title: Comparative proteomic assessment of matrisome enrichment methodologies.
abstract: The matrisome is a complex and heterogeneous collection of extracellular matrix (ECM) and ECM-associated proteins that play important roles in tissue development and homeostasis. While several strategies for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used decellularisation protocols and two extraction methods to characterise the matrisome in four murine organs (heart, mammary gland, lung and liver). We undertook a systematic evaluation of the performance of the individual methods on protein yield, matrisome enrichment capability and the ability to isolate core matrisome and matrisome-associated components. Our data find that sodium dodecyl sulphate (SDS) decellularisation leads to the highest matrisome enrichment efficiency, while the extraction protocol that comprises chemical and trypsin digestion of the ECM fraction consistently identifies the highest number of matrisomal proteins across all types of tissue examined. Matrisome enrichment had a clear benefit over non-enriched tissue for the comprehensive identification of matrisomal components in murine liver and heart. Strikingly, we find that all four matrisome enrichment methods led to significant losses in the soluble matrisome-associated proteins across all organs. Our findings highlight the multiple factors (including tissue type, matrisome class of interest and desired enrichment purity) that influence the choice of enrichment methodology, and we anticipate that these data will serve as a useful guide for the design of future proteomic studies of the matrisome.
authors: Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, U.K.
authors: Lukas
authors: L
authors: Krasny
authors: Proteomics Core Facility, The Institute of Cancer Research, London SW3 6JB, U.K.
authors: Angela
authors: A
authors: Paul
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, U.K. Division of Molecular Pathology, The Institute of Cancer Research, London SW3 6JB, U.K.
authors: Patty
authors: P
authors: Wai
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, U.K.
authors: Beatrice A
authors: BA
authors: Howard
authors: The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, U.K. Division of Molecular Pathology, The Institute of Cancer Research, London SW3 6JB, U.K.
authors: Rachael C
authors: RC
authors: Natrajan
authors: Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, U.K.
authors: Paul H
authors: PH
authors: Huang
mesh_terms: D000818:Animals; D002853:Chromatography, Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D005109:Extracellular Matrix / Q000378:metabolism; D016326:Extracellular Matrix Proteins / Q000378:metabolism; D006801:Humans; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D016326:Extracellular Matrix Proteins
keywords: extracellular matrix; mass spectrometry; matrisome; proteomics; tissue extraction