An integrated approach to epitope analysis II: A system for proteomic-scale prediction of immunological characteristics

Table 5 Summary of analysis of Staphylococcus aureus strains

Output for *Staph aureus* COL	Metric
No. of Proteins in Staph aureus Col proteome	2615
No. of Surface Proteins (with Transmembrane Helices)	649
Number of Proteins with Signal Peptides	255
Sub-proteome analyzed (secreted and membrane affiliated)	835
Total B-cell epitopes > 4 aa long	14,089
Total B-cell epitopes overlapping or borders within 3 aa of a MHC-II high affinity binding peptide	4,527
Percentage of B cell epitopes overlapping or bordering within 3 aa of a MHC-II high affinity binding peptide	32.13%
Total MHC-II high affinity binding peptides	3,230
Output for 15 Strains of *Staph. aureus*	Metric
Proteomes of Staphylococcus aureus strains analyzed	15
Unique CEGs detected (all strains)	5646
CEGs conserved in 15/15 strains	572
Additional CEGs conserved in 14/15 strains	364
Median CEG (amino acids)	25
Minimum CEG (amino acids)	15
Maximum CEG (amino acids)	60
Proteins conserved in 15 strains with conserved CEGs (secreted and membrane affiliated)	140

Staphylococcus aureus COL is used as an example of the properties analyzed and observed within a strain. The data from 15 strains of Staph. aureus is summarized in the lower half of the Table. The strains are listed in Additional File 3, Table S3b. Epitopes conserved in 14 of 15 strains tend to have only a single amino acid change. Epitopes characterized as B cell epitopes are within the top 25% on a permuted population basis. Peptides characterized as a MHC-II high affinity binding peptide are n the top 25% of binding affinities on a permuted population basis as defined in Table 4. A CEG is a coincident epitope group comprising a stretch of amino acids where overlapping or adjacent B-cell epitopes as well as MHC high affinity binding peptides are predicted.