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5.2 Mass Spectrometry Metabolomics Approach

Metabolite profiling and identification is an essential part of the study of how a drug or xenobiotic is absorbed, distributed, metabolized, and eliminated from a biological system. The uptake of almost all organic compounds is followed by metabolism or biotransformation reactions. Among all compounds, drugs and pesticides are the most important as the biotransformation does not always lead to inactivation (detoxification) of the agent but in some instances, may lead to more active (bioactivation) or even more toxic compounds (biotoxification). These sometimes toxic compounds are known as metabolites. Most drugs are eliminated from the body by metabolism, a detoxification process and the metabolites modulate the efficacy of drugs in the treatment of disease with potential characteristics as follows:


  • The metabolites may possess pharmacological activity.

  • Some metabolites may be toxic: Bioactivation, which is bad for the patient

  • Metabolites may provide leads to new and more sophisticated drugs.


Mass spectrometry has emerged as an ideal technique for the identification of almost all structurally diverse metabolites. MS/MS data provides tremendous structural information for any drug metabolite due to its superb speed, high selectivity and high sensitivity Understanding which metabolites are likely to be formed in vivo is essential for interpreting pharmacology, pharmacokinetic and toxicology data.


Gemini Biosciences’ metabolite profiling and identification service uses the Thermo Scientific (Q Exactive) and Waters (Q-TOF) instrumentation to determine high resolution accurate mass of any metabolites and Ultra High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS)

leading to increased sensitivity and enhanced structural characterisation.


Metabolites can be investigated in a number of different matrices including

  • Plasma,

  • Urine,

  • Microsomal incubations,

  • Hepatocyte incubations,

  • Recombinant enzyme incubations, etc.

  • Any biological sample with appropriate sample preparation and collection..


Gemini Biosciences offers a range of metabolite profiling and identification services depending upon the level of detail and interpretation required e.g.


  1. We can provide putative identifications based on accurate metabolite mass measurements to calculate a molecular formula and then search biological and chemical databases.

  2. We can provide a higher level of confidence in the identification of a metabolite by applying mass spectral fragmentation and searching mass spectral libraries (plus using in-silico fragmentation tools).

  3. Gemini Biosciences can match a metabolite identification (i.e. accurate mass, mass spectral fragmentation and retention time) to an authentic chemical standard.


Untargeted LC-MS metabolic profiling analyses are performed using Ultra High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) and applying state-of-the-art Thermo Scientific (Q Exactive) and Waters (Q-TOF) instrumentation.


Targeted LC-MS assays are performed by using Ultra High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) and applying state-of-the-art Thermo Scientific and Waters instrumentation.


Metabolite profiling and identification protocol


























Please contact us  if you require details of our process and a quote.