SMN Newsletter

 
 
 

15th August 2018

Overview  

 

  • Scottish Metabolomics Network Symposium 2018 Advert (from Will Allwood and Jeffery Huang)
  • Scottish Metabolomics Network Lab Visit Training Grants for Early Career Researchers 2018
  • Laboratory of the Quarter: Glasgow Polyomics Facility (from Karl Burgess)
  • Core Technologies in Life Sciences (CTLS) Conference 2018 in Ghent (from Natalie Homer)
  • Cold Spring Harbor Laboratory Metabolomics Course (from David Sumpton)
  • Notes from our Sponsors: Chromatographic Deconvolution (from John Moncur, SpectralWorks Ltd.)
  • Scottish Metabolomics Network Papers
  • Awarded PhD studentships and grants
  • Upcoming Metabolomics (and other) conferences
  • Webinars
  • Further Announcements
  • Vacancies
  • Acknowledgements

 

For twitter updates search for #ScotMetNet


Scottish Metabolomics Network Symposium 2018 Advert (from Will Allwood and Jeffery Huang)

The next Scottish Metabolomics Symposium will be held at the Discovery Point Exhibition Centre on Thursday the 1st and Friday the 2nd of November 2018. More information can be found on the SMN website (events page). You can download a flyer to display in your workplace and a link to the Dundee and Angus Convention Bureau where you can get more information about Dundee as well as discounted rates for hotels and visitor attractions. Early Bird registration (£40) closes 19th September 2018 (Registration will be £60 after this date). Deadline for poster abstracts is the 19th September 2018 (note: abstracts will only be considered from authors who have registered for the SMN18).

Themes will be metabolomics technologies, cancer metabolomics, lipidomics, food and crop chemistry and nutrition and metabolomics in biomarker research. The evening drinks reception will be held on board the RSS Discovery followed by the conference dinner. Enquiries to will.allwood@hutton.ac.uk and wtcrf.education@ed.ac.uk

 Photograph of the RRS Discovery and the Discovery Point Exhibition Centre ( http://www.rrsdiscovery.com)

Photograph of the RRS Discovery and the Discovery Point Exhibition Centre (http://www.rrsdiscovery.com)

 Dr James MacRae (photography courtesy of the Francis Crick Institute/Dave Guttridge)

Dr James MacRae (photography courtesy of the Francis Crick Institute/Dave Guttridge)

This year we are delighted that Dr. James MacRae of the London Metabolmics Network will be attending the SMN 2018 meeting in November in Dundee. This is part of an ongoing initiative to build interactions between national and international Metabolomics groupings. We look forward to welcoming him and hearing his talk entitled “Lipid Metabolism in apicomplexan parasites: Routes for drug therapy?”


Scottish Metabolomics Network Lab Visit Training Grants for Early Career Researchers 2018

We are pleased to be able to offer a new initiative through the SMN:  the SMN Lab Visit Training Grants for Early Career Researchers. We are now seeking to award 3 or 4 Early Career Researchers from our network laboratories a grant to visit and train in another network lab. Applications for these grants are now invited with a Deadline of 29th September 2018, and awards will be made at the Annual Symposium in November 2018 in Dundee. An application form, with more details, can be downloaded here .


Laboratory of the Quarter: Glasgow Polyomics Facility, University of Glasgow (from Karl Burgess)  

Glasgow Polyomics is a multiomics facility based on the Garscube campus of the University of Glasgow. Our team aims to provide a comprehensive coverage of ‘omics experiments from concept design through to data interpretation and publication. Born as the Sir Henry Wellcome Functional Genomics Centre, Glasgow Polyomics expanded in 2008 to include proteomics and metabolomics capabilities to a wide range of academic and industrial customers.

