FIG 1.

Schematic representation of an immunopeptidomic workflow to identify pathogen-derived peptides in infected cells. Infected cells and mock-infected control cells are separately lysed, lysate is subjected to immunoprecipitation with an MHC-specific antibody, and peptides are eluted in acid and separated from MHC proteins using size filtration or solid-phase extraction. Finally, the eluted peptides are analyzed by LC-MS/MS, and mass spectra are searched against a database that includes the proteomes of both the pathogen and the host to identify MHC-associated peptides. Putative pathogen-derived peptides identified in the samples from infected cells can be looked for in the data from the mock-infected control to identify and eliminate some false positives.