What is metabolomics? My definition: Identifying, measuring and tracking the small biochemical intermediates formed during the making, breaking, and interconversion between biochemical molecules to figure out what organisms are up to.

It typically uses mass spectrometry (MS), coupled to liquid chromatography (LC) or gas chromatography (GC) to aid in separation prior to measuring the mass/charge (m/z) ratios of the molecules and/or their fragments to ID them.

You can never measure everything (differences in prep are needed for different types of metabolites, etc.), but you can design your experiment to measure what you care about.
Broadly speaking . . .

Untargeted metabolomics: “Hypothesis-generating” – experiment to measure “all” metabolites to see what’s there; may use prediction programs, etc. to ID “unknowns”; approach statistically

Targeted metabolomics: “Hypothesis testing” – experiment to measure and (potentially) quantify previously-selected analytes to see how much of specific things are there; compare to standards you’ve run

Semi-targeted, “profiling”: A sort of middle ground where you try to identify a large number of compounds based on library database hits, but don’t try to ID unknowns and don’t have personal standards for them all