 Photograph of the Wolfson Wohl Cancer Research Centre where Glasgow Polyomics is situated (photograph courtesy of James Houghton)

Photograph of the Wolfson Wohl Cancer Research Centre where Glasgow Polyomics is situated (photograph courtesy of James Houghton)

The metabolomics team has recently benefited from grants from SULSA and Wellcome Institutional Strategic Support Fund, allowing the expansion to a team of seven members, assisted by the Polyomics administrative team. Headed by Dr Karl Burgess, the expert team is composed of two technicians, two mass spectrometry specialists/technologists and two bioinformaticians/data analysts allowing us to call on a wide body of knowledge and experience. We have experience with a diverse range of sample types and help users design and plan experiments, producing high quality data along with biochemical interpretation leading to high impact publications. We have been involved in a large number of successful grant applications, many with industrial partners, and are happy to discuss and participate in any future applications requiring metabolomics input.

Our close collaboration with Thermo Scientific has led to us focusing on Orbitrap mass spectrometers for our metabolomics platform. Our current instrument portfolio includes an Exactive, Q-Exactive and Fusion (run in conjunction with the Wellcome Centre for Molecular Parasitology) allowing us to carry out experiments ranging from routine screening analysis to specific, targeted fragmentation identifications of novel components. We also have a Thermo ion trap GC-MS that is used for a variety of targeted work.

We routinely run untargeted metabolomics, focussing on small, polar metabolites and our standard analytical platforms are geared towards these types of analyses. We also have a range of targeted methods for specific classes of metabolites and expertise in isotope labelling analysis to further investigate changes discovered via untargeted analysis.

 Erin Manson and Suzanne McGill working at the Thermo Orbitrap Fusion Mass Spectrometer (photograph courtesy of James Houghton)

Erin Manson and Suzanne McGill working at the Thermo Orbitrap Fusion Mass Spectrometer (photograph courtesy of James Houghton)

Interpretation of metabolomics data can be difficult, requiring knowledge of the instrumentation, bioinformatics and biochemical understanding to get the best from an experiment. We provide support for every aspect of metabolomics experiments and our metabolomics software pipeline, Polyomics integrated Metabolomics Pipeline (PiMP), provides an easy way to investigate LC-MS data in the context of biochemical pathways. We have in-house support in complex analyses from an advanced statistics team who can be involved in projects that require advanced statistics, such as data modelling and pattern matching.

  Isabel Vincent (left) taking a customer through her data (photograph courtesy of James Houghton)

 Isabel Vincent (left) taking a customer through her data (photograph courtesy of James Houghton)

For more high throughput users of the service, we also provide training and workshops in PiMP as well as running an “Intro to Omics” course for people that wish to know more about what each ‘omic can be used for.

Our overall goal is to provide a cutting-edge metabolomics service that goes beyond the running of samples and return of raw instrument data. We take pride in the relationships we have built with research groups both at Glasgow University and around the world. If you think metabolomics may aid your research but are unsure where to start, then please don’t hesitate to get in touch (http://www.polyomics.gla.ac.uk/enquiry.php).

Some of our highlight papers include:

  • Newton, James, et al. "Minimally-destructive atmospheric ionisation mass spectrometry authenticates authorship of historical manuscripts." Scientific reports 8.1 (2018): 10944.
  • McMurray, Rebecca J., et al. "Nanoscale surfaces for the long-term maintenance of mesenchymal stem cell phenotype and multipotency." Nature materials 10.8 (2011): 637.
  • Creek, Darren J., et al. "Toward global metabolomics analysis with hydrophilic interaction liquid chromatography–mass spectrometry: improved metabolite identification by retention time prediction." Analytical chemistry 83.22 (2011): 8703-8710.
  • Connolly, James PR, et al. "The host metabolite D-serine contributes to bacterial niche specificity through gene selection." The ISME journal 9.4 (2015): 1039.
  • Haggarty, Jennifer, et al. "Serially coupling hydrophobic interaction and reversed-phase chromatography with simultaneous gradients provides greater coverage of the metabolome." Metabolomics 11.5 (2015): 1465-1470.

