Fig. 4: IceR enables label-free DDA proteomics with DIA performance.
From: IceR improves proteome coverage and data completeness in global and single-cell proteomics
a Fraction of missing values on peptide-level in MaxQuant (grey), DIA (red) and IceR (orange) results for a publicly available data set of 12 spiked proteins into a constant complex background at 8 concentrations (n = 3). b Receiver operating characteristic (ROC) over all pairwise differential expression analyses on protein-level in MaxQuant (grey) and on peptide-level in IceR (orange) and DIA (red) data. Corresponding areas under the ROC (AUROC) are indicated. Dashed vertical line and respective dots represent observed sensitivity at 95% specificity per method. c Cumulative true and false-positive counts over all (28) pairwise DE analyses for MaxQuant (grey), DIA (dark grey) and IceR (orange). Percentages within bars indicate corresponding true positive and false-positive rates. d Fraction of missing values on peptide-level in MaxQuant (grey), DIA (red) and IceR (orange) results for a data set of an E. coli lysate spiked into a constant background at 6 concentrations (n = 3). e Receiver operating characteristic (ROC) over all pairwise differential expression analyses protein-level in MaxQuant (grey) and on peptide-level in IceR (orange) and DIA (red) data. Corresponding areas under the ROC (AUROC) are indicated. Dashed vertical line and respective dots represent observed sensitivity at 95% specificity per method. f Cumulative true and false positives over all (15) pairwise DE analyses for MaxQuant (grey), DIA (dark grey) and IceR (orange). Percentages within bars indicate corresponding true positive and false-positive rates.
