ProteinLynx Global SERVER™ (PLGS) v2.5.3 (Waters, Altrincham, UK) was used to analyze the acquired ion mobility enhanced MSE spectra for protein identification as well as for the label-free relative protein quantification. Data processing and parameter setups were carried out as followed by [44]. The sequence database of the reference strain E. faecalis V583 (NCBI Reference Sequence: NC_004668.1) was used for database search. The false positive rate (FPR) was set to 4% with a randomized database, appended to the original one. The parameters for protein identification were made in such a way that a peptide was required to have at least one fragment ion match, a protein was required to have at least three fragment ion matches, and two peptide matches for identification. The peptides with 50% or more probability to be present in the mixture and detected with a score above 20, as calculated by the software were selected for proteomic analysis [45]. Data sets were normalized using the ‘internal standard-normalization’ function of PLGS and label-free quantitative analysis was performed by comparing the normalized peak area/intensity of identified peptides between the samples.