Core Technologies in Life Sciences (CTLS) Conference 2018 in Ghent (from Natalie Homer)

 CTLS Logo (www.ctls-org.eu)

CTLS Logo (www.ctls-org.eu)

The aim of the Core Technologies for Life Sciences (CTLS) is to ‘bring together scientists, technical and administrative staff working in or in close association with core facilities, research infrastructures and shared resource laboratories in life sciences and biomedicine’.  The third biennial CTLS conference was held from 1st-4th July 2018 in Ghent at the Flanders Institute of Biotechnology, VIB, which is a non-profit research institute in Belgium.

There were plenary and parallel sessions on topics that were of interest to all types of cores, regardless of scientific discipline. These included benchmarking, exchanges on best practice, emerging technologies, finances and contracts, training for core staff and supporting career development at all stages.  A number of software packages that lessen the load for facility management were discussed and showcased by vendors where the capabilities of these packages are a huge jump from self-made processes and procedures developed in isolation.

Discussions revealed that a greater understanding of what is involved in managing and working within a core facility is needed. Retention of staff and their knowledge within a facility is essential for efficient operation and that can only be achieved if there is career development for core scientists. There is a need for ongoing training of core staff for efficient management and operation and a Training Working Group of the CTLS has been established to address this.

There was emphasis placed on the importance of networking and learning from others in terms of operation and management but also facilitating and promoting access to cores. A number of European networks and collaborations presented findings in posters and sessions such as EULIFE and networks such as CORBEL (www.corbel-project.eu) and NEUBIAS (www.neubias.org).

In general CTLS2018 illustrated that those that offer a shared resource, a facility or support research within an institute or university all encounter similar problems and that working together to improve operations and management will only improve cores and add to the scientific outputs of institutes and universities.

 Natalie Homer presenting at the “Emerging Model Systems” session as part of the  CLTS conference in Ghent (photograph courtesy of Valentina Adami, University of Trento, Italy)

Natalie Homer presenting at the “Emerging Model Systems” session as part of the  CLTS conference in Ghent (photograph courtesy of Valentina Adami, University of Trento, Italy)


Cold Spring Harbor Laboratory Metabolomics Course (from David Sumpton)

Since the Cold Spring Harbor laboratory (CSHL) metabolomics course was founded in 2016, members of the metabolomics facility at Beatson Institute have assisted in its organisation and delivery. In June, David Sumpton from the facility returned for his second year.

The course is very technology driven, through a close collaboration with Agilent Technologies and Thermo Fisher Scientific, with a pop-up mass spectrometry lab assembled over a matter of weeks. A wide range of high-end instrumentation is made available for the students, from LC and GC triple quads, LC- time of flight (ToF) and LC-Orbitrap instrumentation. Over a period of two weeks, the students learn both the fundamental theory and application of these different GC/LC-MS methodologies to answer biological questions. Key concepts are further emphasised through practical sessions with considerable amounts of hands-on time. As part of the broader programme, students also hear talks from more than a dozen invited speakers working in the metabolism field. Each speaker gives two presentations, an informal and often interactive chalk talk underlining the main experimental tools they employ in their own research and a more formal big picture scientific talk summarising their work. Speakers this year included Matthew Vander Heiden (Massachusetts Institute of Technology), Teresa Fan (University of Kentucky College of Medicine), our own Eyal Gottlieb (Cancer Research UK, Beatson Institute, Glasgow), a founding instructor of the course, and Steve Gross (Weill Cornell Medical College, New York).

The whole process is extremely challenging but also very rewarding. The Cold Spring Harbor campus is beautiful in summer. The isolation and intense timetable leads to a fully emergence experience, one in which we, along with the students, always learn a great deal.

