Metabolomics

We are New Zealand's largest metabolomics facility, initiating and supporting research spanning agriculture through to human health.

What is metabolomics?

Metabolomics is the measurement of a wide range of different classes of small molecules (metabolites) and the use of statistical tools to analyse and interpret the data. It is a powerful tool for understanding biology and developing new hypotheses.

Biological systems are regulated by a complex interplay between a genetic blueprint and the environment. While genes provide a basis for what can happen, what genes are actually used and to what extent is determined by the interaction between genes and environment. This leads to the phenotype, or what has actually happened.

Small molecules, also known as metabolites, play a major role in determining biological response, and as the end products of the DNA-RNA-protein-metabolite cascade, are also highly informative about how a biological system (e.g. a cell, plant or human) responds in different situations.

By measuring a wide range of metabolites it is possible to get an overview of what is happening to a biological system, and from this develop hypotheses about mechanisms. In this sense, metabolomics is a hypothesis-generating tool, and useful for expanding understanding of how biological systems work and interact.

Metabolomics can also be used to determine composition, and in food and nutrition research can be used to find compositional differences which can be used to better understand products, effects of processing or find biomarkers that are specific for particular foods.

Metabolomics is a branch of analytical chemistry and requires the use of advanced analytical techniques to detect and measure metabolites. At AgResearch we use a number of different mass spectrometers to measure metabolites in samples.

Our capabilities

The AgResearch metabolomics platform runs four main types of analyses:

  • Untargeted metabolomics
  • Untargeted lipidomics
  • Targeted metabolomics
  • Rapid fingerprinting metabolomics

To date, we have analysed a wide range of samples, including human blood and tissue, soil, plants, food, milk, animal samples and breath.

Untargeted metabolomics

This is analysis that aims to measure all the metabolites in a sample, irrespective of if they are identified or not.

We use accurate mass spectrometers coupled to liquid chromatography (Shimadzu LCMS 9030 LC-HRMS instruments) to separate metabolites in a mixture and detect them. We use two different types of chromatography to identify as many metabolites as possible, and generally we will detect a wide range of amino acids, plant secondary metabolites, lipid metabolism intermediates, mono and disaccharides, amines and organic acids.

Untargeted lipidomics

This analysis is similar to untargeted metabolomics except the focus is on lipids.

Lipids are a diverse subclass of metabolites and are involved in many cellular processes. We extract lipids to separate them from other molecules in a sample and use accurate mass spectrometry (Shimadzu LCMS 9030 LC-HRMS) to detect lipids. In a typical sample, around 150-250 lipids can be identified and many more detected. Lipid classes include tri- and diglycerides and phospholipids.

Targeted metabolomics

An analysis of a wide range of known compounds in a sample (measuring ‘target’ metabolites).

We use gas chromatography coupled to a tandem mass spectrometer (Shimadzu GCMS TQ8040) to measure up to 350 different metabolites related to central metabolic pathways. Targeted metabolomics is useful for studies where mechanisms are the focus rather than the discovery of novel compounds. Through our collaboration with Massey University, we also have access to a 700 MHz Nuclear Magnetic Resonance (NMR) spectrometer to conduct NMR metabolomics analyses.

Rapid metabolic fingerprinting

We are investigating novel ways of acquiring metabolomics data, including rapid methods that acquire data directly from a sample within a few seconds. This includes Rapid Evaporative Ionisation Mass Spectrometry (REIMS) and Direct Analysis Real Time-Mass Spectrometry (DART-MS).

Our testing with both methods has shown these to be highly promising methods for screening and gaining novel scientific information from samples. These types of techniques can help to fill the gap between time-consuming lab-based metabolomics analyses used for addressing scientific questions, and metabolomics that could one day be used for data gathering and diagnostics at point-of-care, on farm or in industry. 

AgResearch REIMS traceability tool

AgResearch is developing a method of giving New Zealand exports a "unique fingerprint" that scientifically backs their provenance and could be used to deter supply-chain fraud.

Through the wider AgResearch network, we have access to other analytical methods and instruments, including for fatty acid analysis, amino acid analysis, and rapid biomarker analysis using liquid chromatography coupled to tandem mass spectrometry.

