- Introduction to metabolomics
- Introduction to mass spectrometry data
- Handling and processing metabolomics data in R
- Annotating metabolomics data
CSAMA 2026
Content
Metabolite? Metabolism?
- Key metabolic pathway common to all cells.
- Creates energy by converting glucose to pyruvate.
Metabolite? Metabolism?
- Metabolites: intermediates and products of cellular processes.
Metabolite? Metabolism?
- Metabolites: intermediates and products of cellular processes.
- Why would we want to measure metabolites?
Biological molecules
- Gene
- Transcript
- Protein
- Metabolite
Biological molecules
- Gene
- Transcript
- Protein
- Metabolite
SLC22A5
Biological molecules
- Gene
- Transcript
- Protein
- Metabolite
SLC22A5
Where is it expressed? What’s the abundance? What can affect the abundance?
Biological molecules
- Gene
- Transcript
- Protein
- Metabolite
SLC22A5
Where is it expressed? What’s the abundance? What can affect the abundance?
Biological molecules
- Gene
- Transcript
- Protein
- Metabolite
SLC22A5
SLC22A5 is a transmembrane transporter.
Biological molecules
- Gene
- Transcript
- Protein
- Metabolite
SLC22A5
Quantify metabolites to study SLC22A5’s function and activity.
Metabolome
Set of all metabolites in a system at a time
ℹ️ Studying the metabolome can provide insights into the metabolic state of an organism.
Properties of the metabolome:
- Metabolome influenced by genetic and environmental factors.
- Metabolome is highly dynamic.
Metabolomics?
- Large-scale study of small molecules in a system.
What are we measuring? … depends on context:
- life sciences: metabolites, lipids, …
- plant and food sciences: metabolites, polyphenoles, …
- exposomics: chemicals, pharmaceuticals, …
- environmental sciences: chemicals, metals, …
How are we measuring these small compounds?
- Nuclear Magnetic Resonance (NMR): highly specific, not very sensitive.
- Mass Spectrometry (MS): less specific, highly sensitive, high throughput.
Metabolomics in life sciences
Where can we measure small compounds/metabolites?
- Blood (serum):
- insights into general physiological state of organism.
- mostly liver, kidney, intestine (~microbiome) metabolism.
- Biopsies, tissue slices.
- Urine, stool samples, (food, dust): external influence.
- Cell culture experiments:
- supernatant: what did cells consume/produce?
- cell extracts: insights into mitochondrial metabolism.
How can we measure metabolites?
Properties of metabolites:
- Metabolites are small, electrically uncharged molecules.
How can we measure metabolites?
Properties of metabolites:
Metabolites are small, electrically uncharged molecules.
Can be detected using Mass Spectrometry without e.g. digesting or cleaving them.
How can we measure metabolites?
Properties of metabolites:
Metabolites are small, electrically uncharged molecules.
Can be detected using Mass Spectrometry without e.g. digesting or cleaving them.
Need to create ions to allow measurement by Mass Spectrometry.
How can we measure metabolites?
Properties of metabolites:
Metabolites are small, electrically uncharged molecules.
Can be detected using Mass Spectrometry without e.g. digesting or cleaving them.
Need to create ions to allow measurement by Mass Spectrometry.
Two main setups to measure metabolites:
How can we measure metabolites?
Properties of metabolites:
Metabolites are small, electrically uncharged molecules.
Can be detected using Mass Spectrometry without e.g. digesting or cleaving them.
Need to create ions to allow measurement by Mass Spectrometry.
Two main setups to measure metabolites:
- targeted metabolomics: quantitative measurement of selected metabolites.
How can we measure metabolites?
Properties of metabolites:
Metabolites are small, electrically uncharged molecules.
Can be detected using Mass Spectrometry without e.g. digesting or cleaving them.
Need to create ions to allow measurement by Mass Spectrometry.
Two main setups to measure metabolites:
targeted metabolomics: quantitative measurement of selected metabolites.
untargeted metabolomics: semi-quantitative measurement of all metabolites (detectable with the setup) in a sample.
Mass Spectrometry (MS)
Mass Spectrometry (MS)
mass spectrum