 Photograph of participants of the 2018 CSHL metabolomics course. Bottom row, course instructors: Justin Cross, Memorial Sloan Kettering Cancer Center. Amy Caudy, The Donnelly Centre, University of Toronto, Canada and Adam Rosebrock, Stony Brook School of Medicine, State University of New York. David Sumpton, Beatson Institute metabolomics facility (third from the right, on the backrow) “Cold Spring Harbor Laboratory Meetings & Courses Program” – official course photo)

Photograph of participants of the 2018 CSHL metabolomics course. Bottom row, course instructors: Justin Cross, Memorial Sloan Kettering Cancer Center. Amy Caudy, The Donnelly Centre, University of Toronto, Canada and Adam Rosebrock, Stony Brook School of Medicine, State University of New York. David Sumpton, Beatson Institute metabolomics facility (third from the right, on the backrow) “Cold Spring Harbor Laboratory Meetings & Courses Program” – official course photo)


Notes from our Sponsors: Chromatographic Deconvolution (from John Moncur, SpectralWorks Ltd.)

GC-MS and LC-MS play an important part in the metabolomics workflow. Deriving features from these analytical techniques is a significant part of this workflow.

Peak overlapping or partial co-elution is a common problem in any chromatographic separation technique.  Where a detector which produces spectral characteristics is used, such as a mass spectrometer, the deconvolution of partially overlapping peaks can be achieved without any assumptions being made regarding the peak shape or underlying spectra of the individual components. Figure 1 shows the purpose of chromatographic deconvolution as the resolution between two components is reduced. From fully resolved to unresolved, AnalyzerPro is able to determine the two components in each case.

  Deconvolution of resolved, partially resolved and unresolved components. (courtesy of John Moncur, SpectralWorks, Ltd.)

 Deconvolution of resolved, partially resolved and unresolved components. (courtesy of John Moncur, SpectralWorks, Ltd.)

The benefits of deconvolution can be realised in two ways. The number of features determined in samples may be increased and/or the required chromatographic resolution may be reduced. The effect of the latter is to help reduce analysis time.

Deconvolution brings with it the question of how many data points need to be acquired across a peak? If we reduce the issues of peak fronting and tailing and take the peak width at Full Width Half Maximum (FWHM), typically 8 to 10 sample points would be expected in order to be able to reproducibly generate peak data. Even in the simplest case of partial co-elution, a sampling rate of 20 – 25 data points would not be unreasonable. The closer that the co-eluting components are together, then the more data points are required to generate reliable deconvoluted peak data.

Chromatographic peak deconvolution is very effective at determining multiple components in your samples.  


Scottish Metabolomics Network Papers


Awarded PhD studentships and grants

  • Promovendus – Eurolife Consortium (~£120k): 2018 -2022                                                      Joint PhD Studentship University of Leiden and University of Edinburgh (6 months secondment at University of Edinburgh) “Relieving head pain through modulation of the stress system” (van den Maagdenberg AMJM, Tolner EA, Andrew R, Miejer O)

Metabolomics (and other) Conferences and workshops (in date order)

Androgens 2018 Meeting, 3rd – 5th September 2018.

  • The University of Edinburgh, Edinburgh Medical School: Clinical Sciences.
  • Registration open till 31st August 2018.

Glasgow Polyomics: Introduction to Python for Biologists, 3rd – 7th September 2018.

  • University of Glasgow, Computer Cluster 515, West Medical Building, Glasgow.
  • Registration via enquiry form on website.

Glasgow Polyomics: An Introduction to Omics, 11th-12th September 2018.

  • University of Glasgow, Jura Lab, Library, Main Campus, Glasgow.
  • Registration via enquiry on websit.

Introduction to Metabolomics for the Microbiologist, 19th-21st September 2018.

  • University of Birmingham, Birmingham Metabolomics Training Centre, Birmingham.
  • PhD students and post-doctoral researchers.

Introduction to Metabolomics for the Environmental Scientist, 27th-28th September 2018.

  • University of Birmingham, Birmingham Metabolomics Training Centre, Birmingham.
  • Individuals with no previous experience of metabolomics.

Glasgow Polyomics: Metabolomics Data Analysis Course, 22nd -23rd October 2018.

  • University of Glasgow, Jura Lab, Library, Main Campus, Glasgow.
  • Registration via enquiry form on website.

Introduction to Metabolomics for the Clinical Scientist, 22nd October 2018.

  • University of Birmingham, Birmingham Metabolomics Training Centre, Birmingham.
  • Individuals with no previous experience of metabolomics.

