Discovery strategies for proteomic profiling of airway diseases

Discovery proteomics is defined here as the unbiased (untargeted) differential investigation of protein abundances from biological material resulting from some biological or physical challenge. In this review, we will examine the latest approaches and strategies for discovery investigations of airway disease. We will discuss general and specific sampling strategies, sample preparation, differential separations and quantification-with special attention to posttranslational modifications that are particularly relevant to oxidative stress response of airway tissues, statistical analysis and tools, mass spectrometric identification, and finally bioinformatics tools for pathway analysis.