Abstract
The identification and accurate quantitation of protein abundance has been a major objective of proteomics research. Abundance studies have the potential to provide users with data that can be used to gain a deeper understanding of protein function and regulation and can also help identify cellular pathways and modules that operate under various environmental stress conditions. One of the central missions of the Saccharomyces Genome Database (SGD; https://www.yeastgenome.org) is to work with researchers to identify and incorporate datasets of interest to the wider scientific community, thereby enabling hypothesis-driven research. A large number of studies have detailed efforts to generate proteome-wide abundance data, but deeper analyses of these data have been hampered by the inability to compare results between studies. Recently, a unified protein abundance dataset was generated through the evaluation of more than 20 abundance datasets, which were normalized and converted to common measurement units, in this case molecules per cell. We have incorporated these normalized protein abundance data and associated metadata into the SGD database, as well as the SGD YeastMine data warehouse, resulting in the addition of 56 487 values for untreated cells grown in either rich or defined media and 28 335 values for cells treated with environmental stressors. Abundance data for protein-coding genes are displayed in a sortable, filterable table on Protein pages, available through Locus Summary pages. A median abundance value was incorporated, and a median absolute deviation was calculated for each protein-coding gene and incorporated into SGD. These values are displayed in the Protein section of the Locus Summary page. The inclusion of these data has enhanced the quality and quantity of protein experimental information presented at SGD and provides opportunities for researchers to access and utilize the data to further their research.
Highlights
The Saccharomyces Genome Database (SGD) collects, organizes and presents biological information about the genes and proteins of the budding yeast Saccharomyces cerevisiae [1,2]
Protein pages contain a descriptive overview of each predicted protein, experimental data such as protein abundance and halflife, structural domain information, primary amino acid sequence from a variety of strains with overlaid experimental post-translational modification (PTM) data, physicochemical properties derived from the protein sequence, a list of external identifiers and links to other resources that may be of use to researchers
As we surveyed the literature to collect protein abundance datasets, we concurrently learned that the laboratory of Grant Brown at the University of Toronto was collecting and evaluating protein abundance datasets with the goal of first normalizing the data presented in these studies and converting it into the common units of molecules per cell [26]
Summary
The Saccharomyces Genome Database (SGD) collects, organizes and presents biological information about the genes and proteins of the budding yeast Saccharomyces cerevisiae [1,2]. Doing so provides researchers with context regarding abundance levels relative to other proteins in the proteome and provides baseline information that can be extended to answer questions regarding the regulation of protein levels when cells are grown under stress conditions.
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