Scottish Metabolomics Network Symposium, 1st and 2nd of November 2018.

  • Discovery Point Exhibition Centre, Dundee, registration now open; Early Bird Registration (£40), closes 19th September 2018 (will be £60 after this date). Lab Visiting Training Grants available for Early Career Researchers (Deadline 29th September 2018).

Metabolomics with the Q-Exactive, 19th-21st November 2018.

  • University of Birmingham, Birmingham Metabolomics Training Centre, Birmingham.
  • Individuals with minimal experience of applying LC=MS in metabolomics studies.

Metabolite identification with the Q-Exactive and LTQ Orbitrap, 22nd -23rd November 2018.

  • University of Birmingham, Birmingham Metabolomics Training Centre, Birmingham.
  • PhD students and post-doctoral researchers.

44th Adipose Tissue Discussion Group – Early Career Researcher Workshop, 6th December 2018.

  • Queens Medical Research Institute, Edinburgh.

44th Adipose Tissue Discussion Group Meeting, 7th December 2018.

  • Informatics Forum, University of Edinburgh, George Square, Edinburgh.
  • Speakers include within other Profs Frederick Karpe (Oxford University) and Jimmy Bell (Imperial College). Further information can be obtained from Nik.Morton@ed.ac.uk., rsemple@exseed.ed.ac.uk

2019 Challenges in Analysis of Complex Natural Mixtures- Faraday Discussion, 13th-15th May 2019.

  • Edinburgh, United Kingdom. Deadline Poster Abstracts, 4th March 2019.

Webinars

New:

Agilent: On-going Omics seminar series

  • A good resource to keep up with analytical developments in different laboratories around the world.
  • Webinars are available on demand but also as power point slides.

Metabolomics: Understanding Metabolism in the 21st Century.

  • Course Length: 4 weeks (~3h per week).
  • 2018 Course Dates: Free course – Available now!
  • Recommended Level: Individuals with no previous experience of metabolomics.

Metabolomics Data Processing and Data Analysis.

  • Course Length: 4 weeks (~4 hours per week).
  • 2018 Course Dates: 8th October – 2nd November 2018.
  • Recommended Level: MSc and PhD students in the early stats of analysing metabolomics data.

SCIEX:  Innovation Advisory Board

  • SCIEX account necessary.
  • a series of "lightening talks".
  • An Infusion “Shotgun” Approach for High-Throughput Untargeted Metabolomics by Marialuce Maldini.

SCIEX: The Proteome: Composition and Organization

  • 40 min video watch on demand.

On Demand (Old):

Biomarker Discovery: SWATH Enabled- Metabolomics Differentiates Known Disease Classifications of Prostate Cancer

  • 30 minute video, watch anytime.

High Resolution Mass Spec Performance Without the Complexity

  • Info-kit available upon registration.

High-Throughput Proteomics Applications to Solve Major Biological Problems Around the Metabolic Network 

  • Webinar available upon registration.

Protein Social Networks Studied By SWATH® Acquisition

  • Webinar available upon registration.

Further Announcements

The Metabolomics Society Board has posted proposed amendments to the Society Bylaws for review and comment which can be found here. Member comments are being solicited for 30 days before any further action is taken. Comments can be send to secretary@metabolomicssociety.org.


Vacancies

Anatune GC-MS Support Engineer 

  • UK based, closing date 17th August 2018

CrawfordScientific Training & Technical Consultant

  •  UK based, closing date 31st August 2018.
  • For further information please contact the Technical Services Manager Claire Paterson claire@crawfordscientific.com (pdf document)

Sciex Support Specialist

  • Open position, based in Warrington, UK
  • Small molecule analysis using QTraps and Q-ToFs for customer demos and onsite training

Thank you

Thank you to all the contributors and Naomi Rankin for help and advice. If you have anything you want to add to the next edition of the newsletter, please e-mail Sabine.Freitag@hutton.ac.uk.


