Comparative proteomic assessment of matrisome enrichment methodologies

Area of Science:

• Proteomics
• Extracellular Matrix Biology
• Biochemistry

Background:

• The matrisome, comprising extracellular matrix (ECM) and associated proteins, is crucial for tissue development and homeostasis.
• Existing matrisome enrichment strategies lack comparative performance data across diverse tissue types.

Purpose of the Study:

• To comparatively assess proteomic identification of matrisome components using different enrichment methods across multiple murine organs.
• To evaluate protein yield, matrisome enrichment capability, and isolation of core and associated matrisome components.

Main Methods:

• Comparative proteomic analysis of two decellularisation protocols (including SDS) and two extraction methods.
• Characterization of the matrisome in murine heart, mammary gland, lung, and liver tissues.
• Systematic evaluation of method performance on protein yield and enrichment efficiency.

Main Results:

• SDS decellularisation achieved the highest matrisome enrichment efficiency.
• Chemical and trypsin digestion of the ECM fraction identified the most matrisome proteins across all examined tissues.
• Matrisome enrichment significantly improved identification in liver and heart but led to substantial loss of soluble matrisome-associated proteins.

Conclusions:

• The choice of matrisome enrichment methodology depends on tissue type, matrisome class, and desired purity.
• All tested enrichment methods result in the loss of soluble matrisome-associated proteins.
• These findings provide guidance for optimizing future matrisome proteomic studies.