The Swedish Metabolomics Centre (SMC; SLU/UmU) is a state-of-the-art facility which has specialized in the use of mass spectrometry based methods for the analysis of metabolites in different biological systems. A mass spectrometry laboratory performing research on plant hormones and also in metabolite analysis has been operating at SLU in Umeå since the 1990s. The laboratory has offered metabolite services since 2002 within the framework of the metabolomics platform. Dedicated staff and instrumentation have offered analysis to Swedish researchers in everything from clinical- to plant research. In 2012, a larger grant was obtained from the Knut & Alice Wallenberg Foundation (KAW), with the purpose of expanding the facility to a national knowledge and service centre in metabolite analysis for Swedish researchers. To mark this restart, the facility was renamed the Swedish Metabolomics Centre. Since 2016, Swedish Metabolomics Centre is a platform within the national centre Science for Life Laboratory (www.scilifelab.se).

Since the start in 2002 has far more than 123 000 samples have been analyzed in the facility, ranging from plant to plasma and cerebrospinal fluid samples. The requests since 2013 have originated from more than 100 different researchers, covering all the major institutes of higher education in Sweden. For more information, read this article.

Organization

SMC is divided into two parts; a service platform and Metabolomics 2.0. The purpose of the service platform is to conduct and implement methods in order to perform metabolite analysis for Swedish researchers. Metabolomics 2.0 is SMC's research and development program which is run by SLU, UmU and Chalmers. SMC is supervised by the platform Director, who (together with the Co-director) has general responsibility for the facility, including financial matters and the Metabolomics 2.0 project. The contact person for researchers seeking information about our services and other relevant advice is the Facility Manager. SMC has also appointed a Steering Committee that will be meet annually to decide about changes in service direction, and with the help of the Facility Manager monitor the platform’s performance and customer perceptions. The committee will also prioritize and review larger projects when necessary. Contact details for SMC and Steering committee are listed below.

The service platform works as a professional consultant facility and is divided into three components; SMC-consulting, SMC-service and SMC-open access. SMC-consulting focuses on formalizing customer inquiries into what is possible from an analytical chemical point of view. SMC-service performs analyses efficiently according to standard operating procedures and the defined project descriptions which have been established by the customer and SMC.  The open access facility offers Swedish researchers the possibility of being involved in or performing their analyses independently. An overview of the current organization is shown in the figure below.

Organisation 160304

Platform Director
Thomas Moritz (This email address is being protected from spambots. You need JavaScript enabled to view it.)
UPSC, SLU, Umeå. 
Tel: +46 (0)90-786 8456; +46 (0)702 690 684

Vice Platform Director
Anders Nordström (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Dept. Molecular biology, UmU, Umeå
Tel: +46 (0)90 785 2561

Head of Facility (contact person Service)
Jonas Gullberg (This email address is being protected from spambots. You need JavaScript enabled to view it.
UPSC, SLU, Umeå
Phone: +46 (0)90 786 8393

SMC Steering committee 
Thomas Moritz, SLU;  This email address is being protected from spambots. You need JavaScript enabled to view it. (Chair)
Maria Fällman, UmU;  This email address is being protected from spambots. You need JavaScript enabled to view it.
Gunnar von Heijne, SU; This email address is being protected from spambots. You need JavaScript enabled to view it.
Göran Karlsson, GU; This email address is being protected from spambots. You need JavaScript enabled to view it.
Hindrik Mulder, Lu; This email address is being protected from spambots. You need JavaScript enabled to view it.
Jens B. Nielsen, Chalmers; This email address is being protected from spambots. You need JavaScript enabled to view it.

Steering Committee metabolomics at Chemical-Biological-Centre, Umeå (KBC)
Thomas Moritz, SLU;  This email address is being protected from spambots. You need JavaScript enabled to view it. (Chair)
Johan Trygg, UmU;  This email address is being protected from spambots. You need JavaScript enabled to view it.
Maria Fällman, UmU;  This email address is being protected from spambots. You need JavaScript enabled to view it.
Per Gardeström, UmU;  This email address is being protected from spambots. You need JavaScript enabled to view it.
Stefan Marklund, UmU;  This email address is being protected from spambots. You need JavaScript enabled to view it.
Ove Nilsson, SLU;  This email address is being protected from spambots. You need JavaScript enabled to view it.
Bernt-Eric Uhlin, UmU; This email address is being protected from spambots. You need JavaScript enabled to view it.