 

 

 

Previous Newsletters

May 2018 Newsletter

  • Scottish Metabolomics Network Symposium 2018 Advert (from Will Allwood and Jeffery Huang)
  • Laboratory of the Quarter: The Edinburgh Clinical Research Facility Mass Spectrometry Core (from Ruth Andrew and Natalie Homer)
  • Metabolomics Workshops at the African Centre for Gene Technologies (from Karl Burgess)
  • A Novel Metabolomics Method Developed by the Dundee Team (from Jeffrey Huang)
  • Symposium on Informatics for Stratified Medicine and Biomarker Discovery (from Naomi Rankin)
  • Technical Managers in Universities Conference (from Natalie Homer)
  • Scottish Metabolomics Network Papers
  • Metabolomics (and other) conferences
  • PhD Opportunities
  • Vacancies
  • Acknowledgements

February 2018 Newsletter

  • Scottish Metabolomics Network Symposium 2018 Advert (from Will Allwood and Jeffery Huang)
  • Laboratory of the Quarter: Hutton Lipidomics (and Proteomics) Research Facility at the University of the Highlands and Islands, Inverness (from Phil Whitfield)
  • Metabolomics Profiling Forum 2017 Birmingham Overview (from Karl Burgess)
  • Metabolomics Training at EMBL-EBI (Naomi Rankin)
  • Edinburgh CRF MS Core Update (from Ruth Andrew)
  • Scottish Metabolomics Network Papers
  • Metabolomics (and other) conferences
  • PhD studentships
  • Vacancies
  • Acknowledgements

 

November 2017 Newsletter

  • Scottish Metabolomics Network Symposium 2017 Special
    • Overview (Ruth Andrew)
    • Technical Sessions (Ruth Andrew and David Watson)
    • Biology Sessions (Ruth Andrew and Kevin Rattigan)
  • Scottish Metabolomics Network Symposium 2018 Advert (Will Allwood and Jeffery Huang)
  • Laboratory of the Quarter: HuttonEnvironmental and Biochemical Sciences Group LC- and GC- MS metabolomics, lipidomics and volatile analysis facilities, James Hutton Institute (from Will Allwood)
  • Edinburgh Update (from Natalie Homer)

  • UK Clinical Research Facilities Network (from Natalie Homer)

  • Synthetic Biology Workshop in China (from Karl Burgess)


 

August 2017 Newsletter

  • Scottish Metabolomics Network Symposium 2017 Update (Naomi Rankin and Gavin Blackburn)
  • Laboratory of the Quarter: Cell Metabolism and Homeostasis Group and Metabolomics/Lipidomics Mass Spectrometry Group at the Institute of Genetics and Molecular Medicine (IGMM) (from Andy Finch)
  • Edinburgh Update (from Ruth Andrew and Natalie Homer)
  • UK Clinical Research Facilities Network (from Natalie Homer)
  • EPSRC UK National Mass Spectrometry Facility 30th Anniversary Symposium (from Natalie Homer)
  • Scottish Metabolomics Network Papers
  • Metabolomics (and other) conferences

May 2017 Newsletter

  • Scottish Metabolomics Network Symposium 2017 Update (Naomi Rankin and Gavin Blackburn)
  • Metabolomics Training in South Africa (Karl Burgess)
  • NMR metabolomics training at EMBL-EBI (Naomi Rankin)
  • Updates from Edinburgh (Ruth Andrew)
  • Updates from the University of Glasgow (Naomi Rankin and Karl Burgess)
  • Papers from the Scottish Metabolomics Network
  • Metabolomics and other conferences

December 2016 Newsletter

Special issue on the Scottish Metabolomics Symposium 2016 in Inverness:

  • Overview (from Karl Burgess and Naomi Rankin)
  • Biology Sessions Overview (from Andrew Finch)
  • Technical Sessions Overview (from Natalie Homer)

September 2016 Newsletter

  • Scottish Metabolomics Network Updates (Karl Burgess)
  • Update on Symposium 2016 (Phil Whitfield)
  • Core expansion at Edinburgh CRF (Ruth Andrew)