Study Data
| Project uploaded by: | Ganesh |
| Project ID: | IMP_100062 |
| Title: | The Quantitative Amino Acid Economy of Yeast Reveals Public versus Private Goods and Guides Syntrophic Community Design |
| Project Description: | Quantitative mass spectrometry based estimates of intra and extracellular amino acids in yeast Quantitative metabolic flux into amino acids using 15N ammonium acetate Quantitative mass spectrometry based amino acid amounts in wild-type and mutant yeast |
| Research Area: | Biological Sciences |
| Funding Source: | DBT Wellcome India Alliance (IA/S/21/2/505922), DBT-DFG Indo-German collaboration grant (IC-12025(22)/4/2023-ICD-DBT) Department of Biotechnology |
| Project Contributors: | Shabbir Ahmad, Ganesh Muthu, Sunil Laxman |
| Sr.No | Sample ID | Sample Name | Organism | Source | Sample Preparation Protocol | Sample Type | Experimental Condition | Time of treatment | Variant/Variety | Gender | Age | Replicates | Storage Conditions | Extraction Protocol | Number of files per sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11 | IMSM_104892 | Fig2_Int_2h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium over 2-hours. At specific time points, equal numbers of cells (~2x10^7) were rapidly harvested and immediately quenched by plunging them into an extraction buffer of 60% methanol. | Metabolites | Absolute concentrations of intracellular amino acids in the cells across the indicated times of growth | NA | NA | NA | NA | 3.0 | NA |
The quenched cells were extracted in 75% ethanol. The mixture was then dried down using a speed vacuum (rotatory evaporator). The dried metabolites were subsequently dissolved in 300 µl of mass spectrometry-grade water, and 10 µl of this sample was injected for targeted LC-MS/MS analysis. |
6.0 |
| 12 | IMSM_104893 | Fig2_Int_4h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium over 4-hour. At specific time points, equal numbers of cells (~2x10^7) were rapidly harvested and immediately quenched by plunging them into an extraction buffer of 60% methanol. | Metabolites | Absolute concentrations of intracellular amino acids in the cells across the indicated times of growth | NA | NA | NA | NA | 3.0 | NA |
The quenched cells were extracted in 75% ethanol. The mixture was then dried down using a speed vacuum (rotatory evaporator). The dried metabolites were subsequently dissolved in 300 µl of mass spectrometry-grade water, and 10 µl of this sample was injected for targeted LC-MS/MS analysis. |
6.0 |
| 13 | IMSM_104894 | Fig2_Int_8h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium over 8-hours. At specific time points, equal numbers of cells (~2x10^7) were rapidly harvested and immediately quenched by plunging them into an extraction buffer of 60% methanol. | Metabolites | Absolute concentrations of intracellular amino acids in the cells across the indicated times of growth | NA | NA | NA | NA | 3.0 | NA |
The quenched cells were extracted in 75% ethanol. The mixture was then dried down using a speed vacuum (rotatory evaporator). The dried metabolites were subsequently dissolved in 300 µl of mass spectrometry-grade water, and 10 µl of this sample was injected for targeted LC-MS/MS analysis. |
6.0 |
| 14 | IMSM_104895 | Fig2_Int_12h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium over 12-hours. At specific time points, equal numbers of cells (~2x10^7) were rapidly harvested and immediately quenched by plunging them into an extraction buffer of 60% methanol. | Metabolites | Absolute concentrations of intracellular amino acids in the cells across the indicated times of growth | NA | NA | NA | NA | 3.0 | NA |
The quenched cells were extracted in 75% ethanol. The mixture was then dried down using a speed vacuum (rotatory evaporator). The dried metabolites were subsequently dissolved in 300 µl of mass spectrometry-grade water, and 10 µl of this sample was injected for targeted LC-MS/MS analysis. |
6.0 |
| 15 | IMSM_104896 | Fig2_Int_24h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium over 24-hours. At specific time points, equal numbers of cells (~2x10^7) were rapidly harvested and immediately quenched by plunging them into an extraction buffer of 60% methanol. | Metabolites | Absolute concentrations of intracellular amino acids in the cells across the indicated times of growth | NA | NA | NA | NA | 3.0 | NA |
The quenched cells were extracted in 75% ethanol. The mixture was then dried down using a speed vacuum (rotatory evaporator). The dried metabolites were subsequently dissolved in 300 µl of mass spectrometry-grade water, and 10 µl of this sample was injected for targeted LC-MS/MS analysis. |
6.0 |
| 16 | IMSM_104897 | Fig4A_13C_Asp_4h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | Cells were grown in synthetic defined minimal medium for 4hrs. The cultures were pulsed with 1 mM 13C4-aspartate and incubated for 20 minutes. Following incubation, approximately 1.0 OD of cells were rapidly harvested and quenched. | Metabolites | 13C4-aspartate pulse-labeling of metabolites | NA | NA | NA | NA | 3.0 | NA |
Intracellular metabolites were extracted from the quenched cells using 75% ethanol, dried down, and derivatized. The incorporation of 13C4 into TCA intermediates and other metabolites was analyzed via targeted LC-MS/MS in positive polarity mode. |
6.0 |
