Supporting Information

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Fig. 6. Native MHC is detected on the arrays. The numbers below each fluorescent image indicate the concentration (m g/ml) of MHC in the solution spotted onto the array. (A) HLA-A2 is detected with BB7.2, an antibody that recognizes properly folded A2 associated with light chain. Antibody binding was detected by using goat anti-mouse conjugated to Alexa Fluor 555. (B) HLA-DR1 is detected by using CY3-labeled LB3.1, an antibody that recognizes natively folded empty and peptide-loaded DR1. (C) Denatured HLA-DR1 is detected by using MEM-267, an antibody that recognizes empty or denatured but not peptide-loaded HLA-DR1. Antibody binding was detected by using goat anti-mouse conjugated to Alexa Fluor 555.

Fig. 7. Tetramer staining of AC25 and VA55 3.13 T cells. (Left) The CD4⁺ DR1-PP16-specific T cell clone AC25 binds to DR1-PP16 SA-phycoerythrin tetramers (solid line) but not DR1-Ha SA-phycoerythrin tetramers (dashed line). (Right) The CD8⁺ A2-74A-specific T cell line VA55 3.13 binds to A2-74A SA-allophycocyanin tetramers (solid line) but not A2-165 SA-allophycocyanin tetramers (dashed line).

Fig. 8. EBV-specific response from a short-term line can be detected by a mapping chip. (Upper) A short-term T cell line, raised from a patient with acute infectious mononucleosis, which is ≈13% specific for the EBV protein BZLF-1 by intracellular cytokine staining (data not shown), was analyzed by using a series of overlapping peptides covering the sequence of the protein, each in complex with HLA-DR1. Cells were incubated on a chip at a density of 500 specific cells per mm² or ≈8 × 10⁵ total cells per array. The fluorescence map obtained after a 6-h incubation with the polyclonal T cell line and detection of secreted IFN-g is shown. IFN-g was specifically detected most intensely in the spots with the previously identified EBV epitopes BZLF-1 [196-220] in the overlapping peptide series and the minimal peptide epitope QHY (BZLF-1 [198-210]). (Lower) A map of the chip.