Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics
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Author(s)
Pearce, Oliver M. T.
Del Rosario, Amanda
Ma, Duanduan
Ding, Huiming
Rajeeve, Vinothini
Cutillas, Pedro R.
Balkwill, Frances R.
Naba, Alexandra
Hynes, Richard O
Date Issued
April 2017
Journal
Journal of Proteome Research
Publisher
American Chemical Society (ACS)
Citation
Naba, Alexandra et al. “Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics.” Journal of Proteome Research 16, 8 (July 2017): 3083–3091 © 2017 American Chemical Society
Version
Author's final manuscript
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
MIT Department
Koch Institute for Integrative Cancer Research at MIT
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DOI of Published Version
https://doi.org/10.1021/acs.jproteome.7b00191