Funding

The Swedish Metabolomics Centre has been awarded a major grant from the Knut & Alice Wallenberg (KAW) foundation to support a 8-year program, starting from the 1st of January 2013, with co-funding from SLU and Umeå UniversityThe Kempe foundation is gratefully acknowledged for previous funding. The facility is also receiving direct or indirect support via other grants or projects, e.g. from Erling Perssons Stiftelse (for neuro-metabolomic analyses and instrumentation support), Trees and Crops for the Future, the UPSC Berzelii project (VR/Vinnova; general support) and BBMRI (post-doc support). Since 2016, Swedish Metabolomics Centre is a platform within the national centre Science for Life Laboratory (www.scilifelab.se).

Collaborations

Chemometric expertise (CLiC and BILS)
CLiC (Computational Life Science Cluster) is an umbrella for bioinformatics researchers at Umeå University. It is engaged in advanced bioinformatics research within the fields of genomics, proteomics (including protein modelling) and metabolomics, including the development of chemometric approaches for experimental design and analysis of omics-data.

BILS (Bioinformatics for Life Sciences) is a distributed national research infrastructure supported by Swedish Research Council (Vetenskapsrådet) providing bioinformatics support to life science researchers. It works in close collaboration with SciLifeLab, as a facility within the SciLifeLab Bioinformatics platform, with SNIC (Swedish National Infrastructure for Computing) for storage of bioinformatics data and it is the Swedish contact point to the European infrastructure for biological information (ELIXIR). BILS offers short-term bioinformatics consultation for free, but also for long-term projects for a fee.

SMC enjoys close collaborations with CLiC and BILS, both at research and support levels.

NMR-based metabolite profiling
As mentioned above, SMC performs NMR metabolite profiling through collaboration with the Swedish NMR Centre (Gothenburg and Umeå) and can provide direct requests for NMR analysis.

Chalmers University of Technology - Department of Biology and Biological Engineering (Prof. Jens B. Nielsen)
A major aim for the platform is to support, in collaboration with Prof. Jens B. Nielsen, integrative analysis of metabolomic data by providing access to various metabolic network models (via the web) for all key organisms. This will allow integrative analysis of metabolomic with other, e.g. transcriptomic and proteomic, data. 

SciLifeLab
Science for Life Laboratory, SciLifeLab, is a national center for molecular biosciences with focus on health and environmental research. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.

WABI
WABI is a facility within SciLifeLab Bioinformatics platform, and offers bioinformatics long-term support in the format of “embedded bioinformaticians”- senior bioinformaticians working in your project for an extended time, typically 6 – 12 calendar months. WABI is supported via grant from the Knut and Alice Wallenberg Foundation and is predominantly targeting projects that have generated high-throughput data of kinds that can be produced at the SciLifeLab platforms.

Swedish Metabolomics Centre and WABI have initiated a joint metabolomics-bioinformatics project.

Instrumentation

GC and LC/MS are techniques that combine the physical separation capabilities of chromatography (LC/GC) with mass spectrometry (MS). MS is an analytical technique that measures the mass-to-charge ratios of charged particles. At SMC we have both GC and LC instruments coupled with time-of-flight (TOF), QTOF, QqQ detectors and Orbitrap. A TOF instrument is a single MS detector. The MS detectors (mass filtering) for both the QTOF and QqQ can be used separately or in combination to perform both MS and MS/MS. The Orbitrap is mainly used at SMC for identification in MSmode.

Mass spectrometers funded by WCN, KAW and Kempe foundation, dedicated to metabolomic analyses
LECO Pegasus III, GCTOFMS, 2002
LECO HT, GCTOFMS, 2010
Agilent 6490 UHPLC-QqQMSMS, 2013
Agilent 6490 UHPLC-QqQMSMS, 2013
Agilent 6550 iFunnel Accurate-Mass UHPLC-QTOFMSMS, 2013
Agilent 6550 iFunnel Accurate-Mass UHPLC-QTOFMSMS, 2013
Agilent 6560 Ion Mobility UHPLC-QTOFMSMS, 2015
Agilent 6495 UHPLC-QqQMSMS, 2017

Mass spectrometers at the UPSC mass spectrometer facility
Thermo LTQ-Orbitrap XL, UHPLC-high resolution MSMS, 2009
Agilent 7000, GCQqQMSMS, 2011
Waters SYNAPT G2-Si HDMS, Acquity M-Class, nano source,  2015, Proteomics Core Facility (www.kbc.umu.se/english/proteomics/)
Waters Xevo TQ-S, Aqcuity M-Class, iKey source, 2016, Proteomics Core Facility (www.kbc.umu.se/english/proteomics/)

NMR instrumentation at collaborating sites of the Swedish NMR center (Gothenburg and Umeå). 

TOF=time-of-flight mass spectrometer
Q=quadrupole mass spectrometer
q=quadrupole mass spectrometer with RF, only used as a “collision cell”

Contact

Jonas Gullberg
Head of Facility
This email address is being protected from spambots. You need JavaScript enabled to view it.