Photo: Rebecca Forsberg
On 28-29 of January, over 30 researchers from the Metabolomics Platform and Swedish NMR center met in Umeå. During the lunch-to-lunch retreat, they brainstormed ideas for the future and launched their new initiative that will help find the needle in the haystack of metabolomic data: the Computational Metabolomics Group.
Every year, the Metabolomics platform at SciLifeLab, which SMC is a unit in, meets to share last year's success, gain a clear view of the platform’s scientific standing and brainstorm ideas for the future. The metabolomics platform consists of three units: SMC, CMSI at Chalmers University of Technology and the National Facility for Exposomics at Stockholm University, all with their unique expertise and strengths.
“We want to find new ways in which we can exchange our knowledge and skills, for instance, by enabling staff scientists to spend more time at the other units”, says Annika Johansson, Coordination Officer of the platform and Head of Unit of SMC who hosted the retreat.
This year the Swedish NMR Centre, which also offers metabolomics services, was also invited to participate in the retreat. “By learning more about our respective techniques, discussing future technology development and how to overcome common obstacles, we hope to offer better services for the Swedish research community”, says Annika Johansson.
At the retreat, the platform also initiated a new group that will support users in handling and analyzing metabolomic data: the Computational Metabolomics Group. The group is a joint effort between the Metabolomics platform and the National Bioinformatics Infrastructure Sweden (NBIS).
“We are very excited about this group that will provide support to our users in translating the numbers in Excel sheets into meaningful biological and chemical interpretations", says Annika Johansson.
The group is led by Associate Professor Carl Brunius at CMSI and Katie Bennett, research coordinator at the Computational Analytics Support Platform (CASP).
“Metabolomics is essential for understanding a variety of biological processes, from plants to human health, but studying metabolites together presents the challenge of handling massive datasets. Finding the right information can feel like searching for a needle in a haystack. With the Computational Metabolomics Group, we hope to help users sift through the data”, says Katie Bennett.
The Metabolomics Platform consists of three units
Swedish Metabolomics Centre (SMC) at Umeå University and SLU.
Chalmers Mass Spectrometry Infrastructure (CMSI) at Chalmers University of Technology.
National Facility for Exposomics at Stockholm University.
Invited to the retreat was also
Swedish NMR Centre, situated at Umeå University and University of Gothenburg, and members from the National Bioinformatics Infrastructure (NBIS) involved in the Metabolomics platform.
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Photo: Jenna Lihavainen
The Swedish Metabolomics Centre (SMC) at Umeå University and the Swedish University of Agricultural Sciences (SLU) recently hosted a workshop for young scientists eager to delve into the world of metabolomics. Organised in collaboration with the Metabolomics Unit at the Institute for Molecular Medicine Finland (FIMM), the University of Helsinki and the Laboratory for Molecular Infection Medicine in Sweden (MIMS), the workshop focused on the rapidly evolving role of data analysis in interpreting complex datasets, which are crucial for advancing metabolomics research. Metabolomics, the study of small molecules known as metabolites, plays a crucial role in understanding biological systems.
By analysing the metabolome, researchers can gain insights into molecular mechanisms, such as how organisms respond to drugs or identify new disease markers. This makes metabolomics an essential tool in fields like molecular medicine, where it can help unravel complex biological processes.
The workshop kicked off with a public symposium on “Metabolomics in Molecular Medicine,” featuring keynote talks from invited experts in the field:
· Thomas Moritz (Center for Basic Metabolic Research, University of Copenhagen)
· Michael Zimmermann (European Molecular Biology Laboratory, Heidelberg)
· Anni Nieminen (Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki)
· Ujjwal Neogi (Karolinska Institute)
Close to a hundred participants in the audience learned about the latest advancements and applications of metabolomics, including microbiome-host interactions and the use of fluxomics in understanding molecular phenotypes. Elin Larsson, staff scientist at Umeå University who participated in the workshop, said that “the symposium gave a good overview of the variety of things metabolomics can be used for. The talks also showed the complexity behind it all – it was really inspiring!”.
Over the following two days, 14 elected young researchers engaged in hands-on training that encompassed the key steps in metabolomics workflow. They learned about metabolite extraction, theory behind mass spectrometry, and, most importantly, the intricacies of data analysis and interpretation.
Photos: Jenna Lihavainen and Cecilia Pettersson
“Getting the hands-on practice, especially in data analysis, was perfect for me since I am just about to take the next steps and expand my research using mass spectroscopy. Getting to meet the other participants was extremely useful for sharing ideas and experiences, and I appreciated the insights from the experts”, said Elin Larsson.
This workshop highlighted the synergies between the Swedish SMC and MIMS, alongside the Finnish FIMM/HiLIFE, which can serve as a stepping stone for future collaborations within metabolomics and molecular medicine.
Annika Johansson, Head of the Swedish Metabolomics Centre, concluded that “The collaboration with FIMM has been incredibly inspiring, and invaluable for exchanging ideas and advancing the metabolomics research here in Umeå. We are eager to strengthen our partnership further and are already discussing new ways to keep this collaboration going."
Text by Rebecca Forsberg
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Swedish Metabolomics Centre has been a collaborating partner in the Swedish SciLifeLab SCAPIS Wellness Profiling (S3WP) program. Read the article on Nature Communcations by following the link below.
Tebani, A., Gummesson, A., Zhong, W. et al. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun 11, 4487 (2020).
https://doi.org/10.1038/s41467-020-18148-7
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See the article here:
Diamanti et al. Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes. Sci Rep. 2019;9(1):9653.
https://doi.org/10.1038/s41598-019-45906-5
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Photo: Thomas Kieselbach, Umeå University
Anders Nordström, Vice Platform Director for SMC, has been awarded the Berzelius award by the Swedish Mass Spectrometry Society (SMSS) at the annual symposium March 12th 2019, for his contribution towards developing modern metabolomics. We want to congratulate Anders and wish him good luck with his continued research!
To read more on Kemisamfundets website (in Swedish), click here.
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See the article here:
Falkevall et al., Reducing VEGF-B Signaling Ameliorates Renal Lipotoxicity and Protects against Diabetic Kidney Disease, Cell Metabolism, Volume 25, Issue 3, 7 March 2017, Pages 713-726, ISSN 1550-4131
https://doi.org/10.1016/j.cmet.2017.01.004
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In the accepted service projects, we have run 14 500 samples from a variety of biological matrices and performed in total 25 000 analyses. We currently have 40 active Open Access users, and 43 000 analyzes have been performed in our Open Access service.
| Distribution of accepted projects |
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| Distribution of services provided by SMC |
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Sign up for the workshop by sending an email to
When: Thursday the 28th of January, 09.00 - 15.00
Where: N260
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