Fig. 8.

HLA ligandome physicochemical properties. A, distribution of HLA peptides over the pI range as a function of the first dimension separation technique used. As can be seen, IEF, SCX, and RP-C18 do not discriminate among peptides based on their theoretical pI. The only exception is that peptides with low pI values are clearly underrepresented in the IEF process. This is caused by the actual pI in the pI 3–10 strips, which in fact appeared to be pI 4–10, as also independently checked with a pH indicator after IEF. B, distribution of HLA peptides over the hydrophobicity range depending on the first dimension separation technique used. As can be seen, IEF, SCX, and RP-C18 do not discriminate among peptides based on their hydrophobicity. The plots illustrate that our HLA ligandome is a good representation of the real HLA ligandome.