L604 -L614, 2013. First published September 6, 2013 doi:10.1152/ajplung.00079.2013.-In rodent model systems, the sequential changes in lung morphology resulting from hyperoxic injury are well characterized and are similar to changes in human acute respiratory distress syndrome. In the injured lung, alveolar type two (AT2) epithelial cells play a critical role in restoring the normal alveolar structure. Thus characterizing the changes in AT2 cells will provide insights into the mechanisms underpinning the recovery from lung injury. We applied an unbiased systems-level proteomics approach to elucidate molecular mechanisms contributing to lung repair in a rat hyperoxic lung injury model. AT2 cells were isolated from rat lungs at predetermined intervals during hyperoxic injury and recovery. Protein expression profiles were determined by using iTRAQ with tandem mass spectrometry. Of the 959 distinct proteins identified, 183 significantly changed in abundance during the injury-recovery cycle. Gene ontology enrichment analysis identified cell cycle, cell differentiation, cell metabolism, ion homeostasis, programmed cell death, ubiquitination, and cell migration to be significantly enriched by these proteins. Gene set enrichment analysis of data acquired during lung repair revealed differential expression of gene sets that control multicellular organismal development, systems development, organ development, and chemical homeostasis. More detailed analysis identified activity in two regulatory pathways, JNK and miR 374. A novel short time-series expression miner algorithm identified protein clusters with coherent changes during injury and repair. We concluded that coherent changes occur in the AT2 cell proteome in response to hyperoxic stress. These findings offer guidance regarding the specific molecular mechanisms governing repair of the injured lung. alveolar epithelial cell proteome; acute respiratory distress syndrome; bioinformatics; hyperoxia HEALTHY RATS AND MICE EXPOSED to 100% oxygen develop respiratory failure and death within 2-3 days (2, 20). Histological examination of lungs from these animals shows pathological changes similar to those that occur in human acute respiratory distress syndrome (ARDS), with evidence of apoptosis and necrosis of the alveolar endothelium and epithelium (4, 20). There is evidence that hyperoxia is damaging to the human lung as well (8,24,33).Rodent lung morphology has been well characterized during acute oxygen-lung toxicity and subsequent recovery (19,20,58). In animals, exposure to normobaric hyperoxia for 72 h results in an exudative phase that is characterized by alveolar type I (AT1) epithelial cell death, swelling and necrosis of endothelial cells, interstitial edema, and filling of alveoli with an exudative fluid (19,33). Cessation of oxygen exposure after 60 h leads to a rapid decrease in the number of neutrophils within the first 3 days and an increase in the number of monocytes and lymphocytes, resulting in a normal differential of lung white blood cells by day 7 (58)...