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Metabolomics is defined as “systematic study of the unique chemical fingerprints that specific cellular processes leave behind” [1]. Metabolom includes the final metabolites of a cell, or biological organisms [2]. Herbal metabolomics is unbiased, high-performance and specific analysis of highly complex mixtures of plant extracts. This overall gain for metabolom analysis is at first a result of recent advances in mass spectrometry (MS). Nowadays, about 50,000 herbal compounds have been extracted and identified from plants. It is predicted that the final number would reach 200,000. That’s why metabolomics is a considerable challenge for scientists [3]. Herbal metabolom is very diverse and includes fat-soluble compounds, polar macromolecules, basic and acidic ions, combinations of the constituents, highly stable and oxidative susceptible natural products. Herbal metabolom extraction methods and measurement tools should be selected carefully [4].