Extended Data Fig. 5: EpiScan systematic differences in amino acid representation of MHC-I ligands relative to mass spectrometry. | Nature Biotechnology

Extended Data Fig. 5: EpiScan systematic differences in amino acid representation of MHC-I ligands relative to mass spectrometry.

From: High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform

Extended Data Fig. 5

(a-d) The bar graphs on the left show the fold difference in amino acid representation across all positions and residues for the indicated allele. The bar graphs in the middle and left represent the fold enrichment of cysteine (middle) and proline (right) across each position of MHC-I peptide ligands, relative to the expected frequency based on the overall abundance of cysteine in the random 9-mer library (EpiScan data) or the human proteome (MS data). The MHC-I alleles assayed were (a) HLA-A*02:01, (b) HLA-A*03:01, (c) HLA-B*08:01 and (d) HLA-B*57:01. (e) Peptide tetramer exchange assays on L- versus V-ended 9mer peptides with HLA-A*02:01. Data are from three technical replicates represented as mean ± SEM and curves fit by four parameter nonlinear regression.

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