How do I generate a list of all proteins from which epitopes have been identified for an organism of interest?
In the 'Search' interface on the left side of the IEDB home page, click the Organism Finder under the Epitope Source section to enter the source organism of interest. Select from list of common selections (click on the selection and hit Apply Selection).
If your organism is not in the list, type the genus/species under Find (Use NCBI taxonomy) and hit 'Search.' The Finder will locate your entry within the taxonomy tree and it will be highlighted in blue. Click on this and once the organism appears in the Current Selection box at the top, click Apply Selection.
At the bottom of the home page, hit 'Search' and this will generate a set of Search Result Summary tables.
Find Epitopes in the top table and click on the value in blue under 'positive' to display the list of all positive epitopes reported for the organism of interest plus their derivative protein (Source Antigen).
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link. A download of this data will provide a spreadsheet that can be used to analyze the data (filter on a column to display all of one data type).
Note that the source protein/antigen nomenclature links directly from NCBI. In some cases, the same protein may have slightly or drastically different names. Take care when attempting to compile like proteins.