paragraph: "Since the majority of proteins do not change in abundance in any given stress condition, [investigators] normalized GFP intensities from each study by the mode-shifting method and applied the same linear regression used previously to convert arbitrary units to protein molecules per cell (Table S6). [They] applied a cut-off for changes in protein abundance, corresponding to either a two-fold increase or a two-fold decrease (Table S7). At this cutoff, which is more conservative than that used in most of the individual studies, 1250 of 4263 proteins assessed change in abundance in at least one condition: 580 proteins increase in abundance, and 744 proteins decrease in abundance. The magnitude of abundance changes spans a range of 60-fold for increases and 57-fold for decreases (Table S7, the Lee et al. dataset was excluded from analysis of abundance decreases as its inclusion results in maximum –fold decreases that greatly exceed the dynamic range of GFP fluorescence detection that is evident in Figure 3)." |