lab methods

Swedish Metabolomics Centre is a collaboration between Swedish University of Agricultural Sciences (SLU), Umeå University, and Chalmers University of Technology. Since 2016, Swedish Metabolomics Centre is a part of SciLifeLab.

The Swedish Metabolomics Centre (SMC; SLU/UmU) is a state-of-the-art facility that 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 ( ).

The SMC service has analyzed more than 30 different sample types, ranging from plant and fungi to plasma and cerebrospinal fluid samples. Since 2014 SMC service has been involved in more than 90 publications.

Introduction to metabolomics

Metabolites are important components of all living organisms. It is well known that disturbances in metabolic patterns cause metabolic diseases, which may have dramatic consequences for an organism’s survival. Besides screening of metabolic diseases, focused or general profiling of metabolites (metabolomics) or lipids is necessary in order to understand basic biological processes - processes as nitrogen uptake in plants, interactions between micro- and host organisms, and developmental biology of animals or plants.

A metabolomic analysis combines a number of steps from tissue extraction through the detection and measurement of metabolites to analysis, interpretation, and visualization of the results. All steps may either be untargeted or targeted. The choice depends on the analytical/biological questions posed and various other factors including the classes, stability, and other properties of the metabolites of interest. It also depends on whether or not the samples need to be purified, detection limits, and required analytical accuracy.

Metabolomics methodology can generally be divided into the following three analytical types:

1. Untargeted metabolite profiling
Up to 3000 putative metabolites can be detected using a combination of selected untargeted analytical techniques. Untargeted approaches can cover many classes of metabolites and thus provide broad information about the metabolic state of the analysed samples. However, only a fraction of the detected compounds will be automatically identified or annotated.
2. Targeted metabolite profiling
This refers to the analysis of specific compound classes, e.g. amino acids and amines, fatty acids, eicosanoids, and hormones. Using LC-QqQMSMS and GC-QqQMSMS in multiple-reaction-monitoring (MRM) mode up to 100 selected compounds can be detected and measured in a single analysis. The advantages of targeted approaches are their selectivity and accuracy.
3. Functional group-specific metabolite profiling
This refers to advanced chemical derivatisation and detection strategies to analyse compound-specific structures of both known and unknown compounds. Such strategies can profile, for example, primary and secondary amines, aldehydes, and carboxylic acids.



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 and UmU. 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 Head of Unit.

The SMC service platform works as a professional consultant facility and is divided into three components; Consulting, Service and 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.


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

Head of Unit (contact person Service)
Annika Johansson (This email address is being protected from spambots. You need JavaScript enabled to view it.
Dept. Plant Physiology, UmU, Umeå
Tel: +46 (0)90 786 5551


Chemometric expertise (CASP and NBIS)
(This part is under construction)

The Computational Analytics Support Platform (CASP) is a data analytics service at Umeå University, that supports life science researchers in the analysis of experimental data using data driven tools and strategies. An important role of CASP is acting as an extended support for researchers generating data at the Swedish Metabolomics Centre. The group has strong expertise in data driven life science, in addition to wide domain expert knowledge arising from active engagement with multiple projects in the metabolomics area and beyond. This allows a full understanding of the researcher’s needs, not only in terms of the data analysis, but also in how the data was generated and equally important, the interpretation of the biology behind the project.

CASP provides researchers with modern data analytics tools primarily within multivariate data analysis, but also within AI/deep learning, univariate statistics and statistical experimental design. Support can be provided from day one starting with experimental design, basic and more in-depth data analysis, through to interpretation of results and publishing.

For more information please contact the Platform Manager This email address is being protected from spambots. You need JavaScript enabled to view it. and visit CASP’s webpage.

NBIS (National Bioinformatics Infrastructure Sweden)

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.

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.


GC-MS 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.

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

Mass spectrometers funded by WCN, KAW and Kempe foundation, dedicated to metabolomic analyses
LECO Pegasus BT, GCTOFMS, 2017
Agilent 6490 UHPLC-QqQMSMS, 2013
Agilent 6490 UHPLC-QqQMSMS, 2013
Agilent 6546 Accurate-Mass UHPLC-QTOFMSMS, 2020
Agilent 6546 Accurate-Mass UHPLC-QTOFMSMS, 2020
Agilent 6560 Ion Mobility UHPLC-QTOFMSMS, 2016
Agilent 6495 UHPLC-QqQMSMS, 2017
Agilent 7000, GCQqQMSMS, 2011

Other instrumentation
Agilent RapidFire, 2019
Agilent Bravo, 2019

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


The Swedish Metabolomics Centre has been awarded a major grant from the Knut & Alice Wallenberg (KAW) foundation to support a 5-year program with co-funding from SLU and Umeå UniversityThe Kempe foundation is gratefully acknowledged for previous funding. Since 2016, Swedish Metabolomics Centre is a platform within the national centre Science for Life Laboratory (