Proteomic and Computational Analysis of Bronchoalveolar Proteins during the Course of the Acute Respiratory Distress Syndrome

Rationale: Acute lung injury causes complex changes in protein ex-pression in the lungs. Whereas most prior studies focused on single proteins, newer methods allowing the simultaneous study of many proteins could lead to a better understanding of pathogenesis and new targets for treatment. Objectives: Thepurposeof this studywas toexamine thechanges inpro-tein expression in the bronchoalveolar lavage fluid (BALF) of patients during the course of the acute respiratory distress syndrome (ARDS). Methods: Using two-dimensional difference gel electrophoresis (DIGE), the expressionof proteins in theBALF frompatients onDays 1 (n5 7), 3 (n5 8), and7 (n5 5) ofARDSwere comparedwithfindings in normal volunteers (n5 9). The patterns of protein expressionwere analyzed using principal component analysis (PCA). Biological processes that were enriched in the BALF proteins of patients with ARDS were identified using Gene Ontology (GO) analysis. Protein networks tha