Fig. 3: Effect of conflict assay on the peptide quantitation in Spectronaut analysis.
From: DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
a DIALib-QC assessment reports the number of DIA conflict assays in both libraries. b Comparison of average peak quantities (PQ) of peptide ion GLQTSQDAR.2 between the two libraries (highlighted in orange and green) for the most intense six fragment ions observed in all five DIA/SWATH replicates. c, d Quantitative MS2 analysis based on extracted ion chromatograms (XICs) of peptide GLQTSQDAR.2 with both libraries eluted at the same RT. e, f MS2 spectrum of peptide GLQTSQDAR.2 in both libraries. p++ denotes un-fragmented precursor ion with [M + 2H]2+ charge. g, h Zoomed MS2 spectrum highlighting the overlap of un-fragmented precursor isotopic envelope (M, M + 1, M + 2) with y4+ ion in conflict library. i, j Correlation plots between measured (black) and predicted (red) relative fragment y4+ ion intensity showed higher similarity in the good than in the conflict library.
