MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database

Area of Science:

• Biochemistry
• Proteomics
• Bioinformatics

Background:

• The extracellular matrix (ECM) provides structural organization for cells, tissues, and organs.
• Mass-spectrometry-based proteomics is crucial for profiling the ECM, known as the matrisome.
• MatrisomeDB was initially released in 2020 to aid non-specialists in reusing ECM proteomic datasets.

Purpose of the Study:

• To expand MatrisomeDB with new curated ECM proteomic studies.
• To improve data visualization and accessibility for ECM research.
• To provide tools for enhanced analysis of matrisome data.

Main Methods:

• Curated and integrated data from 25 new studies on the ECM of 24 new tissues.
• Enhanced data visualization with peptide and post-translational modification mapping onto protein structures.
• Developed an abstract-mining tool for protein enrichment analysis.

Main Results:

• MatrisomeDB size has more than doubled, achieving near-complete coverage of the in-silico predicted matrisome.
• New visualizations map detected peptides and post-translational modifications onto protein domains and 3D structures.
• The abstract-mining tool identifies protein enrichment in specific studies.

Conclusions:

• The expanded MatrisomeDB significantly enhances the accessibility and utility of ECM proteomic data.
• Advanced visualization and analysis tools facilitate deeper insights into matrisome composition and function.
• MatrisomeDB serves as a comprehensive resource for researchers studying the extracellular matrix.