A peptide-based vaccine must be bound and presented by major histocompatibility complex class I molecules to elicit a CD8(+) T-cell response. Because class I HLA molecules are highly polymorphic, it has yet to be established how well a vaccine peptide that stimulates one individual's CD8(+) cytotoxic T lymphocytes will be presented by a second individual's different class I molecules. Therefore, to facilitate precise comparisons of class I peptide binding overlaps, we uniquely combined hollow-fiber bioreactors and mass spectrometry to assign precise peptide binding signatures to individual class I HLA molecules. In applying this strategy to HLA-B*1501, we isolated milligram quantities of B*1501-bound peptides and mapped them using mass spectrometry. Repeated analyses consistently assign the same peptide binding signature to B*1501; the degree of peptide binding overlap between any two class I molecules can thus be determined through comparison of their peptide signatures.