Fig. 2.

A, Experimental design for isolation and identification of HLA-DR-bound peptides. HLA-DR bound peptides from two independent preparations of DR⁺Ii⁻ MCF10 vaccine cells and from DR⁺Ii⁺ MCF10 transfectants were purified using affinity chromatography, sequenced using LC-MS/MS, assigned to proteins using SEQUEST, and analyzed using ANN. Peptides with the highest predicted HLA-DR7 binding affinity were selected for further study. B, HLA-DR⁺ MCF10 vaccines and Ii⁺ transfectants present distinct and partially overlapping repertoires of peptides. Values are the number of peptides that are unique or shared between DR⁺Ii⁻ MCF10 vaccine cells and DR⁺Ii⁺ MCF10 transfectants. C, Peptides isolated from HLA-DR7-transfected and CIITA-transfected Ii⁻ and Ii⁺ MCF10 cells are similar in length. D, Peptides isolated from HLA-DR7-transfected Ii⁻ and Ii⁺ MCF10 cells contain nested sequences. Data are from two independent analysis of each preparation of cells.