New & Noteworthy

Proteome-wide abundance data

March 11, 2019

SGD has now incorporated proteome-wide protein abundance data obtained from a comprehensive meta-analysis by Ho et al., 2018. The authors normalized and combined 21 different S. cerevisiae protein abundance datasets—including data from both untreated cells and cells treated with various environmental stressors—to create a unified protein abundance dataset where all values are in the intuitive units of molecules per cell. The original datasets were initially obtained using different methodologies (mass spectrometry, fluorescence microscopy, flow cytometry, and TAP-immunoblot), allowing Ho et al. to evaluate the strengths and weaknesses of these methods in addition to providing the community with a comprehensive reference map of the yeast proteome.

Normalized abundance measurements and associated metadata from untreated and treated cells are displayed in tabular form in the experimental data section of protein-tabbed pages (e.g. CDC28). Several different controlled vocabularies have been employed to standardize the metadata display. In addition, calculated median abundance and median absolute deviation (MAD) values are displayed in the protein section of Locus Summary pages (e.g. PHO85). Two new YeastMine templates have been created to provide access to these data: Gene -> Protein Abundance and Gene -> Median Protein Abundance

Special thanks to Brandon Ho and Grant Brown for generating this comprehensive reference map of protein abundance, and for their help in making this data available to the larger community.

Categories: New Data