I want determine epitopes that presented by tumor cells. epitopes that we don't previous information about them but we know they are different from natural or self epitopes.
You can use a number of epitope predictions tools if you know the antigens. I suggest the one available at http://imed.med.ucm.es/Tools/rankpep.html. If you do not have antigens to target for epitpe prediction I will apply a protemics approach to identify peptide ligands eluted from MHC molecules expressed in the cell surface of the tumor.
I want determine which epitopes are presented in tumor cells, thus epitope prediction don't resolve my problem. How I can elute peptides that presented by MHC tumor cell molecules? peptides that have oncogenic viral source.