High definition ion-mobility mass spectrometry and imaging for metabolomics, lipidomics and glycomics

Lead Research Organisation: University of York
Department Name: Biology


We propose to purchase a high-end mass spectrometer system that is capable of identifying thousands of unique small molecules at a time. This is achieved by the combination of accurate mass measurements, which enables the calculation of molecular formulae, and the ability of the mass spectrometer to separate molecules on the basis of their mass and shape. This last ability - separation on the basis of shape - is achieved using a technique known as ion mobility, which is not standard on most commercially available mass spectrometers. Ion mobility techniques allow molecules that have identical masses and formulae to be separated. This ability is crucial for the correct identification and measurement of several classes of biologically important molecules, including small molecules, lipids, and carbohydrates. We propose two main front-end interfaces that will make full use of the mass spectrometer's capabilities. The first is an imaging interface, where plant or animal tissue slices can be automatically sampled in a two-dimensional plane to build up a picture of where molecules are localised in the sample. As one input to this imaging pipeline, we will also use the output from our newly acquired, separately funded quantitative phase imaging microscope, which enables cell types and behaviours in tissue slices to be visualised and measured without prior staining or fixing. This pipeline - from visible features to mass spectrometry imaging on the same sample - will enable us to relate visible changes observed within tissues to the underlying biochemical processes. Applications range from tracking drug movements between cell types in medical treatments, to locating the sites of plant cell wall degradation in studies where the focus is on optimizing biofuel generation from waste biomass. The second interface uses separation by high-performance liquid chromatography of biological extracts before the mass spectrometer. This will enable us to characterize very complex mixtures, for example from understanding how the lipid make-up of cell membranes in industrially important microbes contributes to robust fermentation, to measuring fine changes in branched carbohydrate structures that are important signalling and recognition molecules in human disease. A common thread in all the different applications will be the complexity and multi-dimensionality of the data produced. All data will require careful filtering and annotation to provide biologically meaningful conclusions; this is not trivial and more often than not requires significant expert manual input and is a productivity bottleneck. To address this often overlooked area, together with the instrument manufacturers, we are committing resources to develop software tools for efficient data analysis.

Technical Summary

We propose to purchase a Synapt G2Si high definition mass spectrometer, with MALDI imaging, DESI, and travelling wave ion mobility (TWIMS) capabilities, for small molecule applications in new metabolomic, lipidomic, glycomic, and chemometric pipelines. We will complement the imaging functionality with a newly acquired and separately funded quantitative phase imaging (QPI) microscope to enable label-free light (ptychography) and fluorescence microscopy of tissue samples. We will work closely with the equipment manufacturers to develop hardware, but more importantly software solutions to optimise the quality and impact of the data produced by these pipelines. BBSRC-funded PIs working across the breadth of the BBSRC remit and strategic priorities will be supported by the new equipment; their research will be facilitated and significantly enhanced by access to the new technologies and functionalities. Integrating the QPI and MALDI/DESI imaging capabilities will significantly extend the information obtainable from microscopic analyses, adding specific molecular information to label-free light microscopic data. TWIMS will enable isobar and isomer resolution, which will appreciably enhance the dimensionality and richness of data from glycans, lipids, metabolites and drug candidates, and allow us to address specific technical challenges central to many of our BBSRC-funded programmes. These challenges include the ability to resolve isomeric unsaturated fatty acyl components of complex lipids, carbohydrate isomers to enhance identification of unexpected structures, and the extremely complex mixtures of metabolites in biomass degradation and anaerobic digestion systems, and in crude extracts of medicinal compound-producing plant systems.

Planned Impact

This equipment will enable impacts in the areas of food security, industrial biotechnology, bioenergy, and heath (tissue-specific drug targeting and development). It will underpin 'omic research in the high impact areas of glycomics, metabolomics and lipidomics. The University of York has a strong history of working with industry, enabled by externally facing facilities such as the BTF and CoEMS. The addition of the Synapt G2Si to the CoEMS will make the facility the preeminent open-access mass spectrometry facility in the UK and so will help deliver impacts through the research it enables not only in York, but across the N8 Consortium and more broadly in the UK. The requested equipment investment will greatly enhance our capability to build commercial partnerships and exploit scientific breakthroughs. This will be done by ensuring that the opportunities for licencing IP, creating commercial ventures and engaging with users are optimised, in addition to building the skills and capabilities of future employees in key areas such as plant breeding, and healthcare technologies.

