Respiratory diseases are important health problem throughout the world. The bronchoalveolar lavage (BAL) fluid obtained by fiber-optic bronchoscopy is a biofluid reflecting the expression of secreted pulmonary proteins and the products of activated cells. The characterization of the BALF proteome provides an opportunity to establish diagnostic and get prognostic indicators of airway diseases. The main part of the chapter is devoted to the description of the most effective and reliable method of BALF sample preparation and processing for proteomic studies. Principal BALF proteome characteristics and the difficulties to work with this fluid are also introduced. Finally, the best conditions for high resolution and high reliability 2-dimensional electrophoresis (DE) of BALF samples are given.
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