  • Published papers

    The following papers are widely accessible online:

    • McKeen, S., Young, W., Mullaney, J., Fraser, K., McNabb, W.C., Roy, N.C. (2019) Infant complementary feeding of prebiotics for the microbiome and immunity. Nutrients DOI: 10.3390/nu11020364
    • Cabrera, D., Wolber, F.M., Dittmer, K., Rogers, C., Ridler, A., Aberdein, D., Parkinson, T., Chambers, P., Fraser, K., Roy, N.C., Kruger, M. (2018) Glucocorticoids affect bone mineral density and bone remodelling in OVX sheep: A pilot study. Bone Reports DOI: 10.1016/j.bonr.2018.11.001
    • Milan, A.M., Hodgkinson, A.J., Mitchell, S.M., Prodhan, U.K., Prosser, C.G., Carpenter, E.A., Fraser, K., Cameron-Smith, D. (2018) Digestive responses to fortified cow or goat dairy drinks: A randomised controlled trial. Nutrients DOI: 10.3390/nu10101492
    • Gerard, P., Schwendel, B.H., Fraser, K., Eden, T. (2018) Effect of narrow-leaved plantain cultivar on development of two geometrid pests, Scopula rubraria and Epyaxa rosearia. New Zealand Journal of Agricultural Research DOI: 10.1080/00288233.2017.1398763
    • Aidoud, N., Delplanque, B., Baudry, C., Garcia, C., Moyon, A., Balasse, L., Guillet, B., Antona, C., Darmaun, D., Fraser, K., Ndiaye, S., Leruyet, P., Martin, J.-C. (2018) A combination of lipidomics, MS imaging, and PET scan imaging reveals differences in cerebral activity in rat pups according to the lipid quality of infant formulas. FASEB Journal DOI: 10.1096/fj.201800034R
    • Bermingham, E.N., Reis, M.G., Subbaraj, A.K., Cameron-Smith, D., Fraser, K., Jonker, A., Craigie, C.R. (2018) Distribution of fatty acids and phospholipids in different table cuts and co-products from New Zealand pasture-fed Wagyu-dairy cross beef cattle. Meat Science DOI: 10.1016/j.meatsci.2018.02.012
    • Cabrera, D., Kruger, M., Wolber, F.M., Roy, N.C., Totman, J.J., Henry, C.J., Cameron-Smith, D., Fraser, K. (2018) Association of plasma lipids and polar metabolites with low bone mineral density in Singaporean-Chinese menopausal women: A pilot study. International Journal of Environmental Research and Public Health DOI: 10.3390/ijerph15051045
    • Matthews, Z.M., Edwards, P.J.B., Kahnt, A., Collett, M.G., Marshall, J.C., Partridge, A.C., Harrison, S.J., Fraser, K., Cao, M., Derrick, P.J. (2018) Serum metabolomics using ultra performance liquid chromatography coupled to mass spectrometry in lactating dairy cows following a single dose of sporidesmin DOI: 10.1007/s11306-018-1358-4
    • Gill, G.P., Bryant, C.J., Fokin, M., Huege, J., Fraser, K., Jones, C., Cao, M., Faville, M.J. (2018) Low pyrrolizidine alkaloid levels in perennial ryegrass is associated with the absence of a homospermidine synthase gene DOI: 10.1186/s12870-018-1269-6
    • Subbaraj, Arvind K., Kim, Yuan H. Brad, Fraser, Karl, & Farouk, Mustafa M. (2016). A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study on colour stability of ovine meat. Meat Science, 117, 163-172.
    • Samuelsson, Linda M., Young, Wayne, Fraser, Karl, Tannock, Gerald, Lee, Julian, & Roy, Nicole C. (2016). Digestive-resistant carbohydrates affect lipid metabolism in rats. Metabolomics, In Press.
    • Roche, Jessica, Love, Jonathan, Guo, Qianqian, Song, Jiancheng, Cao, Mingshu, Fraser, Karl, . . . Jameson, Paula E. (2016). Metabolic changes and associated cytokinin signals in response to nitrate assimilation in roots and shoots of Lolium perenne. Physiologia Plantarum, 156(4), 497-511. doi:10.1111/ppl.12412
