Extended Data Fig. 3: Additional filtering of MHC I IP, MS/MS-detected nuORF peptides.
From: Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
a-d. Impact of filtering on nuORF number, types and false discovery rates. a,b. Total number of nuORF peptides (y axis) identified pre-filtering (solid bars) and retained post-filtering (hashed bars) overall (a) and for different nuORF types (x axis, b). c,d. False discovery rate (y axis) for annotated (gray) and nuORF (pink) peptides across 92 HLA alleles pre- and post-filtering (hashed) overall (c) and for different ORF types (x axis, d). e. Criteria used to filter peptides across ORF types. f. Filtering thresholds across nuORF categories. Filter cutoffs (vertical red lines) across different peptide spectral match scoring features (x axis) for different ORF types (y axis). n = 191897 (annotated), 2050 (5’ uORF), 1619 (Out-of-frame), 1542 (5’ overlap uORF), 855 (lincRNA), 514 (ncRNA Processed Transcript), 497 (3’ dORF), 376 (ncRNA Retained Intron), 341 (Pseudogene), 311 (3’ overlap dORF), 299 (Antisense), 163 (Other). Median, with 25% and 75% (box range), and 1.5 IQR (whiskers) are shown. g. Filtering impact across categories. Percent of peptides (y axis) retained post-filtering across different ORF categories and overall (x axis).
