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

Table 2 Characteristics of the surface and secreted proteome of Staphylococcus aureus COL

Total Proteins	with TMH	with TMH and SP	Secreted
2,615	649	69	186
MHC-I	9-mers	Avg ln(ic50) of group	Total
inside	48,222	9.3	238,320
membrane	51,643	8.4
outside	138,455	9.3
MHC-II	15-mers	Avg ln(ic50) of group	Total
inside	40,422	6.4	210,466
membrane	38,698	4.6
outside	131,346	6.6

Total proteins and protein topology and MHC binding characteristics to different protein domains of Staph aureus COL surface and secreted proteins. Peptides within transmembrane domains to have a significantly higher binding affinity to both MHC-I and MHC-II. The ln(ic50) means shown are for peptides in the dataset for which both their N-terminus and C-terminus in the predicted transmembrane domain. All means were different from one another by ANOVA p < .0001. TMH = transmembrane helix; SP = signal peptide.