Fig. 5. Axes of proteome polarization are similar between untreated and LPS-treated macrophages and correlate with dextran uptake.

a, Untreated and LPS-treated macrophages were analyzed separately by PCA, and PSEA was performed on the corresponding PCs. PCA plots are color coded by the median abundance of proteins annotated with proton transport. b, The uptake of fluorescent dextran by LPS-treated macrophages was measured by flow cytometry, and the cells with the lowest and highest uptake were isolated for protein analysis. The volcano plot displays fold changes for differentially abundant proteins and the associated statistical significance. The corresponding analysis for untreated macrophages is displayed in Extended Data Fig. 10. c, LPS-stimulated macrophages were displayed in the space of their PCs and color coded by the median abundance of low-uptake or high-uptake proteins. The low-uptake proteins correlate with PC1 (Spearman r = 0.55, q ≤ 3 × 10⁻¹⁵), and the high-uptake proteins correlate with PC2 (Spearman r = 0.33, q ≤ 2 × 10⁻⁵).