A leader in the delivery of cutting-edge metabolomic services supporting academia and industry

The UWA node of Metabolomics Australia based at CMCA houses staff and equipment dedicated to servicing academia and industry interested in small molecule analysis.

Our services are focused on quantitative targeted and semi-quantitative, untargeted analysis of small molecules in biological samples in all areas of technology with the aim of providing access to world-leading advances in the field of metabolomics.

Map of CMCA - Level 3, Harry Perkins Institute of Medical Research (campus map location 2237) at latitude -31.9680811 and longitude 115.8115418

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How Can Metabolomics Help?

Metabolite analysis is used to reflect the actual cellular condition and to provide useful indicators (biomarkers) of abnormalities/health, consequences of genetic engineering and adaptations to test compounds such as drugs, environmental factors, as well as a means of discovering new biomolecules (biomarker discovery) and monitoring food quality. In combination with other functional omics analyses such as Genomics or Proteomics, it offers the potential to understand a whole biological system.

We tailor our services towards your needs through the adoption of all aspects of our 5-step metabolite analysis pathway which is focused on delivering the best value and highest quality research outcomes.

Why Us?

Many years of experience enable our team members to work with a large range of sample types originating from many fields of science. This includes plasma, tissue, plant, urine, oceans, microbial extracts, foods and other.

Representing one of four specialist nodes in Australia, we have the experience, team and resources to support your particular project requirements.

If you want to understand more about metabolomics and how it can relate to your biological question, download our services overview, or contact our Node Leader Senior Research Fellow, Dr Michael Clarke.

We are based at the CMCA, Level 3, Harry Perkins Institute of Medical Research, Nedlands Campus, 6 Verdun Street, Nedlands, WA 6009.

Our Advantages

  • Highly experienced specialist team
  • Versatile methods optimised to your needs
  • Variety of applications for metabolite analysis
  • Accommodation of most scientific sample types
  • Cutting edge LC-MS/MS and GC-MS/MS instruments
  • Direct collaboration with metabolomics experts
  • International reference network

Quality Management Approach

Our approach for each project follows a strict quality management system across that spans

  • Project discussion
  • Biological sample selection
  • Data acquisition
  • Data analysis and Metabolite identification
  • Report

Our Services

Our highly experienced team have many years of experience and have actively led, or supported hundreds of research programs for academic and commercial research objectives.

Download our services overview to learn more about our skills in sample preparation, targeted and untargeted metabolomics programs, metabolomics identification and advanced data analysis and reporting.

Sample Preparation

Key to high-performance outcomes is quality sample preparation. We can offer a variety of in-house sample preparation methodologies ensuring high sensitivity and precision of your data analysis.

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Targeted Metabolomics

Targeted metabolomics analysis aims to study and quantify known metabolites. It is a powerful tool for precise and accurate quantitation of specific metabolites in biological and biomedical samples. Targeted metabolite analysis offers a promising route to disease diagnosis, therapeutic management and prognostic prediction in clinical applications and food analytics.

To make our services compatible for a variety of research demands, we can provide fully optimised sample preparation and data analysis spanning complex bio fluids through to tissue types.

  • Vitamins (D and A)
  • Drug pharmacokinetics
  • Polyphenols and flavonoids
  • Dityrosine
  • Amino Acids (AA)
  • Steroids

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Untargeted Metabolomics

Non-targeted metabolomics analysis is most advantageous in the study of both known and unknown metabolites to identify changes in the metabolome in different treatment groups. It is a powerful tool for large-scale early phase diagnosis, and discovery of new biomarkers which are initiated through controlled research changes.

To make our services compatible for a variety of research demands, we can provide fully optimised sample preparation and data analysis spanning complex bio fluids through to plant and tissue types.

  • Polar Metabolites (PM)
  • Volatile Organic Compounds (VOC)
  • Steroids
  • Amino Acids (AA)
  • Polyphenols and Flavonoids in Food

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Data analysis and Metabolite Identification

Supporting our extensive technology capability is the skill of our team to support complex and high-quality results. This includes data extraction, mining and guidance to assist in interpretation of the obtained information which is derived from targeted or untargeted metabolomics approaches.

Our history in supporting commercial and research programmes has resulted in numerous positive project engagements as well as publications across a broad range of research areas.

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Our Instruments

We house a variety of cutting-edge mass spectrometry instruments to be able to accommodate your needs.

