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Background   Acinetobacter baumannii  is a major health problem. The most common infection caused by  A. baumannii  is hospital acquired pneumonia, and the associated mortality rate is approximately 50 %. Neither  in vivo  nor  ex vivo  expression profiling has been performed at the proteomic or transcriptomic level for pneumonia caused by  A. baumannii . In this study, we characterized the proteome of  A. baumannii  under conditions that simulate those found in the airways, to gain some insight into how  A. baumannii  adapts to the host and to improve knowledge about the pathogenesis and virulence of this bacterium. A clinical strain of  A. baumannii  was grown under different conditions: in the presence of bronchoalveolar lavage fluid from infected rats, of RAW 264.7 cells to simulate conditions in the respiratory tract and in control conditions. We used iTRAQ labelling and LC-MALDI-TOF/TOF to investigate how  A. baumannii  responds on exposure to macrophages/BALF.    Results  179 proteins showed differential expression. In both models, proteins involved in the following processes were over-expressed: (i) pathogenesis and virulence (OmpA, YjjK); (ii) cell wall/membrane/envelope biogenesis (MurC); (iii) energy production and conversion (acetyl-CoA hydrolase); and (iv) translation (50S ribosomal protein L9). Proteins involved in the following were under-expressed: (i) lipid metabolism (short-chain dehydrogenase); (ii) amino acid metabolism and transport (aspartate aminotransferase); (iii) unknown function (DNA-binding protein); and (iv) inorganic ion transport and metabolism (hydroperoxidase).    Conclusions  We observed alterations in cell wall synthesis and identified 2 upregulated virulence-associated proteins with >15 peptides/protein in both  ex vivo  models (OmpA and YjjK), suggesting that these proteins are fundamental for pathogenesis and virulence in the airways. This study is the first comprehensive overview of the  ex vivo  proteome of  A. baumannii  and is an important step towards identification of diagnostic biomarkers, novel drug targets and potential vaccine candidates in the fight against pneumonia caused by  A. baumannii .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1608-z) contains supplementary material, which is available to authorized users.

Quantitative proteomic analysis of host—pathogen interactions: a study of Acinetobacter baumannii responses to host airways