Fig 1: Quantitative performance comparison across library-free DIA, biological-library DIA, biological-recombinant spectral library (biological-rPSL) DIA, and recombinant PSL (rPSL) DIA methods.a–c and (G–I) The split violin with overlaid box plots represent the distribution of log2 transformed protein intensities between two experiment groups, with statistical significance of the differences indicated by asterisks (Welch’s t-test; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001) in tissues and cell lysates. In the box plots, the center line represents the median, the box limits indicate the upper and lower quartiles. Proteins (a) S100A8, (b) ITGB1 and (c) CPQ were quantified in both noncancerous (N) and tumour tissues (T), with (n = 12) per group. Proteins (G) ITGAV, (H) PFN1 and (I) MUC1 were quantified in control (C) and treated (Tr) cells with (n = 15) per group. The numbers at the bottom indicate number of samples out of the total n per group, in which the protein was detected. d–f and (J–L) highlight proteins exclusively quantified in tumour tissues and either control or treated cells, with half violins with overlaid box plots representing the protein intensities and distribution of the data for proteins (d) IDO1, (e) ITGB6, and (f) MMP9 across tumour samples only and (J) KRT20, (K) IDO1, and (L) QPRT across either control or treated cells only.