Supplement
Supporting Figures & Tables Supplementary Figure S1. Comparison of metabolite yields as a function of the cell harvesting method and composition of the extraction solvent. Supplementary Figure S2. Variant of Figure 1: Clustered heat map of yeast metabolome variation as a function of growth rate and identity of the limiting nutrient. Supplementary Figure S3. Double-reciprocal plot of dilution rate (equivalent to specific growth rate at steady state) as a function of the residual substrate concentration. Supplementary Figure S4. Variant of Figure 4: Growth-limiting and overflow metabolites, in this case for the auxotrophic limitations. Supplementary Figure S5. Variant of Figure 4: Growth-limiting and overflow metabolites, identified here using data from the natural limitations only (i.e., excluding data from uracil and leucine limitation). Supplementary Figure S6. Specific glucose consumption and ethanol production rates as a function of dilution rate (equivalent to specific growth rate at steady state) in glucose-limited chemostats. Supplementary Figure S7. Culture characteristics in nutrient-limited chemostats. Supplementary Table S4. Media composition. Other Supporting Tables provided as separate Excel documents. Supplementary Table S1. Metabolites analyzed and their associated mass spectrometry parameters. In the Excel workbook, the tab "Compounds_included" provides ionization mode, parent ion mass, product ion mass, collision energy, and chromatography retention time for all compounds that were successfully measured. Compounds that were measured unsuccessfully (e.g., did not yield acceptable signal-to-noise from biological samples) are listed separately under the tab "Compounds_excluded." Supplementary Table S2. Comparison of metabolite yields as a function of the cell harvesting method and composition of the extraction solvent. A two-by-two comparison of cell harvesting method (“MeOH quench” versus “filters”) and extraction solvent composition (“MeOH” versus “ACN”) was performed, using yeast growing exponentially in glucose minimal media (N = 3 independent cultures for each condition). In the Excel workbook, raw data (ion counts) are provided in the first tab, and specific head-to-head comparisons in the subsequent tabs (e.g., the second tab, entitled “Filters-Extract MeOH vs ACN” is a head-to-head comparison, for cells collected by the filtration approach, of the two extraction solvent compositions). The term “MeOH quench” refers to quenching cells in methanol and then isolating the quenched cells by centrifugation; the term “filters” refers to isolating the cells directly by vacuum filtration. The solvent composition “MeOH” refers to 80:20 methanol:water; “ACN” refers to 40:40:20 acetonitrile:methanol:water. Supplementary Table S3. Chemostat properties: dilution rate, klett, cell count, cell volume, and extracellular nutrient concentrations.

Supplement

Supporting Figures & Tables

Supplementary Figure S1. Comparison of metabolite yields as a function of the cell harvesting method and composition of the extraction solvent.

Supplementary Figure S2. Variant of Figure 1: Clustered heat map of yeast metabolome variation as a function of growth rate and identity of the limiting nutrient.

Supplementary Figure S3. Double-reciprocal plot of dilution rate (equivalent to specific growth rate at steady state) as a function of the residual substrate concentration.

Supplementary Figure S4. Variant of Figure 4: Growth-limiting and overflow metabolites, in this case for the auxotrophic limitations.

Supplementary Figure S5. Variant of Figure 4: Growth-limiting and overflow metabolites, identified here using data from the natural limitations only (i.e., excluding data from uracil and leucine limitation).

Supplementary Figure S6. Specific glucose consumption and ethanol production rates as a function of dilution rate (equivalent to specific growth rate at steady state) in glucose-limited chemostats.

Supplementary Figure S7. Culture characteristics in nutrient-limited chemostats.

Supplementary Table S4. Media composition.

Other Supporting Tables provided as separate Excel documents.

Supplementary Table S1. Metabolites analyzed and their associated mass spectrometry parameters. In the Excel workbook, the tab "Compounds_included" provides ionization mode, parent ion mass, product ion mass, collision energy, and chromatography retention time for all compounds that were successfully measured. Compounds that were measured unsuccessfully (e.g., did not yield acceptable signal-to-noise from biological samples) are listed separately under the tab "Compounds_excluded."

Supplementary Table S2. Comparison of metabolite yields as a function of the cell harvesting method and composition of the extraction solvent. A two-by-two comparison of cell harvesting method (“MeOH quench” versus “filters”) and extraction solvent composition (“MeOH” versus “ACN”) was performed, using yeast growing exponentially in glucose minimal media (N = 3 independent cultures for each condition). In the Excel workbook, raw data (ion counts) are provided in the first tab, and specific head-to-head comparisons in the subsequent tabs (e.g., the second tab, entitled “Filters-Extract MeOH vs ACN” is a head-to-head comparison, for cells collected by the filtration approach, of the two extraction solvent compositions). The term “MeOH quench” refers to quenching cells in methanol and then isolating the quenched cells by centrifugation; the term “filters” refers to isolating the cells directly by vacuum filtration. The solvent composition “MeOH” refers to 80:20 methanol:water; “ACN” refers to 40:40:20 acetonitrile:methanol:water.

Supplementary Table S3. Chemostat properties: dilution rate, klett, cell count, cell volume, and extracellular nutrient concentrations.