Question: What is a good way to identify all MHC class I epitopes that are natural ligands? That is, I want to eliminate all epitopes that were, for example, synthesized to test MHC binding, and only look at peptides that are naturally presented and that were generated through natural antigen processing.
I think that limiting the query to peptides eluted from MHC will almost entirely eliminate artificial peptides, but also eliminates many natural peptides that were identified in different ways.
I've tried a number of approaches but almost all of them either limit the output to a fraction of true natural ligands, or else pull out sets of peptides that are clearly artificial variants (something like RPQASGVYM RPLAAGVYM RPLSSGVYM RPLSAGVYM RPASSGVYL RPQAGGVYL RPAASGVYL RPQASGYYL RSASSGYYL RSQASGVYL RSGSSGYYL
Is there some way of finding all the natural peptides, while excluding all non-natural peptides?
Answer: A search of all epitopes defined by MHC ligand elution will produce all naturally processed peptides. However, you can also obtain naturally processed peptides by doing a search of T cell assays with a positive outcome in which the epitope source protein or source organism was used as the antigen and the response was restricted by human MHC class I antigen. The assay will usually show that an epitope-specific T cell clone/line recognized the epitope processed from the intact protein or infected cell. However, since we curate the optimal or minimal epitope (that may be determined in a truncation analysis), the peptide that is actually presented (and not explicitly determined by the assay) may be longer than the epitope needed for recognition. The two types of queries can be done as follows.
Using the homepage search fields on the IEDB 3.0 site, select “Humans” in the “Host” box. In the “Assay” box, check only “MHC Ligand Elution.” For “MHC Restriction,” select “MHC Class I.” Click “Search.”
Alternatively, choose “T Cell Assays” for the assay, leaving the remaining parameters unchanged. Click “Search” and view the results listed in the “T Cell Assays” tab under “Assays.” The data which have the “Antigen Epitope Relation” of Source Antigen or Source Organism represent epitope-specific T cell clones/lines which recognized the epitope processed from the intact protein or infected cell.
These searches were designed to retrieve human class I binding epitopes but can be modified for other species. These types of searches retrieve about 200 epitopes so you can compare those defined by ligand elution versus a T cell assay. You can export the results to an Excel file.