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Analysis of Secreted Proteins

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Proteomics for Biomarker Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1002))

Abstract

Most biological processes including growth, proliferation, differentiation, and apoptosis are coordinated by tightly regulated signaling pathways, which also involve secreted proteins acting in an autocrine and/or paracrine manner. In addition, extracellular signaling molecules affect local niche biology and influence the cross-talking with the surrounding tissues. The understanding of this molecular language may provide an integrated and broader view of cellular regulatory networks under physiological and pathological conditions. In this context, the profiling at a global level of cell secretomes (i.e., the subpopulations of a proteome secreted from the cell) has become an active area of research. The current interest in secretome research also deals with its high potential for the biomarker discovery and the identification of new targets for therapeutic strategies. Several proteomic and mass spectrometry platforms and methodologies have been applied to secretome profiling of conditioned media of cultured cell lines and primary cells. Nevertheless, the analysis of secreted proteins is still a very challenging task, because of the technical difficulties that may hamper the subsequent mass spectrometry analysis. This chapter describes a typical workflow for the analysis of proteins secreted by cultured cells. Crucial issues related to cell culture conditions for the collection of conditioned media, secretome preparation, and mass spectrometry analysis are discussed. Furthermore, an overview of quantitative LC-MS-based approaches, computational tools for data analysis, and strategies for validation of potential secretome biomarkers is also presented.

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Acknowledgments

We gratefully acknowledge Dr. Menotti Ruvo (IBB, CNR of Naples) and Dr. Carla Pasquarello Mosimann (Geneva Proteomics Core Facility) for their useful suggestions and support.

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Authors and Affiliations

  1. Second University of Naples, Caserta, Italy

    Valeria Severino & Angela Chambery

  2. Geneva University, Geneva, Switzerland

    Annarita Farina

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  1. Valeria Severino
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  2. Annarita Farina
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  3. Angela Chambery
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Editors and Affiliations

  1. , Laboratory of Proteomics and Analytical, Frederick National Laboratory for Cancer, N/A, Frederick, 21702-1201, Maryland, USA

    Ming Zhou

  2. , Laboratory of Proteomics and Analytical, Frederick National Laboratory for Cancer, N/A 5540, Frederick, 21702-1201, Maryland, USA

    Timothy Veenstra

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Severino, V., Farina, A., Chambery, A. (2013). Analysis of Secreted Proteins. In: Zhou, M., Veenstra, T. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1002. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-360-2_4

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  • DOI: https://doi.org/10.1007/978-1-62703-360-2_4

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