Results Protein identification A total of 43 dominant protein spots in three gels (Figure 1, 2, and 3) were marked and analyzed after in gel digestion with trypsin using MLDI-TOF-MS and/or ESI-MS/MS [see Additional file 1 and 2]. This included 22 surface associated proteins, 10 cell envelope proteins, and 12 CMM specific differentially expressed proteins. The gels were analyzed quantitatively

to determine the relative abundance of spots and also the fold difference of expression in CMM specific proteins. Since our protein PRIMA-1MET mouse identification was based on ion search at NCBI nonredundant database in the taxonomic group of Bacteria (1348868 entries) or Firmicutes (258665 entries), chances of false positive hits are substantially reduced. Figure 1 A portion of representative 2DE gel showing spots quantitatively over-expressed (>2-fold difference) in CMM grown cells (B) of C. perfringens ATCC13124 as compared to those grown in TPYG medium (A). The spots identified are marked with arrows. Figure 2 2DE gel image of Coomassie-stained structure associated proteins of C. perfringens ATCC13124 from pH 3–10 (17 cm IPG strip). Spots this website identified are indicated with arrows. Figure 3 2DE gel image of Coomassie-stained surface proteins of C. perfringens ATCC13124 from pH

5–8 (17 cm IPG strip). Spots identified are indicated with arrows. We estimated the MW and pI values of the protein spots on the 2-DE gels and compared them with theoretical MW and pI values of corresponding proteins from C. perfringens ATCC13124. Most of the experimental values matched well with theoretical values, indicating unambiguous identification [see Additional file 1]. Any discrepancies between experimental out and theoretical masses might have been caused

by post-translational proteolytic processing and modification. The differences between the two pI values might be attributed to the cleavage of alkaline regions and phosphorylation of multiple residues. CMM induced changes in total cellular protein profile Figures 1A and 1B show a portion of 2-DE gels of total cellular protein from C. perfringens ATCC13124 cells, grown on TPYG and CMM, respectively. The analytical and biological replicates (2 each) of the corresponding 2-DE gels are shown in Additional file 3 and 4. Growth on CMM resulted in over expression of several proteins of which 11 most prominent ones have been identified. To identify the up-regulated proteins, the spots (numbered CMM2-CMM12 in Figure 1) were excised from the gel, digested with trypsin and subjected to MS/MS analysis as detailed in methods. Riboflavin biosynthesis protein, ornithine carbamoyltransferase, cystathionine Ricolinostat beta-lyase, and threonine dehydratase were the predominant proteins that exhibited 2.19 to 8.5 fold increase in the expression level in cells grown on CMM (see Additional file 1, Figure 1).