System Wide Analyses have Underestimated Protein Abundances and Transcriptional Importance in Mammals

System wide surveys in mammals suggest that the protein expressed at the median abundance is present at 8,000 - 16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al., we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than the uncorrected protein data. To estimate the degree to which mRNA expression levels determine protein levels, it is critical to measure the error in protein and mRNA abundance data and to consider all genes. By taking direct measurements of experimental error into account, we estimate that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. By in addition modeling all genes' expression, we show that mRNA levels can explain at least 65% of protein levels for expressed genes and 100% for genes that are not expressed. We also employ a second strategy to determine the contribution of mRNA levels to protein expression. This shows that the median variance in translation rates directly measured by ribosome profiling in three human and mouse cell lines is 4.6 fold less than the variance inferred by Schwanhausser et al. and that based on this mRNA levels are expected to explain ~75% of the variance in expressed protein levels for the 4,212 detected genes and ~82% for all expressed genes. While the magnitude of our differently derived estimates vary, all suggest that the previous studies have significantly underestimated the importance of transcription.