    • Cao, Mingshu, Fraser, Karl, Huege, Jan, Featonby, Tom, Rasmussen, Susanne, & Jones, Chris. (2015). Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics. Metabolomics, 11, 696-706. doi:10.1007/s11306-014-0727-x
    • Johnson, Richard D., Lane, Geoffrey A., Koulman, Albert, Cao, Mingshu, Fraser, Karl, Fleetwood, Damien J., . . . Johnson, Linda J. (2015). A novel family of cyclic oligopeptides derived from ribosomal peptide synthesis of an in planta-induced gene, gigA, in Epichloë endophytes of grasses. Fungal Genetics and Biology, 85, 14-24. doi:http://dx.doi.org/10.1016/j.fgb.2015.10.005
    • Jones, Chris, Hatier, Jean-Hugues, Cao, Mingshu, Fraser, Karl, & Rasmussen, Susanne. (2015). Metabolomics of plant phosphorus-starvation response Annual Plant Reviews Volume 48 (pp. 215-236): John Wiley & Sons, Inc.
    • Leathwick, D. M., Miller, C. M., & Fraser, K. (2015). Selection for anthelmintic resistant Teladorsagia circumcincta in pre-weaned lambs by treating their dams with long-acting moxidectin injection. International Journal for Parasitology: Drugs and Drug Resistance, 5(3), 209-214. doi:http://dx.doi.org/10.1016/j.ijpddr.2015.11.001
    • Wakelin, S. Harrison C. Mander B. Dignam S. Rasmussen S. Monk K. Fraser M. O’Callaghan. (2015). Impacts of endophyte infection of ryegrass on rhizosphere metabolome and microbial community. Crop and Pasture Science, 66, 1049-1057.
    • Subbaraj, Arvind K, Barrett, BrentA, Wakelin, SteveA, & Fraser, Karl. (2015). Using non-targeted direct analysis in real time-mass spectrometry (DART-MS) to discriminate seeds based on endogenous or exogenous chemicals. Analytical and Bioanalytical Chemistry, 407(25), 8047-8058. doi:10.1007/s00216-015-8977-7
    • Fraser, K., Lane, G. A., Otter, D. E., Hemar, Y., Quek, S.-Y., Harrison, S. J. and Rasmussen, S. (2014). Non-targeted analysis by LC-MS of major metabolite changes during the oolong tea manufacturing in New Zealand. Food Chemistry. DOI: 10.1016/j.foodchem.2013.11.054
    • Fraser, K., Lane, G. A., Otter, D. E., Harrison, S. J., Quek, S.-Y., Hemar, Y., & Rasmussen, S. (2014). Monitoring tea fermentation/manufacturing by direct analysis in real time (DART) mass spectrometry. Food Chemistry. DOI: 10.1016/j.foodchem.2013.05.054
    • Cao, M., Fraser, K., Huege, J., Featonby, T., Rasmussen, S. and Jones, C. (2014). Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics. Metabolomics. DOI: 10.1007/s11306-014-0727-x
    • Mackintosh C.G., Cowie C., Fraser K., Johnstone P. and Mason, P.C. (2014). Reduced efficacy of moxidectin and abamectin in young red deer (Cervus elaphus) after 20 years of moxidectin pour-on use on a New Zealand deer farm.Veterinary Parasitology. DOI: 10.1016/j.vetpar.2013.09.028
    • Cao, M., Fraser, K. and Rasmussen, S. (2013). Computational Analyses of Spectral Trees from Electrospray Multi-Stage Mass Spectrometry to Aid Metabolite Identification. Metabolites. DOI:10.3390/metabo3041036
    • Johnson, L.J., Koulman, A., Christensen, M., Lane, G.A., Fraser, K., Forester, N., Johnson, R.D., Bryan, G.T. and Rasmussen, S. (2013). An Extracellular Siderophore Is Required to Maintain the Mutualistic Interaction of Epichloë festucae with Lolium perenne. PLoS Pathogens. DOI: 10.1371/journal.ppat.1003332
    • Fraser, K., Harrison, S.J., Lane, G.A., Otter, D.E., Hemar, Y., Quek, S.-Y. and Rasmussen, S. (2013). Analysis of low molecular weight metabolites in tea using mass spectrometry-based analytical methods. Critical Reviews in Food Science and Nutrition. DOI:10.1080/10408398.2011.619670.
