The node of Metabolomics Australia based at CMCA provides open access to all researchers across Australia, including training, sample analysis by mass spectrometry and consulting.

Our goal is to use our expertise and equipment to fuel cutting-edge research. We strive to form strong collaborations with any interested scientists to increase the value of their research.

Metabolomics Australia was founded in 2007 as the first high-throughput Metabolomics facility in Australia. There are currently five research nodes around the country that house staff and equipment dedicated to servicing researchers interested in small molecule analysis – amongst which Metabolomics Australia at UWA is one. Services are focused on all areas of technology, with the aim of providing access to world-leading advances in analytical techniques for academic and private industry users.

What is Metabolomics?

Metabolomics is defined as the non-targeted detection and quantification of small molecules (metabolites) in biological materials (plasma/urine/tissue/plant/oceans/microbial extracts). The resulting metabolite profiles reflect the actual cellular condition and provide useful indicators (biomarkers) of abnormalities/health, consequences of genetic engineering and adaptations to test compounds (such as drugs) or environmental factors, as well as a means of discovering new biomolecules (biomarker discovery) and monitoring food quality. In combination with other functional omics analyses, it offers the potential to understand a whole biological system.

Metabolomics requires reliable sampling and precise capture of thousands of metabolites from the biological sample of interest. The utilisation of a variety of complementary analytical platforms is crucial for identifying and quantifying the large numbers of chemically diverse primary and secondary metabolites typically found in biological samples. The most commonly used platforms for the detection and measurement of metabolites involves the use of gas chromatography (GC), liquid chromatography (LC), or capillary electrophoresis (CE) coupled with mass spectrometry (MS). Compounds may also be measured directly without chromatographic separation using nuclear magnetic resonance spectroscopy (NMR).

Finally, it requires appropriate informatics for data extraction, mining and interpretation of the obtained information.


Instruments are located at Room 2.28, Bayliss Building, Perth campus.

If you want to understand more about metabolomics and how it can relate to your biological question, contact Senior Research Fellow, Dr Michael Clarke.

Agilent 7890 Series GC with 5975 MSD (X2)

The platform of an Agilent 5975C Series MSD combined with a 7890A GC delivers all of the elements needed for Metabolomics' analysis of complex samples.

The instruments also have Gerstel/CTC autosamplers for online derivatisation and an option for volatile analysis using SPME.


  • Polar Metabolites in multiple sample types
  • Short chain fatty acid analysis in multiple sample types
  • Fatty acid methyl ester analysis in multiple sample types
  • Profiling of volatile organic compounds from solids and liquids

Instrument specifications

  • Gertsel/CTC automated autosampler
  • SPME analysis
  • NIST 2014 Mass Spec database
  • AMDIS Software

Agilent 6340 Ion Trap with 1290 UPLC

The 6300 Series Ion Trap LC/MS system consists of an Agilent LC, an atmospheric pressure ion source with the Ion Trap mass spectrometer coupled to a 1290 UPLC system.

The Ion Trap software controls the instrument and provides the tools to acquire and analyse LC/MS data.


  • MSn analysis of compounds
  • Phospholipid analysis
  • Drug pharmacokinetics
  • Analysis of plant hormones


  • ChemStation–LC control, LC method development and sequence setup and execution
  • 6300 Series Trap Control–IonTrap control, MS method development, acquisition monitoring
  • Data Analysis–compound-based data-mining and-browsing, search and identification (Library Editor), report design (Report Designer) and generation, analysis automation through Visual Basic Scripting
  • Quant Analysis–quantitation

Agilent 6460 QQQ with 2D 1290 UPLC

The Agilent 6460 Triple Quadrupole LC/MS System is equipped with Agilent Jet Stream Technology to provide ultra-sensitive performance for analytes in the most complex matrices.

This makes the 6460 the instrument of choice for a wide range of applications including environmental and food safety analysis, clinical research, and peptide quantitation. The 6460 provides a fast and robust solution for simultaneously quantifying, screening, and confirming analytes using triggered MRM (tMRM). The instrument has 2 x 1290 UPLC systems for two-dimensional separation of complex samples.


  • CDC Certified analysis of Vitamin D in serum
  • Steroid profiling in multiple sample types
  • Drug pharmacokinetics
  • Polyphenols and flavonoids in foods


  • 2D UPLC performance
  • Excellent sensitivity for many applications
  • 1ms dwell time with no collision cell crosstalk
  • Very fast polarity switching for multi-analyte studies
  • Dynamic Multiple Reaction Monitoring (dMRM) to maximise MRM efficiency
  • Triggered Multiple Reaction Monitoring (tMRM) for simultaneous quantitation and confirmation