A proteomics approach to ventilator-induced lung injury might identify protein patterns that contribute to epithelial injury. To identify changes in alveolar type II cells (ATII), rats were mechanically ventilated for 5 hours with a high tidal volume (HTV; 20 ml/kg, no positive end expiratory pressure) or a low tidal volume (LTV; 6 ml/kg, positive end expiratory pressure 4 cmH2O) and compared with pooled controls without mechanical ventilation (SV). ATII were isolated and lysed. Protein expression was compared using the recently introduced cleavable isotope coded affinity tag (ICAT) methodology. After tryptic digestion, cysteine containing peptides were tagged with biotin, extracted using an avidin-coated column and identified by HPLC and mass spectrometry with collision-induced dissociation. Spectra were interrogated against the Swissprot database and quantified using the ProteinProspector software. HTV ventilation resulted in morphologic changes, pulmonary edema and neutrophil influx in the lung. Quantization showed differential expression of several hundred proteins following both HTV and LTV ventilation. Most proteins were upregulated by LTV ventilation compared with SV. For some proteins, upregulation was markedly attenuated after HTV compared with LTV. This was not true for ICAM-1, which correlated with the increased number of neutrophils in these samples. After HTV, surfactant proteins B and D followed different patterns. Since the differentially expressed proteins play important roles in innate immunity and in pulmonary edema fluid clearance, the attenuated response of ATII after HTV ventilation might indicate a clinically relevant impediment.