CSAMA 2024

Content

  • Introduction to metabolomics
  • Introduction to (LC-)MS
  • Handling and processing metabolomics data in R
  • Lab overview: Main preprocessing steps
  • Annotation of metabolomics data

Metabolite? Metabolism?

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.

Metabolomics?

  • Large-scale study of small molecules in a system.

What are we measuring? … depends on context:

  • (human) metabolomics: metabolites, lipids, …
  • plant and food metabolomics: 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.

(Human) Metabolomics

Where can we measure small compounds/metabolites?

  • Blood (serum):
    • insights into general physiological state of organism.
    • venous blood/capillary (arterial) blood.
  • Urine, stool samples, (food, dust): external influence.
  • Cell culture experiments:
    • supernatant: what did cells consume/produce?
    • cell extracts: insights into mitochondrial metabolism.

Metabolomics

Putting metabolomics into context:

  • Genome: what can happen.
  • Transcriptome: what appears to be happening.
  • Proteome: what makes it happen.
  • Metabolome: what actually happened.

Properties of the metabolome:

  • Metabolome is highly dynamic.
  • Metabolome influenced by genetic and environmental factors.

Influence from genetic factors

  • mGWAS: associations between genetic variants and metabolite concentrations.

  • Significant association between variant and carnitine, acetylcarnitine and butyrylcarnitine.
  • SLC22A5: carnitine transporter.
  • Genetic variant in this gene has influence on its function.

How can we measure metabolites?

  • Metabolites small enough to be directly measured by Mass Spectrometry.
  • Most metabolites uncharged - need to create ions first.

Two main setups to measure metabolites:

  • targeted: quantitative measurement of selected metabolites.
  • untargeted: semi-quantitative measurement of all metabolites (detectable with the setup) in a sample.

Mass Spectrometry (MS)

Mass Spectrometry (MS)