Fig. 2: Two complementary methods to assess the accuracy of NewAnce. | Nature Communications

Fig. 2: Two complementary methods to assess the accuracy of NewAnce.

From: Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

Fig. 2

a The percentages of predicted proteome-derived HLA-I binders in 0D5P were assessed with each MS search tool (MaxQuant and Comet at FDR 3%) and NewAnce. b Similar to a, the comparisons were performed for the different non-canonical antigen classes. c Hydrophobicity index calculations by SSRCalc for peptides identified in melanoma 0D5P. The observed mean retention time is plotted against the hydrophobicity indices for NewAnce-identified proteome-derived versus lncRNA-derived non-canonical peptides. d All peptides identified with each tool (MaxQuant, Comet, NewAnce) were analyzed based on their hydrophobicity indices. e Hydrophobicity index calculation for MaxQuant- or f Comet-identified 8- to 14-mer peptides, based on predicted HLA binding. Source data are provided as a Source Data file.

Back to article page