    • Fraser, K., Lane, G. A., Otter, D. E., Hemar, Y., Quek, S-Y., Harrison, S. J. and Rasmussen, S. (2012). Analysis of metabolic markers of tea origin by UHPLC and high resolution mass spectrometry. Food Research International. DOI: 10.1016/j.foodres.2012.10.015.
    • Harrison, S., Xue, H., Lane, G., Jones, C., Villas-Boas, S. and Rasmussen, S. (2012). Investigating neoinulin biosynthesis using recombinant enzymes, isotopic labeling and multistage mass spectrometry on a linear ion trap to discern oligosaccharide fragmentations and structure. Biomacromolecules (submitted).
    • Rasmussen, S., Parsons, A. and Jones C. (2012). Metabolomics of Forage Plants - A Review. Annals of Botany, 110: 1281-1290.
    • Rasmussen, S., Lane, G.A., Mace, W., Parsons, A.J. Fraser, K., and Xue, H. (2012). The use of genomics and metabolomics methods to quantify fungal endosymbionts and alkaloids in grasses. In Hardy, N., Hall, R. (eds.) Plant Metabolomics: Methods and Protocols, Methods in Molecular Biology, 860: 213 - 226. Springer Science+Business Media, LLC.
    • Fraser, K., Harrison, S.J., Lane, G.A., Otter, D.E., Hemar, Y., Quek, S.-Y. and Rasmussen, S. (2012). HPLC MS/MS profiling of proanthocyanidins in teas: a comparative study. Journal of Food Composition and Analysis. 26: 43-51.
    • Fraser, K., Harrison, S.J., Lane, G., Otter, D.E., Hemar, Y., Quek, S.-Y., and Rasmussen S. (2012). Non-targeted analysis of tea by hydrophilic interaction liquid chromatography and high resolution mass spectrometry. Food Chemistry. 134: 1616-1623.
    • Harrison, S., Xue, H., Lane, G., Villas-Boas, S. and Rasmussen, S. (2012) Linear ion trap MSn of enzymatically synthesized 13C-labelled fructans reveals differentiating fragmentation patterns of β (1-2) and β (1-6) fructans and provides a tool for oligosaccharide identification in complex mixtures. Analytical Chemistry 84: 1540–1548.
    • Harrison, S., Fraser, K., Lane, G.A., Villas-Boas, S. and Rasmussen, S. (2012). Automated high-throughput analysis of fractions generated during the isolation of natural products. NZ Journal of Agricultural Research 55: 15-20.
    • Koulman, A., Lee, T.V., Fraser, K., Johnson, L., Arcus, V., Lott, S., Rasmussen, S. and Lane, G.A. (2012). Identification of extracellular siderophores and a related peptide from the endophytic fungus Epichloë festucae in culture and endophyte-infected Lolium perenne. Phytochemistry 75: 128-139.
    • Harrison, S., Fraser, K., Lane, G., Hughes, D., Villas-Boas, S. and Rasmussen, S. (2011). Analysis of High-Molecular-Weight Fructan Polymers in Crude Plant Extracts by High-Resolution LC-MS. Analytical and Bioanalytical Chemistry. 401: 2955-2963.
    • Draper, J., Rasmussen, S. and Zubair, H. (2011). Metabolite Analysis and Metabolomics in the Study of Biotrophic Interactions between Plants and Microbes, in Annual Plant Reviews Volume 43: Biology of Plant Metabolomics (ed R. D. Hall), Wiley-Blackwell, Oxford, UK.
    • Tibe, O. Meagher, L. P. Fraser, K. and Harding D. R. K. (2011). Condensed Tannins and Flavonoids from the Forage Legume Sulla (Hedysarum coronarium). Journal of Agricultural and Food Chemistry 59: 9402–9409.
    • Otter, D., Cao, M., Lin, H-M., Fraser, K., Edmunds, S., Lane, G. and Rowan D. (2011). Identification of Urinary Biomarkers of Colon Inflammation in IL10-/- Mice Using Short-Column LCMS Metabolomics. Journal of Biomedicine and Biotechnology, vol. 2011, Article ID 974701, 12 pages.
