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Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
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2008 (Engelska)Ingår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 80, nr 1, s. 115-22Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Metabolomics studies generate increasingly complex data tables, which are hard to summarize and visualize without appropriate tools. The use of chemometrics tools, e.g., principal component analysis (PCA), partial least-squares to latent structures (PLS), and orthogonal PLS (OPLS), is therefore of great importance as these include efficient, validated, and robust methods for modeling information-rich chemical and biological data. Here the S-plot is proposed as a tool for visualization and interpretation of multivariate classification models, e.g., OPLS discriminate analysis, having two or more classes. The S-plot visualizes both the covariance and correlation between the metabolites and the modeled class designation. Thereby the S-plot helps identifying statistically significant and potentially biochemically significant metabolites, based both on contributions to the model and their reliability. An extension of the S-plot, the SUS-plot (shared and unique structure), is applied to compare the outcome of multiple classification models compared to a common reference, e.g., control. The used example is a gas chromatography coupled mass spectroscopy based metabolomics study in plant biology where two different transgenic poplar lines are compared to wild type. By using OPLS, an improved visualization and discrimination of interesting metabolites could be demonstrated.

Ort, förlag, år, upplaga, sidor
Columbus, OH: American Chemical Society , 2008. Vol. 80, nr 1, s. 115-22
Nationell ämneskategori
Biokemi och molekylärbiologi
Identifikatorer
URN: urn:nbn:se:umu:diva-17996DOI: 10.1021/ac0713510OAI: oai:DiVA.org:umu-17996DiVA, id: diva2:157669
Tillgänglig från: 2008-01-02 Skapad: 2008-01-02 Senast uppdaterad: 2018-06-09
Ingår i avhandling
1. Spectroscopic data and multivariate analysis: tools to study genetic perturbations in poplar trees
Öppna denna publikation i ny flik eller fönster >>Spectroscopic data and multivariate analysis: tools to study genetic perturbations in poplar trees
2007 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

In our society in the 21st century one of the greatest challenges is to provide raw materials to the industry in a sustainable way. This requires increased use of renewable raw materials such as wood. Wood is widely used in pulp, paper and textile industries and ongoing research efforts aim to extend the use of wood in e.g. liquid biofuels and green chemicals. At Umeå Plant Science Center (UPSC) poplar trees are used as model systems to study wood formation. The objective is to understand the function of the genes underlying the wood forming process. This knowledge could result in improved chemical and physical wood properties suitable for different industrial processes. This will in turn meet the demands for a sustainable development.

This thesis presents tools and strategies to unravel information regarding genetic perturbations in poplar trees by the use of nuclear magnetic resonance (NMR) spectroscopy and multivariate analysis (MVA). Furthermore, gas chromatography/mass spectrometry (GC/MS) is briefly discussed in this context. Multivariate methods to find patterns and trends in NMR data have been used for more than 30 years. In the beginning MVA was applied in pattern recognition studies in order to characterize chemical structures with different ligands and in different solvents. Today, the multivariate methods have developed and the research have changed focus towards the study of biofluids from plant extracts, urine, blood plasma, saliva etc. NMR spectra of biofluids can contain thousands of resonances, originating from hundreds of different compounds. This type of complex data can be hard to summarize and interpret without appropriate tools and require sophisticated strategies for data evaluation. Related fields of research are rapidly growing and are here referred to as metabolomics.

Five different research projects are presented which includes analysis of poplar samples where macromolecules such as pectin and also small molecules such as metabolites were analysed by high resolution magic angle spinning (HR/MAS) NMR spectroscopy, 1H-13C HSQC NMR and GC/MS. The discussion topics include modelling of metabolomic time dependencies in combination with genetic variation, validation of orthogonal projections to latent structures (OPLS) models, selection of putative biomarkers related to genetic modification from OPLS-discriminant analysis (DA) models, measuring one of the main components found in the primary cell-walls of poplar i.e. pectin, the use of Fourier transformed two-dimensional (2D) NMR data in OPLS modelling and model complexity in a PLS model.

Ort, förlag, år, upplaga, sidor
Umeå: Kemi, 2007. s. 81
Nyckelord
NMR spectroscopy, Metabolomics, Degree of methylation, S-plot, SUS-plot, Metabonomics, Poplar, MLR, PLS, OPLS, PCA, Pectin, Wood
Nationell ämneskategori
Organisk kemi
Identifikatorer
urn:nbn:se:umu:diva-1396 (URN)978-91-7264-380-2 (ISBN)
Disputation
2007-11-09, N360, Johan bures väg, Umeå, 10:00
Opponent
Handledare
Tillgänglig från: 2007-10-19 Skapad: 2007-10-19 Senast uppdaterad: 2018-06-09Bibliografiskt granskad

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Wiklund, SusanneEdlund, UlfGottfries, JohanTrygg, Johan

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Analytical Chemistry
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