In addition to the imaging, mass spectrometry, and informatics scientific communities, the commercial mass spectrometry, microscopy, and data analysis software industries will directly benefit from the work we propose. Collaborations between York scientists and the instrument manufacturers will bring rapid knowledge transfer from the research users to the commercial suppliers, enabling immediate exploitation of the analytical pipelines the research users will develop and apply.

The applied research that the requested instrumentation will support and enhance at York, will ensure wide-ranging impacts. Users of anaerobic digestion will benefit directly from the results of programmes to improve the efficiency of biomethane production that will be facilitated by the requested instrumentation; energy companies are directly involved to help translate the results into impact. The industrial biotechnology sector will benefit from new data that will inform rational engineering of microbes to produce higher titres of desirable but toxic end-products, and also from data that will help optimise the process of transferring biochemical pathways into heterologous systems. The bioenergy sector will benefit from the improved understanding of biomass degradation that the instrumentation will support and enhance. In all these approaches, impact is ensured by the involvement of key partner companies to directly translate scientific results into industrial and commercial applications. Programmes in drug development for both the developing and the developed world will be facilitated by the imaging and the small molecule analysis pipelines that the instrumentation will enhance. Producers of glycoprotein biologics will benefit directly from developments in glycomic profiling that will be commercialised by instrument and software suppliers; these will provide such companies with commercially-available user-friendly instrumentation and consumable products and kits that will make it possible for them to carry out product analysis and batch control readily in house, to facilitate bringing this important class of therapeutics to market.


10 25 50
Description The equipment was initially set up for use in identifying specific molecules in biological samples, called glycans, that are specialized carbohydrates present on cell surfaces, and play important roles in cell to cell interactions. Glycans are involved in immune response and disease recognition, with structural variety tuning these responses, and structural aberrations leading to disease. The capability of the equipment to separate compound ions base on ion mobility has now given us the ability to more fully structurally characterize biologically important glycans. The instrument has also been set up to generate high-resolution images of the biochemical components in tissue sections using multiple ionization and detection techniques. This will enable researchers to search, for example, for new markers associated with the biochemical pathways and end products of disease.
Exploitation Route The instrument is now up and running after several months of teething problems following installation in the summer of 2018. Two permanent staff are now trained in the operation and deployment of the instrument for users. At least three recent grants have been funded to end users, who will be making use of this instrument in their research programs:
BB/T000740/1 Chong, J.; "Rational design of microbial community mixtures for biogas production"; relevant to this instrument, LC-MS based metabolomics
MR/S01862X/1 Lichmann, B. "The Daphniphyllum alkaloids: biosynthesis, biocatalysts and bioactives from a neglected natural product class"; relevant to this instrument, LC-MS based metabolomics
H2020 EU 851448 Willems, L "RibiTool - Ribitol-phosphate: chemical tools to probe the biology of a unique mammalian carbohydrate"; relevant to this instrument, glycan structural analysis
Sectors Agriculture, Food and Drink,Chemicals,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

Description Advanced spatial profiling of osteoarthritis development
Amount £108,382 (GBP)
Funding ID ShS/PhD/22206 
Organisation Versus Arthritis 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2019 
End 09/2022
Description York Biology-Chemistry Glycoscience Symposium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact The event comprised eight formal talks from research groups across the University of York Biology and Chemistry departments, aimed at those groups who have a research interest in some aspect of glycobiology. These interests range from physical (structural) studies (Chemists) and the role and biochemistry of these molecules in organisms (Biologists). These represented groups who do not normally mix and it was an opportunity for us to highlight (in one of the eight talks) how the new instrument could be used to analyse this class of molecules from both disciplines.
Year(s) Of Engagement Activity 2019