Stages of the workflow
The workflow has been divided into stages. We use the following number codes in the documentation presented here as well as in the R code and workflow diagram.
- Overviews, workflow diagram & useful information
- Metabolite extraction
- Data acquisition (Mass Spectrometry)
- Converting data to open format
- Data pre-processing
- Extracting & formatting peak table & metadata
- Multivariate analysis (PCA) & further analysis (if applicable)
- Putative metabolite identification
- Archiving data & citing resources
⚠️ Stages 1 and 2 are not covered in great detail in this documentation which focusses more on data processing
and analysis.
Resources and further reading
💡 We can’t cover everything in this guide but there are lots of other useful resources out there.
Here are some general metabolomics workflow resources you may find useful:
- Miao Yu’s guide 2021 (particularly useful as links to a lot of literature and other tools that we have not covered here)
- R for Mass Spectrometry 2016 (nearly everything you could need for doing metabolomics in R BUT relies on proficiency in R)