SUMMARYThe cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology.Keywords cell adhesion, extracellular matrix, mass spectrometry, proteomics Intercellular cohesion and communication are fundamental requirements of multicellular organisms. Indeed, the selective adhesion of cells to one another and to the extracellular matrix (ECM) within which they reside is necessary for much of metazoan anatomy and development ( € Ozbek et al. 2010; Hynes 2012). The ECM provides a structural framework for cell binding, and this enables tissues and organs to form. In addition, the composition and organization of the ECM play key roles in determining how cells interact with and respond to their microenvironment (Frantz et al. 2010). Thus, the ECM defines the physical and chemical interactions that control cellular physiology and fate.The identification and quantification of the components of distinct ECMs, the spatial and temporal dynamics of ECM molecules and the interactions underpinning ECM protein networks represent key steps towards understanding the role of the ECM in health and disease. Proteomics, the study of all proteins in a given system, offers an opportunity to address these challenges in a global manner, without the need for investigations based on predetermined molecular candidates. Here, we review recent progress in the isolation and proteomic analysis of extracellular molecules, with a focus on mass spectrometry (MS)-based proteomic strategies aimed at the non-specialist. A complete overview of ECM composition is beyond the scope of this review; rather, we highlight the technical and biological aspects of the latest ECM proteomic studies and discuss implications for futur...