The research question for a metabolomics study needs to be carefully described. At the moment it is not possible to measure the whole metabolome in one run, in contrast to transcriptomics measurements. To make your study to a success you should therefore decide which metabolites may change in your study and may be of most interest. For this selection the following websites may help you:

www.hmdb.ca
On this website under biofluid plasma/serum many metabolites that have been detected in blood are indicated.
www.nugowiki.org 
On this website many metabolites are categorized on for instance their biological function.

Depending on the choice of the metabolites you might be able to select the best platforms for you study (Metabolomics and Separation Techniques).
After you have formulated your research question you should design the experiment. Several biological (Biological design) and analytical (Analytical design) issues should be kept in mind.