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

被引：169

作者：

Naba, Alexandra ^{[1
,6
]}

Pearce, Oliver M. T. ^{[2
]}

Del Rosario, Amanda ^{[3
]}

Ma, Duanduan ^{[4
]}

Ding, Huiming ^{[4
]}

Rajeeve, Vinothini ^{[2
]}

Cutillas, Pedro R. ^{[2
]}

Balkwill, Frances R. ^{[2
]}

Hynes, Richard O. ^{[1
,5
]}

机构：

[1] MIT, Koch Inst Integrat Canc Res, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[2] Queen Mary Univ London, Barts Canc Inst, London EC1M 6BQ, England

[3] MIT, Koch Inst Integrat Canc Res, Prote Core Facil, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[4] MIT, Koch Inst Integrat Canc Res, Bioinformat & Comp Facil, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[5] MIT, Howard Hughes Med Inst, Cambridge, MA 02139 USA

[6] Univ Illinois, Dept Physiol & Biophys, Chicago, IL 60607 USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2017年 / 16卷 / 08期

基金：

欧洲研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

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

D O I：

10.1021/acs.jproteome.7b00191

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：3083 / 3091

页数：9

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