g. flagellin (FliC/FlaA) and type IV pilin types (PilA)). Transcriptomic analyses are able to quantitate gene expression accurately up to 4.7 orders

of magnitude [76], however proteomic strategies such as iTRAQ only achieve measurement of around 2 orders of magnitude. Technical limitations of the iTRAQ method may lead to an underestimation of the magnitude of change [77], while many proteins are below the limit of detection by 2-DE. Clear examples of iTRAQ ratio underestimation are seen in proteins that are unique to a particular strain, such as AES_7165 (unique to AES-1R), which despite being absent in PAO1 and PA14 only achieved measured ratios of 4.15 and 4.90, respectively. Conclusions A complementary proteomic approach combining gel-based (2-DE) and gel-free (2-DLC-MS/MS with

check details iTRAQ tags) techniques was employed to quantitatively compare the proteomes of P. aeruginosa strains PAO1, PA14 and AES-1R (an acute, transmissible CF isolate). Proteins associated with AES-1R belonged to a variety of functional groups including Wortmannin virulence factors, antibiotic resistance, LPS and fatty acid biosynthesis, and several MS-275 mouse hypothetical proteins. Proteins involved in the acquisition of iron were elevated in AES-1R compared to PAO1, while being decreased compared to PA14. These results confirm that CF-associated P. aeruginosa strains express a unique protein profile indicative of phenotypic adaptations to their environment and that provide traits conferring an advantage in colonization of the CF lung micro-environment. Identification of the proteins used by transmissible strains will aid in the elucidation of novel intervention strategies to reduce the burden of P. aeruginosa infection in CF patients. Acknowledgements This work was supported by the National Health and Medical Research Council of Australia (NHMRC 632788 to S.J.C.). N.J.H. is the recipient of an NHMRC Dora Lush Biomedical Research Scholarship and a stipend

from the Australian Cystic Fibrosis Research Trust (ACFRT). N.S. is the recipient of an Australian Postgraduate Award. The authors wish to thank Dr. Torsten Seemann from the Victorian Bioinformatics Consortium for assistance with annotation of the AES-1R genome sequence and bioinformatics Tyrosine-protein kinase BLK support for proteomics data searches. Electronic supplementary material Additional file 1: Growth curves for P. aeruginosa AES-1R, PAO1 and PA14 grown to stationary phase in LB medium. Dotted line and *, harvest time for PAO1 and PA14; #, for AES-1R. (JPEG 348 KB) Additional file 2: Table containing identification of differentially abundant proteins in P. aeruginosa AES-1R compared to PAO1 and PA14 using 2-DE. (PDF 143 KB) Additional file 3: Table containing identification of differentially abundant proteins in P.