Fig. 3: Empirically corrected libraries improve peptide and missense variant detection rates.
From: Generating high quality libraries for DIA MS with empirically corrected peptide predictions
a The average number of yeast (N = 4) and HeLa (N = 3) peptides in single-injection DIA detected using library-free searching with Pecan, searching with a combined SCX fractionated and high-pH reverse-phase fractionated DDA spectrum library, or searching with a predicted spectrum library, before or after empirical correction with the chromatogram library method. Match-between-runs was not enabled for any search strategy so that replicates are independent measurements demonstrating the technical variability for each approach. b The number of HeLa missense variants detected in the total DIA library, single-injection DIA (N = 3), or a meta-analysis of 40 published DDA experiments27, each filtered to a 1% peptide/protein FDR. c Retention time predictions differ somewhat from empirical data from GPF-DIA for homologous peptides: YFYTSMSRPGR from HLA-A (F33Y,V36M), YFYTAMSRPGR from HLA-B, and YFYTAVSRPGR from HLA-C. d Relative +1H y-type and b-type fragmentation patterns above 200m/z for the same peptides are shown as butterfly plots with empirical intensities (blue) above predicted intensities (red). e All three peptides are in the HLA peptide binding/presentation region, as indicated by YFYTSMSRPGR (red) in HLA-A (blue) relative to an antigenic peptide (green) in PDB structure 1AO7. Source data are provided as a Source Data file.
