MUSERMET: MultiUSER equipment for small molecule identification in untargeted METabolomics

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

Many of the projects in the newly formed Liverpool Centre for Metabolomics Research involve a requirement for the sophisticated, detailed, and RAPID analysis of biological samples to identify and measure the many hundreds or thousands of small molecules (metabolites) that they contain. This is done by separating them in a flowing stream (liquid chromatography) followed by their estimation on the basis of their masses and the masses of any fragments that may be produced therefrom (as these form a unique 'signature'). Classically, a major bottleneck has been the IDENTIFICATION of the metabolites represented by what may otherwise be highly reproducible times of the appearance of these mass spectral peaks or signatures. An instrument called the Orbitrap ID-X tribrid, together with an integrated suite of software (to which we shall add), offers a real chance of solving this 'spectrum-to-structure' problem. It may be applied to the solution of multiple problems within the BBSRC remit, and we illustrate several.

The aim of this proposal is to secure such an instrument for an extensive User Community in Liverpool and elsewhere. The instrument, while based on established Orbitrap technology, is both novel and unique, and no such instrument is currently available within the UK. This would be a 'first', and we have accordingly secured a substantial contribution from the applicant Universities.

Technical Summary

Many of the projects in the newly formed Liverpool Centre for Metabolomics Research involve a requirement for the sophisticated, detailed, and RAPID analysis of biological samples to identify and measure the small many hundreds or thousands of molecules (metabolites) that they contain. This is typically done using liquid chromatography followed by high-resolution mass spectrometry, including the masses of any fragments that may be produced. Classically, a major bottleneck has been the IDENTIFICATION of the metabolites represented by what may otherwise be highly reproducible retention times and MS^n mass spectra. An instrument called the Orbitrap ID-X tribrid, together with an integrated suite of software (to which we shall add), offers a real chance of proving the necessary spectra and solving this 'spectrum-to-structure' problem. It may be applied to multiple problems within the BBSRC remit, and we illustrate several.

The aim of this proposal is to secure such an instrument for an extensive User Community in Liverpool and elsewhere. The instrument, while based on established Orbitrap technology, is both novel and unique, and no such instrument is available within the UK.

Planned Impact

WHO WILL BENEFIT: Companies will benefit in a number of ways, by (i) gaining access to knowledge of methods used for the rapid analysis of biological systems using state-of-the-art XC-MS instrumentation and its attendant analytics, and e.g. (ii) knowledge of how to improve the production of various compounds, whether they are substrates, intermediary metabolites, nutraceuticals, drugs, or bioactives in any kind of products. So far as industrial biotechnology more generally is concerned, companies will benefit from knowledge of a novel strategy for rapid cell analysis.

HOW WILL THEY BENEFIT: As is our practice, all pertinent data are made available via the Web, and OA publishing has long been our norm. We also hold frequent workshops to assist dissemination of research results. We have pioneered in the Altmetrics field for digital dissemination - indeed a recent Nature article (Kwok R: Altmetrics make their mark. Nature 2013; 500:491-492) highlighted the fact that the PI's paper Hull D, Pettifer SR, Kell DB: Defrosting the digital library: bibliographic tools for the next generation web. PLoS Comput Biol 2008; 4:e1000204 was the most accessed in ANY PLoS journal, with over 53,000 accesses! (it is past 108,000 now) - the PI's paper Kell DB: Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genom 2009; 2:2 has over 98,000 accesses, increasing at ~50 per day).We shall work closely with University KT staff and industrial IP offices to secure intellectual property rights for any useful inventions that we discover. Having secured IP, future development work can take place, and several routes to commercialisation can be explored. For example, all pharmaceutical companies have their own relevant groups, with whom we are in contact. Finally, having secured IP, we shall, of course, seek actively to communicate our scientific findings to the wider research community through scientific meetings, scholarly publications and press releases.

THE WIDER COMMUNITY: DBK (@dbkell) and RG (@RoyGoodacre) are well known and regular tweeters (the latter also runs the @metabolomics twitter feed), and social media will provide a novel and useful means of disseminating our findings. Both are regular attenees at thee MetaboMeeting and International Metabolomics Society's conferences.

COMMUNICATIONS: We will communicate with relevant industrial partners both directly and via the meetings of relevant learned societies (we are members of several). In year three of the Project, we will organise a half-day meeting to explain our research to interested industrial scientists. However, we will also provide a video link to facilitate the participation of
those who are unable to travel to Liverpool.

