Data collection and generation
a. If using secondary metabolomics data, data can be downloaded from public repository
b. Sample collection and handling.
- Handling: Appropriate handling methods include use appropriate sample collection protocol (e.g., use appropriate kits for the type of samples being collected, spike quality control samples when collecting, etc.); use appropriate sample transportation method (e.g., keep samples in a box of dry ice during transporting process); use appropriate barcoding/indexing process such as keeping samples cold, wearing gloves and using two hands to hold samples when carrying samples; replicate sampling; pretreatment of tissue samples; etc.
- Storage: Keep samples in a freezer with -80C degree and monitor the temperature of the freezer; index samples in the freezer so that we will be able to know the sample position in the freezer quickly when need it.
- Extraction: Use appropriate methods to extract metabolites from samples.
- QC samples: Get samples containing known concentration of known analytes in order to control the quality of analysis.
c. Sample pre-processing using instrument such as mass spectromatry (MS) or nuclear magnetic resonance (NMR)
- NMR: nuclear magnetic resonance (NMR) identify metabolites based on their resonance frequency.
- Separation + MS: mass spectrometry (MS) ionizes metabolites and measures mass to charge ratio to identify potential identity of the metabolite. Separation can be done via gas chromatography or liquid chromatography, which are suitable for different metabolites.