Table 1.
Composition of culture medium.
Figure 1.
Peptide content of bacterial lysates and medium.
Contourplots showing all polypeptides detected in the 5 lots of Pro-SymbioFlor and culture medium, displayed in three dimensions (x-axis: migration time in Minutes, y-axis: mass in logarithmic scale and Da, peak height (z-axis): signal intensity).
Figure 2.
Similarity of different lots based on peptide content.
Graphical representation of the presence of identical peptides. A) Shown is the absolute number of detected peptides in the 5 different Pro-Symbioflor lots and in the culture medium and B) peptide abundance based on relative ion counts of each lot.
Table 2.
Percentage of identical peptides present in a lot (expressed as the percentage of the total signal intensity in the lot) compared to the other lots.
Figure 3.
Expression profiles of sequenced bacterial peptides.
Contourplots of the sequenced polypeptides originating from E. coli and E. faecalis in the 5 lots of Pro-Symbioflor and culture medium. To improve visualization of the peptides in this contourplot, the abundance of the peptides was artificially amplified with a factor 3 in relation to Figure 1. The 9 signals shown in culture medium are false positive hits by sequencing via LC-MS/MS. Given that 390 bacterial peptides were identified we obtained an acceptable false discovery rate of below 5%.
Figure 4.
Ontology based characterization of the peptides identified by CE/MS.
Based on the Uniprot identifiers the involvement of a protein (defined by one or more CE/MS peptides) in a biological process, molecular function and cellular component was determined. The pie-charts show the percentage of proteins in each group. Only classes represented by 4 or more proteins are shown. Classes for which we identified less than 4 proteins are indicated and grouped as “others”. A) Classification for E. coli and B) classification for E. faecalis.
Figure 5.
Expression profiles of peptides originating from the medium.
Contourplots of the sequenced polypeptides originating from the culture medium only. To improve visualization of the peptides in this contourplot, the abundance of the peptides was artificially amplified with a factor 3 in relation to figure 1.