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. 2021 Apr 9;20:100080. doi: 10.1016/j.mcpro.2021.100080

Fig. 6.

Fig. 6

Prosit-predicted MS/MS spectra for the identification of canonical and noncanonical peptides. A schematic overview of the application of sample-specific or multi-HLA library for DIA immunopeptidomics in combination with libraries generated from Prosit-predicted MS/MS spectra of canonical and noncanonical peptides (A). EG.Cscore distribution of all OD5P peptides and of the 39 TAAs detected in DIA analyzed with the BigLib library (DDA-to-DIA) and the predicted BigLib (DDA-to-Prosit-to-DIA) (B). Examples of extracted ion chromatograms for the peptide RYNADISTF detected in the DDA-to-DIA (C) and the DDA-to-Prosit-to-DIA (D) approaches. Summary of the identified HLA-I peptides form the novel ORF of the ABCB5 gene (E). Extracted ion chromatograms of the ABCB5 KYKDRTNILF peptide that have been detected with the DDA-to-DIA (F) and with the Prosit-to-DIA approach as doubly (G) and triply (H) charged ions. Extracted ion chromatograms of the ABCB5+ KDRTNILFI (I) and DRTNILFIF (J). Extracted ion chromatograms for precursors (MS1) and fragments (MS2) are aligned for each peptide and are shown across the technical replicates. The asterisk indicates a manual extraction of transitions that did not pass the q value threshold. DDA, data-dependent MS/MS acquisition; DIA, data-independent acquisition; HLA, human leukocyte antigen; MS/MS, tandem MS; TAAs, tumor-associated antigens.