Publications

10 25 50
 
Title Ergothioneine: the new super antioxidant 
Description Scientific animation 
Type Of Art Film/Video/Animation 
Year Produced 2020 
Impact Created to inform lay as well as professional audiences. 
URL https://www.youtube.com/watch?v=SDiYMPpbUpk
 
Description Some activities/projects that the IDX has been used for:

COVID-19 Longitudinal study sample acquired on this instrument. Preliminary results published within this article: Roberts, I., Wright Muelas, M., Taylor, J.M. et al. Untargeted metabolomics of COVID-19 patient serum reveals potential prognostic markers of both severity and outcome. Metabolomics 18, 6 (2022). https://doi.org/10.1007/s11306-021-01859-3. Related BBSRC grant: Untargeted metabolomics of serum samples during COVID-19 disease progression - BB/V003976/1.

BARLEY METABOLITES: Untargeted metabolite analysis of barley to discern effects of strains on beer flavouring. Project on-going. Progressing to semi-targeted. Initial work focussed on determining suitable sample preparation methods for consistent MS results.

BEER AGING: Untargeted metabolite analysis of beer metabolite changes arising from aging.

ANIMAL FAECES: Untargeted metabolite analysis to consider health assessment of (zoo) animals. Project on-going. Progressing to targeted analysis. Initial work focussed on determining suitable sample preparation methods for consistent MS results.

EICOSANOIDS - PROOF OF CONCEPT: Semi-targeted analysis of samples for eicosanoids. Proof of concept from sample preparation to analysis, for grant application.

FUNGAL ALLERGIES: Untargeted metabolite analyses involving BAL and sera, with tissue held in reserve. Investigations pertain to respiratory tract related samples. Initial work focussed on determining suitable sample preparation methods for consistent MS results. Project ongoing. Future work expect to be targeted.

MUSSEL METABOLITES: Untargeted metabolite analysis from three different types of tissue sample investigating stressors. Initial work focussed on determining suitable sample preparation methods for consistent MS results, allowing for matched on-column injections for each sample in relation to individual starting material. Project ongoing.

ROUND ROBIN ANALYSIS/INTER-LABORATORY: Global multi-lab matching analysis of HILIC and LIPID samples to discern consistency of results between labs. Untargeted analysis. Project ongoing.

GI INFECTION: Untargeted metabolite analysis from human faecal matter. Initial work focussed on determining suitable sample preparation methods for consistent MS results. Project currently on hold.
Exploitation Route Use of untargeted/targeted metabolite analysis results to improve outcomes in the ongoing research noted above.
Sectors Pharmaceuticals and Medical Biotechnology

 
Description NxNW: Innovation to Commercialisation of University Research (ICURe) Programme
Amount £45,000 (GBP)
Organisation Queen's University Belfast 
Sector Academic/University
Country United Kingdom
Start 05/2020 
End 10/2020
 
Description Daye 
Organisation Daye
Country United Kingdom 
Sector Private 
PI Contribution Member of Medical Advisory Board. Approached to join due to extensive research in the area of the gut microbiome.
Collaborator Contribution The company is developing and optimising intuitive, scientifically robust sexual and reproductive health products.
Impact The company have created and marketed new products.
Start Year 2019
 
Title METHODS FOR PRODUCTION OF ERGOTHIONEINE 
Description The present invention relates to microbial factories, in particular yeast factories, for production of ergothioneine. Also provided are methods for producing ergothioneine in a yeast cell, as well as useful nucleic acids, polypeptides, vectors and host cells. 
IP Reference WO2020221795 
Protection Patent granted
Year Protection Granted 2020
Licensed No
Impact The present invention relates to microbial factories, in particular yeast factories, for production of ergothioneine. Also provided are methods for producing ergothioneine in a yeast cell, as well as useful nucleic acids, polypeptides, vectors and host cells. Ergothioneine (ERG) (2-mercaptohistidine trimethylbetaine, (2S)-3-(2-Thioxo-2,3-dihydro-1 H-imidazol-4-yl)-2-(trimethylammonio)propanoate) is a naturally occurring antioxidant that can be found universally in plants and mammals; it possess
 
Description Webinar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Kell DB (2020) How drugs really get into cells: why passive bilayer diffusion is a myth. ACS webinar, 55 min + questions, freely available online at https://www.acs.org/content/acs/en/acs-webinars/drug-discovery/so-lute-carriers.html
Year(s) Of Engagement Activity 2020
URL https://www.acs.org/content/acs/en/acs-webinars/drug-discovery/so-lute-carriers.html