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J Proteome Res. 2017 Aug 4;16(8):3083-3091. doi: 10.1021/acs.jproteome.7b00191. Epub 2017 Jul 19.

Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics.

Author information

1
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
2
Barts Cancer Institute, Queen Mary University of London , London EC1M 6BQ, United Kingdom.
3
Proteomics Core Facility, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
4
Bioinformatics and Computing Facility, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.
5
Howard Hughes Medical Institute, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

Abstract

The extracellular matrix (ECM) is a complex meshwork of insoluble fibrillar proteins and signaling factors interacting together to provide architectural and instructional cues to the surrounding cells. Alterations in ECM organization or composition and excessive ECM deposition have been observed in diseases such as fibrosis, cardiovascular diseases, and cancer. We provide here optimized protocols to solubilize ECM proteins from normal or tumor tissues, digest the proteins into peptides, analyze ECM peptides by mass spectrometry, and interpret the mass spectrometric data. In addition, we present here two novel R-script-based web tools allowing rapid annotation and relative quantification of ECM proteins, peptides, and intensity/abundance in mass spectrometric data output files. We illustrate this protocol with ECMs obtained from two pairs of tissues, which differ in ECM content and cellularity: triple-negative breast cancer and adjacent mammary tissue, and omental metastasis from high-grade serous ovarian cancer and normal omentum. The complete proteomics data set generated in this study has been deposited to the public repository ProteomeXchange with the data set identifier: PXD005554.

KEYWORDS:

collagens; extracellular matrix; hydroxylation; mass-spectrometry-based proteomics; matrisome; microenvironment

PMID:
28675934
DOI:
10.1021/acs.jproteome.7b00191
[Indexed for MEDLINE]

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