Abstract:
BACKGROUND : Phosphorylation is the most frequent post-translational modification made to proteins and may regulate
protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP)
phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many
phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the
total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast). RESULTS : In all, 187
HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia.
Estimates of the number of phosphoproteins and p-sites were inferred by two METHODS : Capture-Recapture, and fitting the
saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also
adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in
total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast,
respectively, whereas estimates for Arabidopsis were not as reliable. CONCLUSIONS : Most of the phosphoproteins have been
discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites
are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP
phosphoproteomics appears to be capable of capturing 70% to 95% of total phosphoproteins, but only 40% to 60% of total
p-sites.
