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.
00 - Overviews, workflow diagram + useful information 01 - Metabolite extraction 02 - Data acquisition (Mass Spectrometry) 03 - Converting data to open format 04 - Data pre-processing 05 - Extracting + formatting peak table + metadata 06 - Multivariate analysis (PCA) + further analysis (if applicable) 07 - Putative metabolite identification 08 - Archiving data + citing resources
N.B. Stages 01 and 02 are not covered in great detail in this documentation which focusses more on data processing and analysis.
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: