Analysis of the extracellular matrix and secreted vesicle proteomes by mass spectrometry

The extracellular matrix (ECM) and secreted vesicles are unique structures outside of cells that carry out dynamic biological functions. ECM is created by most cell types and is responsible for the three-dimensional structure of the tissue or organ in which they are originated. Many cells also produce or secrete specialized vesicles into the ECM, which are thought to influence the extracellular environment. ECM is not s a physical structure to connect cells in a tissue or organ. The proteins in ECM and secreted vesicles are critical to cell function, differentiation, motility, and cell-to-cell interaction. Although a number of major structural proteins of ECM and secreted vesicles have long been known, an appreciation of the role of less-abundant non-collagenous proteins has just begun to emerge. This chapter outlines a series of methods used to isolate and enrich ECM constituents and secreted vesicles from bone-forming osteoblast cells, enabling comprehensive profiles of their proteomes to be obtained by mass spectrometry. These methods can be easily adapted to study ECM and secreted vesicles in other cell types, primary cell cultures derived from animal models, or tissue specimens.