The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

Area of Science:

• Proteomics
• Yeast molecular biology
• Post-translational modifications

Background:

• Phosphorylation is a key post-translational modification regulating protein function.
• Understanding phosphorylation networks is crucial for deciphering cellular signaling pathways.
• The Saccharomyces cerevisiae proteome offers a model system for studying fundamental cellular processes.

Purpose of the Study:

• To update and expand the PhosphoGRID database with new experimentally verified in vivo phosphorylation sites.
• To provide comprehensive annotations for phosphosites, including associated kinases/phosphatases and functional effects.
• To facilitate the development of predictive models for phosphorylation-based signaling networks.

Main Methods:

• Curating and integrating data from high-throughput (HTP) mass spectrometry studies.
• Incorporating data from focused low-throughput (LTP) studies.
• Annotating phosphosites with protein kinases, phosphatases, conditions, and functional impacts.

Main Results:

• The PhosphoGRID version 2.0 dataset includes 20,177 unique phosphorylated residues and 1,614 unique phosphosites from LTP studies.
• This represents a four-fold increase in unique phosphorylated residues compared to version 1.0.
• A significant overlap exists between HTP and LTP data, with 45% of functionally defined LTP sites found in at least two HTP studies.

Conclusions:

• The expanded PhosphoGRID database provides a rich resource for yeast phosphoproteomics research.
• The near-saturation of phosphoprotein coverage suggests a comprehensive understanding of yeast phosphorylation.
• Integration of HTP and LTP data holds promise for building predictive models of cellular signaling.