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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Updated: Mar 14, 2026

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis

Published on: July 23, 2015

Targeted proteomics effectively quantifies differences between native lung and detergent-decellularized lung

Elizabeth A Calle¹, Ryan C Hill², Katherine L Leiby¹

¹Department of Biomedical Engineering, Yale University, New Haven, CT 06519, USA; Yale School of Medicine, Yale University, New Haven, CT 06519, USA.

Acta Biomaterialia

|October 4, 2016

Summary

This summary is machine-generated.

A new method quantifies extracellular matrix (ECM) proteins in tissue scaffolds. Mild decellularization preserves significantly more ECM proteins, crucial for regenerative medicine and whole organ engineering.

Keywords:

Decellularization Extracellular matrix Quantitative proteomics Regenerative medicine Tissue engineering

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Area of Science:

Biomaterials Science
Regenerative Medicine
Proteomics

Background:

Extracellular matrix (ECM) is vital for tissue regeneration and widely used in regenerative medicine.
Understanding ECM composition in scaffolds is critical but challenging.
Current decellularization methods may compromise scaffold integrity.

Purpose of the Study:

To develop and apply an advanced proteomic method for quantifying ECM proteins in native and decellularized lung tissues.
To compare the efficacy of a mild decellularization technique versus a standard method in preserving ECM components.
To assess the impact of ECM retention on cell proliferation in engineered scaffolds.

Main Methods:

Utilized quantitative proteomics with ¹³C-labeled peptides for precise protein quantification.
Analyzed native lung tissue and scaffolds produced by two different decellularization methods.
Quantified 71 specific ECM proteins, including laminins and proteoglycans.
Assessed cell proliferation (PCNA staining) on decellularized scaffolds.

Main Results:

A mild "Triton/SDC" decellularization technique retained up to 27-fold more ECM proteins compared to a previous method.
Key basement membrane and ECM-associated proteins, such as laminins and proteoglycans, were well-preserved.
Scaffolds with higher ECM retention supported robust cell proliferation.
The proteomic method achieved picomole-level measurements of numerous matrix proteins.

Conclusions:

Mild decellularization preserves native ECM composition more effectively, crucial for regenerative medicine.
This quantitative proteomic approach enables better understanding and quality control of ECM scaffolds.
The findings advance tissue engineering, particularly for whole organ regeneration, by ensuring high-fidelity biomaterial substrates.