Figure 4: Analysis of DIA samples.

a–f, Similarity of DIA samples at the peptide level, analysed by PCA and MDS. Each sample contained 5000 cells, and triplicate samples were analysed for each of the 12 conditions. Data for the 1872 most abundant proteins, as defined by DDA analysis, were extracted from the DIA dataset for both PCA (a–c) and MDS (d–f) analyses. For PCA samples, percentage of the variance contributed by each principal component is indicated in the axis. a, d: Unnormalized. b, e: Global normalization. c, f: Fractional normalization (intensity for a given peptide divided by the sum of all peptide intensities). g, Distribution of fractional intensity values for peptides in each DIA sample. Box plot definitions are the same as in Fig. 2e,f.