Were centrifuged at 140006g for 5 min to remove insoluble material and 150 mL of the supernatants were transferred to high pressure liquid chromatography vials (Waters, USA). MudPIT analysis was performed according to the method described by Delahunty 22948146 and Yates (2005) using a ThermoFinnegan LTQ Orbitrap tandem mass spectrometer with a nano-electrospray ion source operated with a fragment-ion mass tolerance of 0.5 Daltons. Proteins in the sample were identified by matching the peptides predicted from the tandem mass spectra data against the complete L. monocytogenes non-redundant database of the National Centre for Biotechnology Institute (NCBI) using the Computational Proteomics Analysis System (CPAS) Version 8.1 (www.labkey.org). Searches were semi-tryptic, with fixed modifications (cysteine carbamidomethylation-57 Daltons) MedChemExpress Met-Enkephalin allowing no missed cleavages, and used the X!Tandem algorithm (www.thegpm.org/tandem/). Spectra counts within each sample were determined using TPP Xpress Quantitation software (Version 2.1) in conjunction with X!Tandem. Functional assignment of protein identifications was predicted manually using The Institute for Genomic ResearchComprehensive Microbial Resource (JCVI-CMR) (http://cmr.jcvi. org/tigr-scripts/CMR/GenomePage.cgi?org = ntlm01), GenoList L. monocytogenes serovar 1/2a EGD-e database (Version 3) (http:// genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/ goToTaxoRank?level = Listeria 
monocytogenes 20EGD-e), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/). All searches were run through the Trans Proteomic Pipeline (TPP; Version 3.4) for statistical purposes. The TPP analysis utilised the “Peptide Prophet” and “Protein Prophet” algorithms as previously described [14] to enable the level of false positive peptide and protein identifications to be estimated and to generate a peptide and protein error rate. Identifications with an average peptide prophet error rate (APPER) and protein error rate (PER) of .0.3/1, and protein identifications assigned based on a single unique peptide, were not considered for further analysis. Relative protein abundances between growth conditions were determined using the spectra counting method [15]. Spectra counts were averaged between biological replicates and normalised to account for sampling depth [16]. Statistical significance of differences in spectra abundances for protein identifications between samples was assessed using a likelihood ratio test 15755315 for independence (G-test) adjusted using the William’s correction (Gadj) to reduce false positive rates [17,18]. Significance was assigned at p#0.05 (Gadj 3.841). Only those protein 
identifications that met the AVP filtering criteria (APPER and PER of .0.3/1) and that differed significantly from the control treatment are discussed.Uncoupling of Oxidative PhosphorylationOxidative phosphorylation was uncoupled in alkaline adapted L. monocytogenes EGD-e cells using the ionophore carbonyl cyanide m-chlorophenyl hydrazone (CCCP; Sigma-Aldrich, Australia) [6,19]. Cultures were adapted to growth at pH7.3 and 9.0 as described previously. Replicate 10 mL cultures of each pH condition were prepared, incubated at 37uC, and CCCP was added to give a final concentration of 5 uM at mid-exponential growth phase (OD <0.4). Growth was measured turbidimetrically at 600 nm using a Spectronic 20D spectrophotometer (Milton Roy, USA) until the optical density ceased to change.Lag phase Determination Following an.Were centrifuged at 140006g for 5 min to remove insoluble material and 150 mL of the supernatants were transferred to high pressure liquid chromatography vials (Waters, USA). MudPIT analysis was performed according to the method described by Delahunty 22948146 and Yates (2005) using a ThermoFinnegan LTQ Orbitrap tandem mass spectrometer with a nano-electrospray ion source operated with a fragment-ion mass tolerance of 0.5 Daltons. Proteins in the sample were identified by matching the peptides predicted from the tandem mass spectra data against the complete L. monocytogenes non-redundant database of the National Centre for Biotechnology Institute (NCBI) using the Computational Proteomics Analysis System (CPAS) Version 8.1 (www.labkey.org). Searches were semi-tryptic, with fixed modifications (cysteine carbamidomethylation-57 Daltons) allowing no missed cleavages, and used the X!Tandem algorithm (www.thegpm.org/tandem/). Spectra counts within each sample were determined using TPP Xpress Quantitation software (Version 2.1) in conjunction with X!Tandem. Functional assignment of protein identifications was predicted manually using The Institute for Genomic ResearchComprehensive Microbial Resource (JCVI-CMR) (http://cmr.jcvi. org/tigr-scripts/CMR/GenomePage.cgi?org = ntlm01), GenoList L. monocytogenes serovar 1/2a EGD-e database (Version 3) (http:// genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/ goToTaxoRank?level = Listeria monocytogenes 20EGD-e), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/). All searches were run through the Trans Proteomic Pipeline (TPP; Version 3.4) for statistical purposes. The TPP analysis utilised the “Peptide Prophet” and “Protein Prophet” algorithms as previously described [14] to enable the level of false positive peptide and protein identifications to be estimated and to generate a peptide and protein error rate. Identifications with an average peptide prophet error rate (APPER) and protein error rate (PER) of .0.3/1, and protein identifications assigned based on a single unique peptide, were not considered for further analysis. Relative protein abundances between growth conditions were determined using the spectra counting method [15]. Spectra counts were averaged between biological replicates and normalised to account for sampling depth [16]. Statistical significance of differences in spectra abundances for protein identifications between samples was assessed using a likelihood ratio test 15755315 for independence (G-test) adjusted using the William’s correction (Gadj) to reduce false positive rates [17,18]. Significance was assigned at p#0.05 (Gadj 3.841). Only those protein identifications that met the filtering criteria (APPER and PER of .0.3/1) and that differed significantly from the control treatment are discussed.Uncoupling of Oxidative PhosphorylationOxidative phosphorylation was uncoupled in alkaline adapted L. monocytogenes EGD-e cells using the ionophore carbonyl cyanide m-chlorophenyl hydrazone (CCCP; Sigma-Aldrich, Australia) [6,19]. Cultures were adapted to growth at pH7.3 and 9.0 as described previously. Replicate 10 mL cultures of each pH condition were prepared, incubated at 37uC, and CCCP was added to give a final concentration of 5 uM at mid-exponential growth phase (OD <0.4). Growth was measured turbidimetrically at 600 nm using a Spectronic 20D spectrophotometer (Milton Roy, USA) until the optical density ceased to change.Lag phase Determination Following an.
