Figure 2. The quantitative protein mass spectrometry.

• A Observed values versus real values for ratios of ¹⁵N ribosomal proteins to ¹⁴N ribosomal proteins. Black dots are the mean values, with error bars representing the range of the values for all ribosomal proteins. The dashed line represents perfect agreement between the observed values and real values.
• B Observed values versus real values for ratios of ¹⁵N proteins to ¹⁴N proteins from whole-cell lysates. Black dots are the median values for more than 600 proteins. The error bar for each median value indicates the quartiles. The dashed line represents perfect agreement between the observed values and real values. Additional characterizations are shown in Supplementary Figs S3 and S4.
• C The expression matrix and clustering results. The matrix is composed of 1,053 proteins (rows) and 14 conditions (columns); see Supplementary Table S2. The first five columns are for C-limitation, the next five columns for A-limitation, and the last four columns for R-limitation. For each mode of growth limitation, the growth rate increases from left to right. The matrix is log2-transformed, with expression values at the standard condition as zero (see Materials and Methods), represented as black color. Red color indicates negative values, green color positive values, and gray color missing entries. A dendrogram generated by clustering analysis is shown on the left of the expression matrix (see Materials and Methods), with the five major clusters shown on the right side of the matrix. The data are estimated to cover ˜80% of the proteome; see Supplementary Fig S5.