| 17 | IMSM_104898 | Fig4A_13C_Asp_24h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | Cells were grown in synthetic defined minimal medium for 24hrs. The cultures were pulsed with 1 mM 13C4-aspartate and incubated for 20 minutes. Following incubation, approximately 1.0 OD of cells were rapidly harvested and quenched. | Metabolites | 13C4-aspartate pulse-labeling of metabolites | NA | NA | NA | NA | 3.0 | NA |
Intracellular metabolites were extracted from the quenched cells using 75% ethanol, dried down, and derivatized. The incorporation of 13C4 into TCA intermediates and other metabolites was analyzed via targeted LC-MS/MS in positive polarity mode. |
6.0 |
| 18 | IMSM_104899 | Fig4B_4h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium to the 4-hour time point. The cells were then pulsed with 1 mM deuterated alanine (d4-alanine) and incubated for exactly 5 minutes. Following this short incubation, the cells were immediately harvested and quenched in cold 60% methanol to arrest metabolism. | Metabolites | 13C4-aspartate pulse-labeling of metabolites | NA | NA | NA | NA | 3.0 | NA |
Intracellular metabolites were extracted from the quenched cell pellets using 75% ethanol. The metabolite extract was dried down using a speed vacuum and subsequently dissolved in mass spectrometry-grade water. The relative incorporation of the d4-label into pyruvate was then estimated using targeted LC-MS/MS. |
6.0 |
| 19 | IMSM_104900 | Fig4B_24h | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in synthetic defined minimal medium to the 24-hour time point. The cells were then pulsed with 1 mM deuterated alanine (d4-alanine) and incubated for exactly 5 minutes. Following this short incubation, the cells were immediately harvested and quenched in cold 60% methanol to arrest metabolism. | Metabolites | 13C4-aspartate pulse-labeling of metabolites | NA | NA | NA | NA | 3.0 | NA |
Intracellular metabolites were extracted from the quenched cell pellets using 75% ethanol. The metabolite extract was dried down using a speed vacuum and subsequently dissolved in mass spectrometry-grade water. The relative incorporation of the d4-label into pyruvate was then estimated using targeted LC-MS/MS. |
6.0 |
| 20 | IMSM_104901 | Fig5_ctrl12_H_Ex_35_mM | Saccharomyces cerevisiae | 4932 | Metabolites from S.cerevisiae cells grown in different conditions | S. cerevisiae cultures were grown in a minimal medium. At 12hours, 1 ml of culture was collected and centrifuged for 5 minutes at 7000 rpm at room temperature to pellet the cells. Between 250 to 500 µl of the cell-free supernatant was carefully collected for metabolite extraction. | Metabolites | Extracellular amino acids concentration from cells collected in standard minimal medium (SD, with ~35 mM ammonium sulfate) after 12 hr of growth | NA | NA | NA | NA | 3.0 | NA |
The cell-free supernatant was mixed with 75% ethanol to extract extracellular amino acids. The mixture was vortexed for 1.0 minute and placed on ice for a few minutes. Samples were then centrifuged at 16000 rpm for 12 minutes at room temperature. 750 µl of the resulting clear supernatant was transferred to new tubes and dried using a speed vacuum. Dried metabolites were stored at -80°C prior to LC-MS/MS analysis. |
6.0 |
| Sr.No | MS Exp ID | Sample Name/ID | Mass Spectrometer Type | MS Instrument Name | MS Instrument type | MS Ionization Method | Ion Mode/Scan Polarity | Data Transformation (Software/s Used) |
|---|---|---|---|---|---|---|---|---|
| 1 | IME_103334 | Fig1_2hour / IMSM_104830 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 2 | IME_103335 | Fig1_2hour / IMSM_104830 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 3 | IME_103336 | Fig1_2hour / IMSM_104830 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 4 | IME_103337 | Fig1_2hour / IMSM_104830 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 5 | IME_103338 | Fig1_2hour / IMSM_104830 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 6 | IME_103339 | Fig1_2hour / IMSM_104830 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 7 | IME_103340 | Fig1_4hour / IMSM_104883 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 8 | IME_103341 | Fig1_4hour / IMSM_104883 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 9 | IME_103342 | Fig1_4hour / IMSM_104883 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| 10 | IME_103343 | Fig1_4hour / IMSM_104883 | LCMS (Liquid Chromatography- Mass Spectrometry) | ABI Sciex 5500 QTrap | Triple quadrupole | Electrospray Ionization - ESI | Positive | MultiQuant |
| Sr.No | First name | Last name | Organization | Designation | |
|---|---|---|---|---|---|
| 1 | Sunil | Laxman | sunil@instem.res.in | BRIC inStem | principal_investigator |
| 2 | Ganesh | Muthu | ganeshm@instem.res.in | BRIC inStem | research_scholar |
| 3 | Shabbir | Ahmad | shabbirmd@instem.res.in | BRIC inStem | postdoctoral_researcher |
| Sr.No | ftprun ID | MS Exp ID | MS Data Files |
|---|---|---|---|
| 1 | IMR_103938 | IME_103334 | Fig1_2hour_A.wiff |
| 2 | IMR_103939 | IME_103335 | Fig1_2hour_A.wiff.scan |
| 3 | IMR_103940 | IME_103336 | Fig1_2hour_B.wiff |
| 4 | IMR_103941 | IME_103337 | Fig1_2hour_B.wiff.scan |
| 5 | IMR_103942 | IME_103338 | Fig1_2hour_C.wiff |
| 6 | IMR_103943 | IME_103339 | Fig1_2hour_C.wiff.scan |
| 7 | IMR_103944 | IME_103340 | Fig1_4hour_A.wiff |
| 8 | IMR_103945 | IME_103341 | Fig1_4hour_A.wiff.scan |
| 9 | IMR_103946 | IME_103342 | Fig1_4hour_B.wiff |
| 10 | IMR_103947 | IME_103343 | Fig1_4hour_B.wiff.scan |