Metabolomics Facility

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Extraction and derivatization

Gullberg J, Jonsson P, Nordström A, Sjöström M, Moritz T (2004) Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal Biochem 331: 283-295.
A, J.; Trygg, J.; Gullberg.; Johansson, A.I.; Jonsson, P.; Antti, A.; Marklund, S.L.; Moritz, T. Extraction and GC/MS analysis of the human blood plasma metabolome. Anal. Chem. 2005, 77, 8086-8094.

Data processing H-MCR

Jonsson P, Gullberg J, Nordström A, Kusano M, Kowalczyk M, Sjöström M, Moritz T (2004) A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Anal Chem 76: 1738-1745
Jonsson P, Johansson AI, Gullberg J, Trygg J, A J, Grung B, Marklund S, Sjöström M, Antti H, Moritz T (2005) High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Anal Chem 77: 5635-5642
Jonsson P, Johansson ES, Wuolikainen A, Lindberg J, Schuppe-Koistinen I, Kusano M, Sjöström M, Trygg J, Moritz T, Antti H (2006) Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data - A potential tool for multi-parametric diagnosis. J Prot Res 5: 1407-1414

Mass spectra library identification

Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, Lundgren K, Roessner-Tunali U, Forbes MG, Willmitzer L, Fernie AR, Kopka J (2005) GC-MS libraries for the rapid identification of metabolites in complex biological samples. Febs Letters 579: 1332-1337

Multivariate analysis

Trygg J, Gullberg J, Johansson AI, Jonsson P, Moritz T (2006) Chemometrics in metabolomics-An introduction. In Plant metabolomics (Ed Saito K, Dixon RA, Willmitzer L) Spinger-Verlag.

Trygg J, Holmes E, Lundstedt T (2007) Chemometrics in metabonomics. J Proteome Res 6: 469-479

Metabolomics has attracted increasing interest in recent years, since it has the power and scope to resolve funda- mental biological issues that cannot be readily addressed using other approaches. It also provides a means to identify “biomarkers” related to diverse disease and developmental states of plants, animals (including humans) and other or- ganisms. The UPSC mass spectrometry laboratory houses a national academic metabolomics platform, the WCN metabolomics facility, which was launched in 2002 as part of the Wallenberg Consortium North functional genom- ics initiative. So far, more than 45 000 samples have been analyzed in the facility, ranging from plant to plasma and cerebrospinal fluid samples.

During the last decade, the sequencing of genomes of various prokaryotic and eukaryotic species has revolutionised biology. The data that these efforts have yielded facilitate analyses that provide insights into the genetic basis of similarities and differences between diverse organisms. They also create new possibilities for investigating the fundamental biology of different organisms, as well as the genetic basis of various diseases. Analysis of gene function by targeted knockouts and mutations, and the measurement of gene products, such as mRNA and protein species, are currently the main methods
used in functional genomics. However, these methods do not provide all the information needed to determine how changes in mRNA or protein profiles are linked to changes in biological function. Complex regulatory interactions occur at all levels in eukaryotic cells, and a change at one level in the network does not necessarily lead to a significant change in function or phenotype. Nevertheless, in order to understand many aspects of biology and gene function, broad phenotypic characterisation is also essential. In addition to the abovementioned methods and traditional morphological and anatomical observations, this requires thorough analysis of metabolite profiles, including characterisation of metabolomes, metabolite network analysis and flux determinations.
Metabolomics analysis is usually divided into several steps: 1. Design of Experiment, 2. Sampling and extraction of metabolites, 3. Chemical analysis of metabolites, for example by mass spectrometry or NMR, 4. Data processing of MS-files, 5. Statistical analysis of data, 7. Visualisation of data. All of these steps are essential in metabolomic analyses and require careful optimization. At UPSC, we are focusing on developing all parts of the metabolomics chain, using competences from a wide range of areas, e.g. biology, analytical chemistry and chemometrics.

Access to the facility

The Metabolomics facility at Umeå Plant Science received substantial support from the Wallenberg Consortium North (WCN; www.wcn.se), and the facility is open for the universities associated to the WCN.

Funding

The facility is now receiving funding from SLU. Wallenberg and The Kempe foundation are highly acknowledged for previous funding.

Scientific director
Thomas Moritz
UPSC, SLU, Umeå.
Tel: 090-786 84 56

Research engineer mass spectrometry and contact person
Krister Lundgren
UPSC, SLU, Umeå
Tel: 090-786 82 42

Chemometrical expertise

Johan Trygg (co-director)
Research group for chemometrics, UmU, Umeå
This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Henrik Antti
Research group for chemometrics, UmU, Umeå
This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Steering committee
Not decided yet.

The steering committee will, if necessary, be responsible to allocate instrument time to the different projects.

Services at the Metabolomics facility

The main services at the facility are the following:

Advice regarding design of metabolomics experiment
Advice regarding extraction protocols
Extraction of samples (depends on the type of samples)
Mass spectrometry analysis
Basic multivariate analysis on obtained results (PCA, PLS, PLS-DA, O-PLS, OPLS-DA)
Simple presentation of obtained results. Only the differences between samples will be presented

The services at the facility will not include:

Extensive identification of unknown compounds.
Extensive multivariate analysis on obtained results.

If above mentioned services are necessary, please contact the facility for information about collaborations within different research groups at UPSC or the Chemometrical group at UmU.

Instrumentation at the metabolomics facility

Mass spectrometers funded by WCN and Kempe fundation, and dedicated to metabolomics
LECO Pegasus III, Gas chromatography - mass spectrometry/time-of-flight analyser (GC/TOFMS)
Waters Acquity UPLC - LCT premier time-of-flight (Tof) mass spectrometer (UPLC/TOFMS)
Thermo LTQ-Orbitrap XL LC/MS (UHPLC-high resolution MS/MS)
Agilent 6460 QQQ LC/MS (triple-stage quadropole mass spectrometer)
Bruker Esquire 3000 plus, Liquid chromatography mass spectrometer (LC/MS)

Mass spectrometers at the UPSC mass spectrometer facility
JEOL JMS-MStation GC/MS (magnetic-sector mass spectrometer)
Micromass Quattro Ultima LC/MS (triple-stage quadrupole mass spectrometer)
Micromass Q-TOF Ultima LC/MS (quadrupole/time-of-flight mass spectrometer)
Applied Biosystem Voyager-DE STR (Maldi-TOF)

Above instruments might, when necessary, be used within the metabolomics facility.

Book instruments online. (You need to be logged in to manage bookings)

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September 2010

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