Response to 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, eaaw8457
DOI: 10.1126/sciimmunol.aaw8457


  • Fig. 1 Selected charts associated with our response to Rolfs et al.’s reanalysis of our data.

    (A) Venn diagram representation of the overlap (indicated in each segment) of scan numbers across four fractions from the same sample. This highlights the potential for incorrect sequence assignments if a fraction number is not associated with each scan number. (B) Correlation between scan number and HI in the complete HLA-A*01:01 dataset. As shown in this figure, there is not a clear correlation between scan number and HI for linear or spliced peptides, and (C) the performance of HI prediction is variable depending on the HLA allomorph selected, with HLA-B*57:01 peptides showing a higher correlation. (D) Ratio of the number of linear and spliced peptides across different PEAKS scores within the 1% FDR cutoff. The subset chosen by Rolfs et al. is therefore biased toward linear peptides, and it is not representative of the overall distribution. (E) Effect of applying two different FDR calculation methods to the distribution of linear and spliced peptides from the HLA-A*01:01 and HLA-A*02:03 datasets. In method 1, the −10logP PEAKS score, corresponding to a 1% FDR cutoff from the first database search (i.e., against the conventional human proteome database), was applied to the output from the second database search (i.e., containing the conventional human proteome database and spliced peptides). Method 2 is the original method we used in (1).

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