Experimental design flowchart. a. Conditions of bacterial populations and type of proteins extracted by comparisons. b. Example of experimental design for the comparison of two strains. Protein samples to be compared were stained with either Cy3 or Cy5 fluorescent dyes. Three biological reps of each sample to be compared were combined in several gels to provide statistical power for comparisons. The pool of gels is normalized in order to compare spots from different gels. Spots were identified and localized across gels and their abundance compared statistically. A list of differentially expressed spots was analyzed and a subset of the total number of spots of interest were excised and sequenced by MS analysis.