A lot of the difficulties in analysis and/ or workflows come from the complexities of experimental structure. A lot of terms are used interchangeably in different contexts. Most tools for untargeted metabolomics are set up for 1 factor analysis with two or three levels e.g.
However, we quite often have more complex experimental designs when coming from other fields e.g.
Before you start, think about the following questions and make a note of what you’re expecting in terms of which groups of metabolite fingerprints could be similar and which could be different to each other. I don’t mean hypothesise but more, think logically about what you’re asking in your analysis and how your data will be grouped.
Get your meta-data (e.g. treatment information) organised early.