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Metabolomics

Principal contact: Dr. J. William (Will) Allwood (will.allwood@hutton.ac.uk)

Metabolomics involves the large-scale study of small molecules, also known as metabolites (polar and lipophilic primary metabolites, secondary metabolites, and volatiles), within plant tissues, foods, microbial and mammalian cells, biofluids, or any other given organism. The collective analysis of small molecules and how they interact in a biological system is known as the metabolome. Metabolomics involves the identification and comparative (or relative) quantification of the thousands of cellular metabolites and their interactions, involving LC-MS (MS/MS and multi stage MSn), GC-MS and NMR analytical approaches, combined with a range of informatics techniques in data processing, quality assurance, compound identification and metabolic network modelling. The application of univariate and multivariate statistical analyses is also a key step in defining significant differences in metabolite abundance between test and control samples.

Lipidomics involves the large-scale study of pathways and networks of cellular lipids (without regard to other metabolite classes) in biological systems and is regarded as a subset of the metabolome. The term, lipidome, describes the complete lipid profile within a given biological system. Lipidomics involves the identification and comparative (relative) quantification (based upon LC-MS, MS/MS and MSn approaches) of the thousands of cellular lipids (phospholipids, free fatty acids, mono- (MAGs), di- (DAGs) and tri-acyl glycerides (TAGs), ceramides, sterols, prenols, saccharolipids and polyketides) and their interactions with other lipids, proteins and metabolites.

These rapidly expanding fields complement the huge progress made in genomics and proteomics, all of which constitute the systems biology approach. Whilst initial metabolomics and/or lipidomics analyses are based upon sample characterisation and relative quantification between test and control samples (commonly applied in gene function analysis, plant/crop breeding populations, abiotic or biotic perturbed and non-perturbed samples, natural product discovery and pharmacodynamics), it can also lead to the further development of targeted methods providing absolute quantification of any given metabolite/lipid or suite of metabolites/lipids.

At the James Hutton Institute/James Hutton Limited we have over twenty years of experience in performing LC- and GC-MS metabolomics studies, with specialism in the analysis of plant tissues and foodstuffs, especially fruits, potato, legumes and cereals such as barley, oats and wheat. Dr. Will Allwood also has a vast experience in the metabolomic analysis of biofluids (urine, blood plasma and serum), microbes and human cell cultures, as well as biotic and abiotic perturbation in model plant species such as Arabidopsis thaliana and Brachypodium distachyon.

LC-MS capabilities

Thermo - Dionex U3000 - LTQ Orbitrap XL MS

The Thermo Dionex U3000 is an 1100 bar UHPLC system with the capability to collect online fractions in conjunction with MS analyses. The Orbitrap is a hybrid mass spectrometer that combines Orbitrap technology with an LTQ™ linear ion trap.  This instrument gives exact mass measurement (3-5ppm) within the FT Orbitrap system.  It is able to perform MSn experiments, online with LC by applying data collection within the LTQ, and also offline with accurate mass ion trees (based upon pre collected LC fractions) obtained by the FT Orbitrap. Such analyses permit compound elucidation in complex mixtures. This is our go to system for metabolomics analysis.

Agilent 1260 Infinity HPLC and 6224 Accurate Mass Time of Fight TOF MS

The Agilent 1260 Infinity is a 600 bar HPLC system that is combined with accurate mass (<5ppm) TOF/MS capabilities provided by the 6224 MS system. Whilst lacking MS/MS capabilities, it is still possible to perform pseudo MS/MS experiments through applying high energies to the ESI source. The system is applied to LC-MS based metabolomics studies and semi-targeted metabolite analyses where the target compounds have been previously characterised via MS/MS analysis on the Thermo - Dionex U3000 - LTQ Orbitrap XL MS.

Agilent 1260 Infinity HPLC and 6460 QQQ MS

This instrument combines the Agilent 1260 Infinity 600 bar HPLC system with the 6460 QQQ MS. QQQ-MS provides high dynamic range, sensitivity, and compound selectivity, thus lending itself to targeted metabolite quantitation. Example applications include the targeted quantification of acrylamide, phytohormones, glucosinolates, carotenoids and isoprenoids.

Thermo Accela HPLC - LCQ Fleet MS

This instrument combines a Thermo Accela 600 bar HPLC system with the LCQ Fleet Ion Trap MS. The system provides nominal mass full-scan and MSn capabilities. It is generally applied as a non-routine LC-MS system to perform preliminary analyses of new compound matrices and as a first pass towards compound characterisation.

GC-MS capabilities

Thermo Trace GC Ultra – DSQ II MS

This instrument combines the Thermo Trace Ultra Gas Chromatography system interfaced with Electron Ionisation and the high scan speed DSQ II single quadrupole MS system. We have two systems interfaced with conventional liquid handling sample injectors that are applied to the analysis of central metabolites in MOX-TMS derivatised samples, as well as a third system that is interfaced with a Solid Phase Micro Extraction (SPME) system, permitting the collection and analysis of volatile organic compounds (VOCs), typically applied to aroma related flavour analyses.

For further information and discussion of your metabolomics and lipidomics requirements, please contact Will.Allwood@hutton.ac.uk.

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Scottish Metabolomics Network: http://scottishmetabolomics.net/

Metabolic Profiling Forum: https://thempf.org/mpf_cms3/index.php

Metabolomics Society: http://metabolomicssociety.org/

Research

Areas of Interest


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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.