Extended Data Fig. 3: Supplement for Fig. 2.

(a) Cell cycle distribution and steady-state growth rate is unaffected by the different SILAC labels. Cell size mutants have doubling times similar to wild type (~90 min) when growing asynchronously in synthetic complete media with 2% glucose. (b) Growth behavior before and after G1 arrest in different SILAC media. The curved trajectory indicates a declining specific growth rate ~200 minutes after washout. Measurements of volume and optical density were collected in parallel on the same cultures. Y-axis is relative to 135 min, which is when ~95% of cells are in G1 phase. (c) The attainment of differentially sized cells was confirmed using a Coulter counter. Color gradients correspond to replicate cultures grown with light, medium, and heavy SILAC labels. (d) PC1 vs PC2 plotted for both orthogonal experimental systems. (e) Illustration of the protein slope calculation from relative changes in peptide concentration and cell size for both orthogonal experimental systems. See methods for a detailed explanation of the protein slope calculation. (f) To determine if protein abundance predicts size-scaling behavior, the individual proteins were grouped into abundance quartiles (depicted in the left plot). We only considered the ion intensity from the “small” cell SILAC channel in each of three G1 arrest time replicate experiments. The right plot depicts the distribution of mean slope values (G1 arrest time, n=3) for the proteins in each abundance quartile. Box region represents the median and interquartile range (IQR). Tails extend to 1.5x the IQR. (g) Correlation of protein slopes calculated from the two orthogonal experimental systems. Each slope value is the mean of three replicates for both systems. For the left panel, the mean volume measurements from the cell size mutants (C) were used to calculate the protein slope. For the right panel, the mean volume measurements from (C) were weighted by the relative DNA content shown in (A). Blue dots are x-binned data and error bars represent the 99% confidence interval. The “adjusted” plot is shown in Fig. 2. (h) Heatmap depicting the relative concentrations of ~4000 budding yeast proteins in the G1 arrest time experiment shown in (c) and (d). Proteins are ordered from top to bottom by descending protein slope value.