Outline of the computational analyses to merge various TAP-, GFP-, and mass spectrometry-based studies to derive yeast proteome abundance in molecules per cell (mpc). Functional enrichment can be identified at high and low abundance measurements, but 67% of the proteome is maintained within 1000 – 10000 mpc. Further biological insight was derived by comparing the unified dataset with other genomic approaches to measure RNA abundance, and protein abundance in stress conditions.

The Brown lab, together with Anastasia Baryshnikova at Calico Labs, used computational analyses to normalize and convert 21 yeast protein abundance studies to the intuitive measurement of molecules per cell. They provide precise and accurate abundance measurements for greater than 90% of yeast proteins, making it the most comprehensive quantitation of the yeast proteome, and any eukaryotic cell, to date.

With this unified dataset in hand, comparative and multivariate outlier analyses were performed to examine how cells respond to environmental stress at the protein level, how RNA compares with protein levels, and to further explore functional organization of yeast proteome at the abundance level. One surprising finding was that the environmental stress response, reported over a decade ago for mRNA levels, is not completely translated to the protein level. One other reassuring finding was that protein fusion tags (i.e. GFP or TAP fusion tags) have a limited effect on protein abundance.

Their findings are published in the journal Cell Systems. This study provides a tool that will be useful for the yeast community, and it provides further biological insight into the proteome of a eukaryotic cell, using the yeast model system.

The study was funded by the Canadian Cancer Society Research Institute.

Their study was highlighted on the Cosmos and CBC News websites.