We are location at Level 3, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun Street, Nedlands, WA 6009

Contact our Node Leader Senior Research Fellow, Dr Michael Clarke for more information.

Thermo Scientific Orbitrap ID-X Tribrid Mass Spectrometer System

The ID-X system consists of a Vanquish UPLC system coupled to a tribrid mass spectrometer furnished with an atmospheric pressure ion source. The mass spectrometer combines a quadrupole, ion trap and high-resolution, accurate-mass (HRAM) Orbitrap mass analysers for acquiring multi-stage mass spectrometry (MSn) data. Collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation techniques are available at any stage of MSn. This unique architecture allows for multiple data independent and data dependant acquisition modes to be carried out using the Thermo Scientific Acquire X data acquisition tool. Thermo Scientific Compound Discoverer data analysis software streamlines unknown identification, determination of differences and elucidation of biological pathways.


A high-throughput, untargeted metabolomics method focused on the global detection of small molecules in biological samples is currently under development.


  • Mass range: m/z 50-2,000
  • Orbitrap mass analyser resolution: 7,500-500,000 (FWHM) at m/z 200
  • Mass accuracy:
    • <3 ppm RMS using external calibration
    • <1 ppm RMS using internal calibration
  • MS scan power: MSn, for n = 1-10

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Shimadzu GCMS-TQ 8050 coupled with a PAL 3 automated sampling system

The ultra- high sensitive GCMS-TQ 8050 is capable of performing unprecedented quantitative and qualitative analyses of ultra-trace concentrations of components, down to the femtogram level. This supports the metabolite analysis of a variety of science areas such as Biology, Marine, Biomedicine, and Food sciences. The PAL 3 automated sampling system enables optimal derivatisation techniques as well as options for tailored volatile organic compound (VOC) analysis using specified solid-phase micro-extraction (SPME) and headspace (HS) techniques.


Here at Metabolomics Australia at UWA, we specialise in the following metabolite analysis approaches:

  • Polar Metabolites
  • Volatile Organic Compounds

Instrument specifications

  • PAL 3 automated Sampling System
  • SPME and HS Analysis
  • Smart Metabolite Database
  • NIST Standard Reference Database 2017
  • Shimadzu Software Suite

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Agilent 6475 QQQ with 2D 1290 Infinity II UPLC

The Agilent 6475 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 6475 the instrument of choice for a wide range of applications including environmental and food safety analysis, clinical research, and peptide quantitation. The 6475 provides a fast and robust solution for simultaneously quantifying, screening, and confirming analytes using triggered MRM (tMRM). The instrument has 2 x 1290 Infinity II 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

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Shimadzu CLAM-2030 LCMS-8060 System

The Shimadzu Clinical Laboratory Automated sample preparation Module (CLAM-2030) is a fully automated sample preparation module based on extensive blood coagulation analyser technology. The CLAM-2030 integrates with Ultra High Performance Liquid Chromatography/Mass Spectrometer (UHPLC-MS) instruments, enabling the CLAM-2030 to sample directly from tubes and blood tubes, perform basic processing steps and then introduce the prepared aliquot to the UHPLC prior to analysis by the ultra-sensitive LCMS-8060 triple quadrupole mass spectrometer (LCMS-8060 also functions as a stand-alone instrument). This simplifies the use of high end instrumentation and improves efficiency for the throughput of laboratory samples, as well as reducing the risk of sample error by use of bar coding technology.


  • Targeted metabolite analysis
  • Drug pharmacokinetics
  • Steroid profiling in blood serum (CLAM) or multiple sample types (LCMS)

Instrument (MS) Specifications

  • 2D UPLC performance
  • Excellent sensitivity for many applications, particularly for negative polarity
  • 5ms polarity switching to detect more compounds, more efficiently
  • Fully automated MRM optimisation to improve compound detection

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Shimadzu 9030 QTOF - on loan from Shimadzu for testing

The Shimadzu Quadrupole Time-of-Flight Mass Spectrometer (QTof MS) integrates with the Shimadzu Ultra High-Performance Liquid Chromatograph (UHPLC) offering high resolution mass spectrometry to detect compounds in complex matrices with confidence at ultra-trace levels. The ion optics, fast scanning quadrupole filters and efficient collision cell is coupled for the first time to Shimadzu's time-of-flight mass spectrometer technology.

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