Functional analysis tools for post-translational modification: a post-translational modification database for...

Area of Science:

• Biochemistry
• Bioinformatics
• Proteomics

Background:

• Post-translational modifications (PTMs) are crucial for protein function, with nearly 200 types identified.
• High-resolution mass spectrometry has revealed numerous PTM sites, enhancing our understanding of cellular regulation.
• Existing PTM databases often lack quantitative analysis, visualization tools, or support for multiple PTM types.

Purpose of the Study:

• To introduce the Functional Analysis Tools for Post-Translational Modifications (FAT-PTM) database.
• To provide a comprehensive platform for visualizing and analyzing diverse PTM data.
• To facilitate hypothesis generation and pattern identification in PTM data.

Main Methods:

• Development of the FAT-PTM database, supporting eight PTM types and over 49,000 PTM sites.
• Integration of tools for visualizing protein-centric PTM networks.
• Inclusion of quantitative phosphorylation data and PTMs in metabolic pathways.

Main Results:

• The FAT-PTM database supports eight PTM types and over 49,000 PTM sites from Arabidopsis thaliana.
• Tools are available for visualizing PTM networks, quantitative phosphoproteomic data, and PTMs in metabolic pathways.
• The database facilitates the identification of co-modified protein groups.

Conclusions:

• FAT-PTM serves as a robust platform for sharing and visualizing PTM data.
• It enables hypothesis development for target proteins and identification of PTM patterns in signaling and metabolic pathways.
• The database enhances the comprehensive understanding of PTMs in cellular regulation.