Bronchoalveolar Lavage: Quantitative Mass Spectrometry-Based Proteomics Analysis in Lung Diseases

Bronchoalveolar lavage (BAL) fluid, obtained by a relatively noninvasive procedure, is used as a practice for diagnosis of various lung diseases as source of cells for cytology analysis. The acellular component of BAL potentially can complement and be a key for the establishment of diagnostic or as a prognostic indicator. This chapter discusses the aspects of standardization of BAL sample preparation and processing and its implications on the BAL fluid proteome quantitative analysis by high-throughput mass spectrometry. The detailed conditions for quantitative analysis of BAL proteome in the context of biomarker discovery are introduced.