After the 2nd dimension, and fixation in equilibration buffer [concentrated H3PO4 (VWR, 20621.295), 150 g/l ammoniumsulfate (Merck, 1.01217), 18% ethanol] for 30 min, the gel was stained with 1 ml 20.0 g/l Coomassie Brillant Blue 250 G (Merck, 1.15444). VRT752271 Relevant protein spots were excised from the gel. The gel pieces were then washed and digested with trypsin as described by Sørensen et al. (2009) [34]. Desalting, concentration, and loading

on MALDI target Gel-loader tips (Eppendorf) packed with Poros reverse phase 20 R2 (Applied Biosystems, 1-1128-02) was used as chromatographic columns for desalting and up-concentration of the digested protein sample prior to spectrometric analysis. The peptide digest was treated and loaded on MALDI target as described

by Sørensen et al. (2009) [34]. Identification of proteins by MALDI-TOF MS A MALDI-TOF-TOF instrument CYT387 order (4800 Proteomics analyzer, Applied Biosystems, Foster City, CA) was used to identify proteins. The MS/MS spectra were analysed using Data Explore v4.6 (Applied Biosystems). Mascot MS/MS Ions Search (Matrix Science, http://​www.​matrixscience.​com) was used to search for matching protein sequences within the NCBI database ( http://​www.​ncbi.​nlm.​nih.​gov/​). ifenprodil The taxonomy was restricted to C. jejuni. The mass tolerance was limited to 70 ppm for peptide mass fingerprinting and to 0.6 Da for peptide sequence data. Primer design and quantitative real time PCR (qRT-PCR) validation of proteome data To examine if there is any correlation between induced proteins during acid stress with changes in mRNA level, a qRT-PCR study on C. jejuni strain NCTC 11168

was performed. Besides the induced proteins, the expression of the ferric uptake regulator (fur) was also included since it has been shown that Fur regulates genes involved in iron transport, metabolisms and oxidative stress defence [18–20]. The following were selected as internal and reference genes: lpxC (encoding UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase) [24] and rpoA (encoding the α-subunit of the RNA polymerase) (Table  2). The Primer Express software version 2.0 (Applied Biosystems) was used to design primers. PCR primers (Table  2) were purchased from TAG Copenhagen (Copenhagen, Denmark).