Fig. 7: HLA class I ligandome of JY and Raji cells employing Thunder-DDA-PASEF, combining wild type (WT) and spike-transfected cells (S1 and S2).

HLAIps were enriched from three cultures of each WT cell line and two different cultures of each transfected cell line and each sample was analyzed in triplicate. a Size distribution of total peptides identified from JY and Raji cells. b Number of 8-13-mer peptides identified in each workflow and the proportion predicted as HLA binders (HLAIp, rank ≤ 2%) or non-binders (NB, rank > 2%) to the respective HLA types. c Charge distribution for the predicted HLAIps. d Supervised clustering (GibbsCluster-2.0 via MhcVizPipe) showing the peptide sequence motifs corresponding to the specific allele motifs for JY and Raji HLAIps, respectively. e Total number of predicted HLAIps identified in JY, Raji, and in total. f Protein groups covered by the HLAIps identified. g Distribution of the number of HLAIps per protein group represented as boxplots (center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range) (top) and histogram (bottom); y-axis cut-off at 12 for simplicity; thus, including 5569 and 6044 protein groups for JY and Raji, respectively; and excluding 0.77% and 1.43% of the protein groups (with 13–53 Binders/Protein) for JY and Raji, respectively. h Overlap of HLAI ligand peptides (left) and protein groups (right) between JY and Raji.