Fig. 2: β-cell immunopeptidome and chymotrypsin cleavage motifs.
a, b Relative representation of the top 40 source proteins in ECN90 β-cells (a) and human islets (b), ranked according to the number of peptides detected in the IFN-α-treated condition. The color scale is proportional to the percent peptides (conventional and PTM) identified for each protein out of the total peptides in a given condition. PTM peptides were counted as such only for PTMs defined as likely biological (they were otherwise counted as unmodified); cis-spliced peptides were excluded. Percent values and peptide numbers are listed on the right. Source proteins enriched in IFN-α-treated cells (log2 fold change, FC ≥ 1) or in basal condition (log2 FC ≤ − 1) are indicated. The complete heatmap is provided in Supplementary Fig. 2. HLA-I-bound peptides eluted from primary human islets are listed in Supplementary Data 5 and compared with those eluted from ECN90 β-cells in Supplementary Data 6. c, d Number (c) and percent (d) of HLA-I-eluted peptides across all 4 biological replicates carrying a chymotrypsin cleavage motif in basal and IFN-α-treated ECN90 β-cells. High-affinity cleavage motifs were defined as C-terminal Y, F, or W not followed by a P aa; low-affinity cleavage motifs were defined as C-terminal M or L not followed by a P aa. Additional analyses are reported in Supplementary Fig. 3 and Supplementary Data 7. ***p < 0.0001 by Fisher exact test.
