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MatrisomeDB: the ECM-protein knowledge database.

Xinhao Shao1, Isra N Taha2, Karl R Clauser3

  • 1College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA.

Nucleic Acids Research
|October 6, 2019
PubMed
Summary
This summary is machine-generated.

MatrisomeDB is a comprehensive database of extracellular matrix (ECM) proteomic data. This updated release includes extensive human and mouse ECM proteoforms and peptide data, aiding tissue analysis.

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Area of Science:

  • Proteomics
  • Extracellular Matrix Biology
  • Bioinformatics

Background:

  • The extracellular matrix (ECM) is crucial for tissue organization and homeostasis.
  • Mass-spectrometry-based proteomics is a key method for ECM characterization.
  • Existing ECM proteomic data is fragmented across studies.

Purpose of the Study:

  • To present an updated and expanded release of MatrisomeDB, a curated proteomic database for the ECM.
  • To facilitate direct comparison of ECM composition across diverse biological contexts.
  • To provide a comprehensive resource for building an ECM atlas.

Main Methods:

  • Retrieved and reprocessed raw mass spectrometry data from 17 studies.
  • Standardized search parameters and criteria for data analysis.
  • Integrated proteomic data from normal tissues, cancers, and other diseases.

Main Results:

  • The new MatrisomeDB release contains 847 human and 791 mouse ECM proteoforms.
  • Includes over 350,000 human and 600,000 mouse ECM-derived peptide-to-spectrum matches.
  • Generates tissue distribution maps, peptide coverage maps, and post-translational modification lists.

Conclusions:

  • MatrisomeDB is the most complete collection of ECM proteomic data available.
  • This resource enables detailed analysis and comparison of ECM composition.
  • Facilitates the creation of a comprehensive atlas of the extracellular matrix.