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Quantitative Metabolomics of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Published: January 5th, 2021



1Department of Biology, Concordia University, 2Centre for Biological Applications of Mass Spectrometry, Concordia University

We present a protocol for the identification and quantitation of major classes of water-soluble metabolites in the yeast Saccharomyces cerevisiae. The described method is versatile, robust, and sensitive. It allows the separation of structural isomers and stereoisomeric forms of water-soluble metabolites from each other.

Metabolomics is a methodology used for the identification and quantification of many low-molecular-weight intermediates and products of metabolism within a cell, tissue, organ, biological fluid, or organism. Metabolomics traditionally focuses on water-soluble metabolites. The water-soluble metabolome is the final product of a complex cellular network that integrates various genomic, epigenomic, transcriptomic, proteomic, and environmental factors. Hence, the metabolomic analysis directly assesses the outcome of the action for all these factors in a plethora of biological processes within various organisms. One of these organisms is the budding yeast Saccharomyces cerevisiae, a unicellular eukaryote with the fully sequenced genome. Because S. cerevisiae is amenable to comprehensive molecular analyses, it is used as a model for dissecting mechanisms underlying many biological processes within the eukaryotic cell. A versatile analytical method for the robust, sensitive, and accurate quantitative assessment of the water-soluble metabolome would provide the essential methodology for dissecting these mechanisms. Here we present a protocol for the optimized conditions of metabolic activity quenching in and water-soluble metabolite extraction from S. cerevisiae cells. The protocol also describes the use of liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) for the quantitative analysis of the extracted water-soluble metabolites. The LC-MS/MS method of non-targeted metabolomics described here is versatile and robust. It enables the identification and quantification of more than 370 water-soluble metabolites with diverse structural, physical, and chemical properties, including different structural isomers and stereoisomeric forms of these metabolites. These metabolites include various energy carrier molecules, nucleotides, amino acids, monosaccharides, intermediates of glycolysis, and tricarboxylic cycle intermediates. The LC-MS/MS method of non-targeted metabolomics is sensitive and allows the identification and quantitation of some water-soluble metabolites at concentrations as low as 0.05 pmol/µL. The method has been successfully used for assessing water-soluble metabolomes of wild-type and mutant yeast cells cultured under different conditions.

Water-soluble metabolites are low-molecular-weight intermediates and products of metabolism that contribute to essential cellular processes. These evolutionarily conserved processes include the conversion of nutrients into usable energy, synthesis of macromolecules, cellular growth and signaling, cell cycle control, regulation of gene expression, stress response, post-translational regulation of metabolism, maintenance of mitochondrial functionality, vesicular cellular trafficking, autophagy, cellular aging, and regulated cell death1,2,3.

Many of t....

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1. Making and sterilizing a medium for growing yeast

  1. Make 180 mL of a complete yeast extract with bactopeptone (YP) medium. The complete YP medium contains 1% (w/v) yeast extract and 2% (w/v) bactopeptone.
  2. Distribute 180 mL of the YP medium equally into four 250 mL Erlenmeyer flasks. Each of these flasks contains 45 mL of the YP medium.
  3. Sterilize the flasks with YP medium by autoclaving at 15 psi/121 °C for 45 min.

2. Wild-type yeast strain


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To improve a quantitative assessment of water-soluble metabolites within a yeast cell, we optimized the conditions of cell quenching for metabolite detection. Cell quenching for this purpose involves a rapid arrest of all enzymatic reactions within a cell31,33,37,38. Such an arrest of cellular metabolic activity is an essential step of any method for the quantit.......

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To successfully use the protocol described here, follow the preventive measures described below. Chloroform and methanol extract various substances from laboratory plasticware. Therefore, handle them with caution. Avoid the use of plastics in steps that involve contact with any of these two organic solvents. Use borosilicate glass pipettes for these steps. Rise these pipettes with chloroform and methanol before use. Use only micropipette tips and tubes made of polypropylene that is resistant to organic solvents. During s.......

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We are grateful to current and former members of the Titorenko laboratory for discussions. We acknowledge the Centre for Biological Applications of Mass Spectrometry, the Centre for Structural and Functional Genomics, and the Centre for Microscopy and Cellular Imaging (all at Concordia University) for outstanding services. This study was supported by grants from the Natural Sciences and Engineering Research Council (NSERC) of Canada (RGPIN 2014-04482 and CRDPJ 515900 - 17). K.M. was supported by the Concordia University Armand C. Archambault Fellowship and the Concordia University Dean of Arts and Sciences Award of Excellence.


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Name Company Catalog Number Comments
Acetonitrile Fisher Scientific A9554
Ammonium acetate Fisher Scientific A11450
Ammonium bicarbonate Sigma 9830
Bactopeptone Fisher Scientific BP1420-2
Chloroform Fisher Scientific C297-4
Glucose Fisher Scientific D16-10
L-histidine Sigma H8125
L-leucine Sigma L8912
L-lysine Sigma L5501
Methanol Fisher Scientific A4564
Methanol Fisher Scientific A4564
Propidium iodide Thermo Scientific R37108
Uracil Sigma U0750
Yeast extract Fisher Scientific BP1422-2
Hardware equipment
500 ml centrifuge bottles Beckman 355664
Agilent 1100 series LC system Agilent Technologies G1312A
Beckman Coulter Centrifuge Beckman 6254249
Beckman Coulter Centrifuge Rotor Beckman JA-10
Centra CL2 clinical centrifuge Thermo Scientific 004260F
Digital thermometer Omega HH509
Foam Tube Holder Kit with Retainer Thermo Scientific 02-215-388
SeQuant ZIC-pHILIC zwitterionic-phase column (5µm polymer 150 x 2.1 mm) Sigma Milipore 150460
Thermo Orbitrap Velos MS Fisher Scientific ETD-10600
Ultrasonic sonicator Fisher Scientific 15337416
Vortex Fisher Scientific 2215365
ZORBAX Bonus-RP, 80Å, 2.1 x 150 mm, 5 µm Agilent Technologies 883725-901
Laboratory materials
2-mL Glass sample vials with Teflon lined caps Fisher Scientific 60180A-SV9-1P
Glass beads (acid-washed, 425-600 μm) Sigma-Aldrich G8772
Hemacytometer Fisher Scientific 267110
15-mL High-speed glass centrifuge tubes with Teflon lined caps PYREX 05-550
Compound Discoverer 3.1 Fisher Scientific V3.1
Yeast strain
Yeast strain BY4742 Dharmacon YSC1049

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