I have a general question. In auto-immune muscle diseases, self-peptides are loaded onto MHC class I or class II molecules and presented to immune cells, eliciting an auto-immune reaction. I was wondering why it seems to be impossible to isolate and sequence the loaded peptide, and why it can't be identified by performing a peptide blast (=a bio-informatics approach). Why can't it be done when it is already known that the peptide is bound into the cleft of MHC molecules?
isolation and sequencing of peptide on MHC class I
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