J Proteome Res 2004, 3:595–603.PubMedCrossRef 21. Carroll J, Altman MC, Fearnley IM, Walker JE: Identification

of membrane proteins by tandem mass spectrometry of protein ions. Proc Natl Acad Sci USA 2007, 104:14330–14335.PubMedCrossRef 22. Kapp EA, Schutz F, Connolly LM, Chakel JA, Meza JE, Miller CA, et al.: An MX69 purchase evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 2005, 5:3475–3490.PubMedCrossRef 23. Gilks WR, Audit B, de Angelis D, Tsoka S, Ouzounis CA: Modeling the percolation of annotation errors in a database of protein ARS-1620 cell line sequences. Bioinformatics 2002, 18:1641–1649.PubMedCrossRef 24. Lommatzsch J, Templin MF, Kraft AR, Vollmer W, Holtje JV: Outer membrane localization of murein hydrolases: MltA, a third lipoprotein lytic transglycosylase in Escherichia coli. J Bacteriol 1997, 179:5465–5470.PubMed 25. Rhen M, Sukupolvi S: The role of the traT gene of the Salmonella typhimurium virulence plasmid for serum resistance and growth within liver macrophages. Microb Pathog 1988, 5:275–285.PubMedCrossRef 26. Laubacher ME, Ades SE: The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance. J Bacteriol 2008, 190:2065–2074.PubMedCrossRef 27. Thulasiraman V, Lin S, Gheorghiu L, Lathrop J, Lomas L, Hammond D, et al.: Reduction of the concentration

difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis 2005, 26:3561–3571.PubMedCrossRef 28. Kaback HR: Bacterial Membranes. In Methods in EnzymologyEnzyme purification and related C59 techniques. Edited by: William BJ. Academic Press; 1971:99–120. 29. Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A, et al.: Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Arch Microbiol 2006, 184:362–377.PubMedCrossRef 30. Juncker AS, Willenbrock H, von Heijne G, Brunak S, Nielsen H, Krogh A: Prediction of lipoprotein signal peptides in Gram-negative bacteria.

Protein Sci 2003, 12:1652–1662.PubMedCrossRef Lepirudin 31. Szafron D, Lu P, Greiner R, Wishart DS, Poulin B, Eisner R, et al.: Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res 2004, 32:W365-W371.PubMedCrossRef 32. Yu CS, Lin CJ, Hwang JK: Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 2004, 13:1402–1406.PubMedCrossRef 33. Gardy JL, Spencer C, Wang K, Ester M, Tusnady GE, Simon I, et al.: PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res 2003, 31:3613–3617.PubMedCrossRef 34. Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, et al.: PSORTb v.2.