Metabolism studies play a pivotal role in drug discovery and development since the active metabolites is critical to toxicological profile, efficacy and designing new drug candidates. From the instrumentation standpoint, liquid chromatography/mass spectrometry (LC/MS) has secured a central analytical technique for metabolite identification with the continuous developments and improvements in LC and MS technologies. Recently, a wide range of experimental strategies and post acquisition data processing and mining modes have emerged driven by the need to identify and characterize metabolites at ever increasing sensitivity and in ever more complex samples. In this article, the classical and practical mass spectrometry-based techniques, such as low resolution MS (quadruple, ion trap, linear ion trap, etc), high resolution MS (time-of-flight, hybrid time-of-flight instruments, Qrbitrap, Fourier transform ion cyclotron resonance MS, etc) and corresponding post acquisition data processing and mining modes (precursor ion filtering, neutral loss filtering, mass defect filter, isotope-pattern-filtering, etc) are described comprehensively. In addition, this review is also devote to discuss several novel MS technologies (ambient ionization techniques, ion mobility MS, imaging MS, LC/NMR/MS, etc) that hold additional promise for the advancement of metabolism studies.