    • Rasmussen, S., Parsons, A.J., and Newman, J.A. (2009). Metabolomics Analysis of Lolium perenne – Neotyphodium lolii Symbiosis: More Than Just Alkaloids? Phytochemistry Reviews 8: 535-550.
    • Harrison, S.J., Fraser, K., Lane, G.A., Villas-Boas, S., and Rasmussen, S. (2009). A Reverse-Phase Liquid Chromatography/ Mass Spectrometry Method for the Analysis of High-Molecular-Weight Fructooligosaccharides. Analytical Biochemistry 395: 113-115.
    • Koulman, A., Lane, G.A., Harrison, S.J. and Volmer, D.A. (2009). From Differentiating Metabolites to Biomarkers. Analytical and Bioanalytical Chemistry 394: 663-670.
    • Koulman, A., Cao, M., Faville, M., Lane, G., Mace, W., and Rasmussen, S. (2009). Semi-Quantitative and Structural Metabolic Phenotyping by Direct Infusion Ion Trap Mass Spectrometry and its Application in Genetical Metabolomics. Rapid Communications in Mass Spectrometry 23: 2253-2263.
    • Rasmussen, S., Parsons, A.J., Fraser, K., Xue, H., and Newman, J.A. (2008). Metabolic Profiles of Lolium perenne are Differentially Affected by Nitrogen Supply, Carbohydrate Content and Fungal Endophyte Infection. Plant Physiology 146: 1440-1453.
    • Rasmussen, S., Parsons, A.J., Popay, A., Xue, H., and Newman, J.A. (2008). Plant-Endophyte-Herbivore Interactions: More Than Just Alkaloids? Plant Signaling & Behavior 3: 1-4.
    • Cao, M., Koulman, A., Johnson, L.J., Lane, G.A., and Rasmussen, S. (2008). Advanced Data-Mining Strategies for the Analysis of Metabolomic DIMSMS Data from the Association of Lolium perenne with its Endophytic Fungus Neotyphodium lolii. Plant Physiology 146: 1501-1514.
    • Koulman, A., Seeliger, C., Edwards, P.J.B., Fraser, K., Simpson, W., Johnson, L., Cao, M., Rasmussen S., and Lane, G.A. (2008). E/Z-Thesinine-O-4’-a-Rhamnoside, Pyrrolizidine Conjugates Produced by Grasses (Poaceae). Phytochemistry 69: 1927-1932.
    • Ryan, G., Parsons, A.J., Rasmussen, S., and Newman, J.A. (2008). Can Optimality Models and an ‘Optimality Research Program’ Help us Understand Some Plant-Fungal Relationships? Fungal Ecology 1: 115-123.
    • Rasmussen, S., Parsons, A.J., Bassett, S., Christensen, M.J., Hume, D.E., Johnson, L.J., Johnson, R.D., Simpson, W.R., Stacke, C., Voisey, C.R., Xue, H., and Newman, J.A. (2007). High Nitrogen Supply and Carbohydrate Content Reduce Fungal Endophyte and Alkaloid Concentration in Lolium perenne. New Phytologist 173: 787-797.
    • Koulman, A., Tapper, B.A., Fraser, K., Cao, M., Lane, G.A., and Rasmussen S. (2007). High-Throughput Direct Infusion Mass Spectrometry: A New Method for Metabolomics. Rapid Communications in Mass Spectrometry 21: 421-428.
    • Koulman, A., Lane, G.A., Christensen, M.J., Fraser, K. and Tapper, B.A. (2007). Peramine and Other Fungal Alkaloids Are Exuded in the Guttation Fluid of Endophyte-Infected Grasses. Phytochemistry 68: 355-360.
    • Villas-Boas, S.G., Rasmussen, S., and Lane, G.A. (2005). Metabolomics or Metabolite Profiles? Trends in Biotechnology 23: 385-386.
    • Rowan, D.D., Hunt, M.B., Cooney, J.M., Koulman, A., Rasmussen, S., and Lane, G.A. (2005). Plant Metabolomics: New Challenges for Chemists. Chemistry in NZ 69: 24-28.

Key contacts

Research

Alastair Ross

Senior Scientist
Research

Karl Fraser

Senior Scientist
Research

Arvind Subbaraj

Scientist
Research

Linda Samuelsson

Science Team Leader - Food Chemistry and Structure
Research

Mingshu Cao

Senior Scientist

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