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Development of advanced tools for metabolic profiling using NMR data

Principal Supervisor: Professor Geerten W. Vuister, Department of Molecular and Cell Biology

Co-supervisor: Dr. Timothy J. Ragan

PhD project title: Development of advanced tools for metabolic profiling using NMR data

University of Registration: University of Leicester

Project outline:

Background: Metabolomics is the study of the metabolome, defined as the complete collection of metabolites found within a cell, tissue, biofluid or organism. A metabolite is a small molecule, with a molecular weight < ~1.5 KDa, which is either an intermediate or end product of a biological pathway. The collection of metabolites are thought to reflect the underpinning biology and changes in response to environment, stimuli and time. The metabolic profile is also thought to be indicative for disease and potentially can provide for diagnostic tools well ahead of the actual appearance of disease symptoms and provide for an avenue of personalised health care.

Currently, there are two major techniques that are used for metabolic profiling. The first, mass-spectrometry (MS), is very sensitive in detecting the various molecules but suffers from limitations due to sample preparation requirements. The second commonly used technique, Nuclear Magnetic Resonance (NMR), has the advantage of an exquisite ‘chemical resolution’ and much less stringent sample preparation requirements; however, the sensitivity of NMR is several orders of magnitude less than MS. Combinations of the two techniques have also been employed, where the weakness of one is being alleviated by the strength of the other technique.

In this project, we will primarily focus on the usage of NMR for metabolomics profiling. In the so-called untargeted approach, the aim is to univocally identify the metabolites from the NMR data recorded on relatively native, non-purified samples. It requires advanced data analysis routines, pattern recognition and cross referencing with databases with prior (spectroscopic) information. Of particular interest are the responses and changes of the metabolic profile over time as results of a stimulus, a disease, a treatment with drugs, etc. In a targeted approach, samples are first purified, typically to reduce the complexity of the data, with the aim to focus specifically on certain molecules.

Aim: The overall of this project is to develop a set of integrated and new tools for the analysis of NMR metabolomics data, encapsulated in tested and validated workflows.

Approach: The project encompasses the following steps:

  • Technical evaluation of existing NMR software packages and/or routines for the analysis of metabolomics NMR data; this will yield a full understanding of the merits of different packages.
  • Design, testing and implementation of suitable tools for visual inspection, including automatic spectral colouring by experimental condition and automated alignment and normalisation of spectra.
  • Design, testing and implementation of suitable routines for accessing various metabolomics databases, including scientific evaluation of the quality and consistency of their contents.
  • Design, testing and implementation of suitable tools for identification of metabolites and the determination of metabolite concentrations across a series of spectra. This needs tools for automatic peak identification, as well as binning, integration and peak-fitting capabilities; scientific assessments of robustness and consistency.
  • Development of chemometric analysis by new and improved pattern recognition and data analysis tools.
  • Encapsulation of the different data analysis steps in tested and verified workflows by using existing and newly acquired metabolomics datasets (jointly with collaborators).

The project will be conducted using the Collaborative Computational Project for NMR (CCPN) Analysis version-3 (Analysis-V3) as a development platform. CCPN develops new state-of-the-art tools in NMR data analysis and NMR structural biology. The 28 partners of CCPN jointly cover all aspects of biomolecular NMR. Specifically for the project, we will draw upon our experts partners in metabolomics in the Crick Institute (Prof. Driscoll) and the University of Birmingham (Prof. Gunther).

Relevance to BBSRC and Approvals

BBSRC Strategic Research Priority: Bioenergy and Industrial Biotechnology

Techniques that will be undertaken during the project:

  • NMR sample preparation (in collaboration)
  • NMR spectroscopy of metabolic samples (in collaboration)
  • Developing advanced coding skills.
  • Advanced techniques to work with databases.
  • Advanced data analysis and mathematical skills

Contact: Professor Geerten W. Vuister, University of Leicester