Metabolic target analysis is used when you want to analyze a single/group of metabolite (s). It is used when you have a hypothesis in mind. Metabolite profiling is used for global analysis of metabolites. it is generally used for framing a hypothesis for further studies.

With Targeted Analysis you know what compound(s) you are looking for.  With Profiling Analysis you are looking more at the overall signal patterns. 

Thank you @Schmitt.  Does that mean targeted analysis involves quantification of targeted compound while Profiling Analysis could involve characterization and identification?

Yes, targeted analysis is quantitative or at least semi-quantitative and in some cases "relative quantitation" of particular metabolytes between subject groups is the goal rather than determining exact concentrations.  Profiling is more like a broad screening analysis which can be very useful for discovery of new biomarkers...things perhaps you didn't even know were there, or were not there, as the case may be.  Targeted analyses can be used to confirm the findings from profiling analysis. 

@Schmitt. Thank you so much. Its just that this is a new area I am planning delving into in my research activities. I am planning of studying biochemical responses of plants (secondary metabolites) in terms of targeted analysis to heavy metals stress as possible biomarkers. Once again, thank you so much

1. Metabolite target analysis is an approach that is restricted to metabolites for example a particular enzyme system that would be directly affected by any perturbation

2. Metabolite profiling focus on a specific group of metabolites (for example lipids) or those associated with a specific pathway; within clinical and pharmaceutical analysis, this is often called metabolic profiling, which is used to trace the fate of a drug or metabolite