Qualitatively both have the same number of metabolites, but quantitatively, upregulated means more (higher levels) of metabolites and downregulated means less (lower levels) of metabolites.

Hope this helps.

Eef Dirksen Got it. It means if the trend is down-regulated in out specific treatment, we can say that this treatment is not good for extracting the value of that metabolite. Is it right?

I guess that is one way to put it, yes.

Normally two, or several, (e.g. disease) states are compared and then gene expression, protein expression or levels of metabolites are compared, resulting in either up-, or down-regulated trends of certain species that can help elucidating the biochemical mechanisms underlying the (disease) state(s).

Up and Down are indicated in both way, it depend on your treatment. Sometimes down regulated is need in some treatment. In my opinion I see both when it touch my criteria and statistical significant.