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dc.contributor.authorNaba, A
dc.contributor.authorPearce, OM
dc.contributor.authorDel Rosario, A
dc.contributor.authorMa, D
dc.contributor.authorDing, H
dc.contributor.authorRajeeve, V
dc.contributor.authorCutillas, PR
dc.contributor.authorBalkwill, FR
dc.contributor.authorHynes, RO
dc.identifier.citationCharacterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics Alexandra Naba, Oliver M. T. Pearce, Amanda Del Rosario, Duanduan Ma, Huiming Ding, Vinothini Rajeeve, Pedro R. Cutillas, Frances R. Balkwill, and Richard O. Hynes Journal of Proteome Research Article ASAP DOI: 10.1021/acs.jproteome.7b00191en_US
dc.description.abstractThe 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, cardio-vascular 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 dataset generated in this study has been deposited to the public repository ProteomeXchange with the dataset identifier: PXD005554.en_US
dc.description.sponsorshipNational Cancer Institute – Tumor Microenvironment Network (U54 CA126515/CA163109), DoD BRCP Innovator Award (BC131410) to ROH, the Howard Hughes Medical Institute of which ROH is investigator, and in part by the Cancer Center Support (Core) Grant P30-CA14051 from the National Cancer Institute. OP and FB were funded by the European Research Council (ERC322566) and Cancer Research UK (A16354)en_US
dc.publisherAmerican Chemical Societyen_US
dc.relation.ispartofJ Proteome Res
dc.rightsThis document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Proteome Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see
dc.titleCharacterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomicsen_US
pubs.organisational-group/Queen Mary University of London
pubs.organisational-group/Queen Mary University of London/Faculty of Medicine & Dentistry
pubs.organisational-group/Queen Mary University of London/Faculty of Medicine & Dentistry/Barts Cancer Institute
pubs.organisational-group/Queen Mary University of London/Faculty of Medicine & Dentistry/Barts Cancer Institute/Cancer & Inflammation
pubs.organisational-group/Queen Mary University of London/Impact Leads
pubs.publication-statusPublished online

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