Fig. 4

Analysis of HLA-DR immunopeptidomes using two replicates and two different staring cell counts. 5e7_R1 is the first replicate with 5 × 10⁷ cells, while 5e7_R2 is the second replicate with the same initial cell counts. 1e8_R1 is the first replicate with 1 × 10⁸ cells while 1e8_R2 is the second replicate using the same cell count. A is the number of unique peptides observed in each immunopeptidome. B is a Custer map based on peptide overlap between each pair of experiments. C is a cluster map based on protein overlap between each pair of experiments. D is a multi-dimensional scaling (MDS) plot using immunopeptidomics coverage as a distance metric