Journal
JOURNAL OF PROTEOME RESEARCH
Volume 16, Issue 8, Pages 3083-3091Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.7b00191
Keywords
extracellular matrix; matrisome; collagens; niicroenvironment; hydroxylation; mass-spectrometry-based proteomics
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Funding
- National Cancer Institute - Tumor Micro environment Network [U54 CA126515/CA163109]
- DoD BRCP Innovator Award [BC131410]
- Howard Hughes Medical Institute
- Cancer Center Support (Core) Grant from the National Cancer Institute [P30-CA14051]
- European Research Council [ERC322566]
- Cancer Research UK [A16354]
- BBSRC [BB/M006174/1] Funding Source: UKRI
- CDMRP [BC131410, 672084] Funding Source: Federal RePORTER
- Biotechnology and Biological Sciences Research Council [BB/M006174/1] Funding Source: researchfish
- Cancer Research UK [16354] Funding Source: researchfish
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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.
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