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?
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isolation and sequencing of peptide on MHC class I
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