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University of Gothenburg
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Photo: Anna-Lena Lundqvist
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Metabolomics – what is it?

Metabolomics research focuses on the analysis of small (<1.5kDa) molecules (metabolites) and their temporal and systematic variation altered by internal or external factors. In short, metabolomics is the identification and quantification of all metabolites in a biological sample detected by the present technology at a given condition and/or point in time. For NMR, this encompasses about 50 to a few hundred metabolites depending on the matrix analyzed. At the Swedish NMR Centre we have experience of a number of different biological matrices for metabolomics analysis, the majority being human origin (serum/plasma, urine, feces and extracts of different tissues such as muscle, liver and brain) but also including samples from model organisms such as mouse, rat, yeast, insects, macroalgae, mammalian cell cultures and bacteria.

The two dominant analytical techniques in metabolomics is mass spectrometry and NMR. The former is available to researchers in Sweden primarily through the Swedish Metabolomics Centre, which also has a node in Gothenburg in the Chalmers Mass Spectrometry Infrastructure. The Swedish NMR Centre in Gothenburg and Umeå offers NMR-based metabolomics, with access to both expertise in sample collection for solid-state NMR (e.g. biopsies) and for bioliquids, and also support for statistical analysis of collected data is available.

For NMR, a typical metabolomics sample means detection and quantification of 50 to a few hundred metabolites depending on sample matrix. At the SNC we have experience in a broad palette of matrices. The majority of samples are of human origin (serum, plasma, urine, fecal water, extracts of different tissues such as liver, brain and muscles) but we also have experience in handling samples from mice, rat, yeast, nematodes, insects, macroalgae, mammalian cell cultures and bacteria.

Metabolomics instrumentation

The instrumentation at the site in Gothenburg includes cooled sample changers hooked up to 600MHz and 800 MHz spectrometers. The 600MHz spectrometer is set up as a Bruker IVDr platform (more information from Bruker) making results obtained in Gothenburg directly comparable to results obtained elsewhere in the world, allowing for big collaborations as well as longitudinal studies where samples are recorded at different times.

The workflow guarantess minimal degradation and high quality of samples using highly automated procedures with an unbroken cold chain, generating NMR data of high international standard which is essential for downstream biological interpretation of metabolomics data.

 

The reproducibility of metabolomics measurement by adhering to the IVDr standard operating procedures is excellent, as shown here for spectra of a quantification reference between Apr 208 and Mar 2020 where the CV is well below 5%.
Photo: Anders Pedersen

Did you have coffee or tea for breakfast?

1D NMR spectra of urine gives a direct fingerprint of which metabolites that are present above a certain concentration threshold. The answer to the question can be found in the multivariate analysis of the spectra. Similarly, it is possible to train statistical models for other characteristics such as diet variants, disease versus healthy controls etc. The goal is to find typical metabolite profiles that reflect different metabolic states and after that be able to build models where the state/projected outcome for unknown samples can be predicted with high certainty.

Information on costs and sample matrices

We offer access to metabolomics measurements in projects ranging from pure service to full statistical analysis of data.

For metabolomics, a per-sample cost model is employed. In projects where the IVDr functionality is desired, i.e. automatic quantitation of metabolites and/or lipoprotein profiling, the cost is 200 SEK per sample. For samples where IVDr is not requested or for other sample matrices, the cost is 150 SEK per sample.

Depending on the agreed support level at project start, additional costs for staff hours may apply. For pure service projects (sample handling, data acquisition, data processing and data delivery) 10 hours of free staff time is included with the requirement that the NMR Centre is acknowledged in any resulting publication using the data. For collaborative projects 40 hours of free staff time is included with the requirement that at least one NMR Centre staff is included as coauthor on any resulting publication. In both cases, staff time spent in excess of the free 10 and 40 hours, respectively, will be charged at 700 SEK per hour.

Plasma/serum, sample preparation through dilution 50/50:

  • B.I.Lisa automatic lipoprotein profiling (IVDr)
  • B.I.Quant automatic quantitation of ~40 metabolites (IVDr)
  • Biobank QC quality control of sample matrix and data quality (IVDr)
  • At least 110 µl sample, preferably 325 µl

Plasma/serum, sample preparation through methanol precipitation:

  • Automatic deproteinization with methanol precipitation using an Agilent Bravo liquid handling robot
  • Compatible with internal standard quantitation
  • Offers additional metabolites compared to dilution sample preparation
  • At least 150 µl sample

Urine, sample preparation through dilution 10/90:

  • B.I.Quant automatic quantitation of up to 150 metabolites (IVDr)
  • Biobank QC quality control of sample matrix and data quality (IVDr)
  • At least 200 µl sample, preferably 650 µl or more