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Visualization and interpretation of OPLS models based on 2D NMR Data
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
2008 (Engelska)Ingår i: Chemometrics and Intelligent Laboratory Systems, ISSN 0169-7439, E-ISSN 1873-3239, Vol. 92, nr 2, s. 110-117Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Multivariate analysis on spectroscopic 1H NMR data is well established in metabolomics and other fields where the composition of complex samples is studied. However, biomarker identification can be hampered by overlapping resonances. 2D NMR data provides a more detailed “fingerprint” of the chemical structure and composition of the sample with greatly improved spectral resolution compared to 1H NMR data. In this report, we demonstrate a procedure for the construction of multivariate models based on frequency domain 2D NMR data where the loadings can be visualized as highly informative 2D loading spectra. This method is based on the analysis of raw spectral data without any need for peak picking or integration prior to analysis. Spectral features such as line widths and peak positions are thus retained. Hence, the loadings can be visualized and interpreted on a molecular level as pseudo 2D spectra in order to identify potential biomarkers. To demonstrate this strategy we have analyzed HSQC spectra acquired from populus phloem plant extracts originating from a set of designed experiments with OPLS regression.

Ort, förlag, år, upplaga, sidor
Elsevier, 2008. Vol. 92, nr 2, s. 110-117
Nyckelord [en]
Metabolomics, Two-dimensional NMR spectroscopy, HSQC, Multivariate Data Analysis, OPLS, S-plot
Nationell ämneskategori
Kemi
Identifikatorer
URN: urn:nbn:se:umu:diva-2652DOI: 10.1016/j.chemolab.2008.01.003ISI: 000257223900002Scopus ID: 2-s2.0-43849098252OAI: oai:DiVA.org:umu-2652DiVA, id: diva2:140879
Anmärkning

Originally included in thesis in manuscript form.

Tillgänglig från: 2007-10-19 Skapad: 2007-10-19 Senast uppdaterad: 2022-06-28Bibliografiskt granskad
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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Hedenström, MattiasWiklund, SusanneEdlund, Ulf

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