Science Immunology

Supplementary Materials

The PDF file includes:

  • Methods
  • Fig. S1. De novo library hybrid workflow for identification of cis- and trans-spliced p-HLA.
  • Fig. S2. De novo sequencing algorithm evaluation for p-HLA identification.
  • Fig. S3. Motif analysis of 9– and 10–amino acid length peptides of p-HLA eluted from 17 different monoallelic cell lines.
  • Fig. S4. NetMHC binding prediction of linear and spliced peptides.
  • Fig. S5. Comparison of MS/MS spectra of synthetic peptides versus their corresponding eluted peptide.
  • Fig. S6. Relative quantification of spliced and linear p-HLA eluted from C1R-B*57:01 cells.
  • Fig. S7. Ratio of observed versus expected paired amino acids in spliced junctions.
  • Fig. S8. The effect of adding PTMs to the library search in the de novo library hybrid workflow on the identification of spliced peptides.
  • Table S1. Percentage of peptides (linear or spliced) matching to RNA-seq data.
  • Table S2. Pearson correlation information for comparison between synthetic peptides and corresponding eluted p-HLA from C1R-B*57:01 cells.
  • Table S3. Data collection and refinement statistics for p-B*57:01 crystal structures.
  • Legends for table S4 and table S5
  • References (3951)

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Other Supplementary Material for this manuscript includes the following:

  • Table S4 (Microsoft Excel format). Sequences of 8-mer to 12-mer of linear and spliced peptides for all 17 allelic datasets.
  • Table S5 (Microsoft Excel format). Raw data file.

Files in this Data Supplement: