1. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics
- Author
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Frances R. Balkwill, Huiming Ding, Duanduan Ma, Richard O. Hynes, Oliver M. T. Pearce, Vinothini Rajeeve, Alexandra Naba, Amanda M. Del Rosario, and Pedro R. Cutillas
- Subjects
Proteomics ,0301 basic medicine ,Triple Negative Breast Neoplasms ,Biology ,Bioinformatics ,Biochemistry ,Mass Spectrometry ,Article ,Extracellular matrix ,03 medical and health sciences ,0302 clinical medicine ,Fibrosis ,medicine ,Humans ,Breast ,Uncategorized ,Ovarian Neoplasms ,Extracellular Matrix Proteins ,Cancer ,Molecular Sequence Annotation ,General Chemistry ,medicine.disease ,Mass spectrometric ,Extracellular Matrix ,Cell biology ,Serous fluid ,030104 developmental biology ,Solubilization ,030220 oncology & carcinogenesis ,Omental metastasis ,Female ,Omentum - 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.
- Published
- 2022
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