2019
DOI: 10.1126/sciimmunol.aaw8457
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Response to Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

Abstract: This is our response to the Technical Comment by Rolfset al.where we point out errors in their reanalysis of our data.

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Cited by 23 publications
(17 citation statements)
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“…Methionine oxidation, deamidation (NQ), N-terminal acetylation and phosphorylation (STY) were set as variable PTMs. Although spliced peptides have been identified in cellular proteomes and immunopeptidomes ( Faridi et al., 2019 ; Liepe et al., 2016 , 2019 ; Mishto and Liepe 2017 ), they were not included in the analysis. Results were filtered for 1% FDR based on peptide spectrum matches (PSMs) using a target decoy approach with a randomized decoy database ( Table S2 ).…”
Section: Methodsmentioning
confidence: 99%
“…Methionine oxidation, deamidation (NQ), N-terminal acetylation and phosphorylation (STY) were set as variable PTMs. Although spliced peptides have been identified in cellular proteomes and immunopeptidomes ( Faridi et al., 2019 ; Liepe et al., 2016 , 2019 ; Mishto and Liepe 2017 ), they were not included in the analysis. Results were filtered for 1% FDR based on peptide spectrum matches (PSMs) using a target decoy approach with a randomized decoy database ( Table S2 ).…”
Section: Methodsmentioning
confidence: 99%
“…In addition to mRNA splicing, proteasomal splicing might also be a source of TSAs 93,94 , although their formation and frequency of occurrence currently remains controversial [95][96][97][98] . Basic characterizations of antigenic peptides produced by peptide splicing in the proteasome have already been conducted using cDNA-based approaches 51,99 .…”
Section: Wwwnaturecom/nrclinoncmentioning
confidence: 99%
“…Putative spliced sequences reported by Liepe and colleagues [12,13] and us [7] have attracted considerable criticism, with others preferring to describe these species as unanticipated or alternative reading frames, highly chemically post‐translationally modified species or no explanation given at all [18,20,34,37–39]. One of the debates focuses upon other possible explanations for proposed spliced peptides.…”
Section: The Debate On the Existence Prevalence And Importance Of Spliced Peptidesmentioning
confidence: 99%