Technical CommentANTIGEN PRESENTATION

Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

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Science Immunology  16 Aug 2019:
Vol. 4, Issue 38, eaaw1622
DOI: 10.1126/sciimmunol.aaw1622

Figures

  • Fig. 1 Analysis of a subset of the data from Faridi et al. shows no evidence for a substantial number of posttranslationally spliced HLA-I peptides.

    (A) Predicted hydrophobicity index against the MS/MS scan numbers for nonspliced (blue) and spliced (red) peptide sequences identified by Faridi et al. for the HLA-A*01:01 sample. (B) Distribution of unique nonspliced (blue) and spliced (red) peptide sequences identified by Faridi et al. for the HLA-A*01:01 sample as a function of the PEAKS de novo score. The ratio of spliced peptides to all identified peptides at or above each score is shown with a line. (C) Percentage of the spliced peptide contribution to the ligandome found by our reanalysis of the HLA-A*01:01 and HLA-A*02:03 samples with the PEAKS software as a function of the error level. (D) Percentage of the spliced peptide contribution to the ligandome found by our reanalysis of the HLA-A*01:01 and HLA-B*07:02 samples with the Comet software as a function of the Comet error level.

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