Fig. 3: A full-factorial proteomic design reveals prominence of synergistic effects on differential protein abundance.

a Experimental design of WT, hxk1-1 and hxk1-2 given all 12 combinations of +/- Fe and +/Glc (n = 3–4; see Supplementary Fig. 6a for culture photographs). Proteomics was conducted on treatment replicates from the same experimental batch. b Number of gene models (y-axis, left) and % of gene models (right) with TMT-labeled peptides. Bar colors indicate genes ≥2 unique representative peptides and detected in all conditions (blue), genes with ≥2 unique representative peptides but are undetected in some conditions (light blue), genes with peptides with just one detected peptide (tan), and genes with no detected peptides (n.d., gray). c Principal components analysis of peptides detected in all treatments. d Full linear model tested against proteins as a function of Fe, Glc, and strain (WT vs. hxk1-2) (see Methods). e Results of a data-filtering pipeline to categorize proteins by the variables that have significant impacts on their proteome (Supplementary Data 3). Height of each heatmap corresponds to the number of proteins (y-axis) associated with significant linear model terms (x-axis). Source data are provided in the Source Data File.