Change search
ReferencesLink to record
Permanent link

Direct link
Cell specific chemotyping and multivariate imaging by combined FT-IR microspectroscopy and OPLS analysis reveals the chemical landscape of secondary xylem
Swedish University of Agricultural Sciences (SLU), Sweden. (Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology)
Umeå University, Faculty of Science and Technology, Department of Chemistry. (Computational Life Science Cluster (CLiC))
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Science and Technology, Department of Chemistry. (Computational Life Science Cluster (CLiC))
Show others and affiliations
2011 (English)In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 66, no 5, 903-914 p.Article in journal (Refereed) Published
Abstract [en]

Fourier-transform infrared (FT-IR) spectroscopy combined with microscopy enables acquiring chemical information from native plant cell walls with high spatial resolution. Combined with a 64 x 64 focal plane array (FPA) detector 4096 spectra from a 0.3 x 0.3 mm image can be simultaneously obtained, where each spectrum represents a compositional and structural "fingerprint" of all cell wall components. For optimal use and analysis of such large amount of information, multivariate approaches are preferred. Here, FT-IR microspectroscopy with FPA detection is combined with orthogonal projections to latent structures discriminant analysis (OPLS-DA). This allows for 1) the extraction of spectra from specific cell types, 2) identification and characterization of different chemotypes using the full spectral information, and 3) further visualising the pattern of identified chemotypes by multivariate imaging. As proof of concept, the chemotypes of Populus tremula xylem cell types are described. The approach revealed unknown features about chemical plasticity and patterns of lignin composition in wood fibers that would have remained hidden in the dataset with traditional data analysis. The applicability of the method on Arabidopsis xylem, and its usefulness in mutant chemotyping is also demonstrated. The methodological approach is not limited to xylem tissues but can be applied to any plant organ/tissue also using other microspectroscopy techniques such as Raman- and UV-microspectroscopy.

Place, publisher, year, edition, pages
Blackwell Publishing Ltd , 2011. Vol. 66, no 5, 903-914 p.
Keyword [en]
FT-IR microspectroscopy, cell wall, lignin composition, wood, poplar, Arabidopsis
URN: urn:nbn:se:umu:diva-41255DOI: 10.1111/j.1365-313X.2011.04542.xPubMedID: 21332846OAI: diva2:405339
Available from: 2011-03-22 Created: 2011-03-22 Last updated: 2013-02-14Bibliographically approved
In thesis
1. Improving interpretation by orthogonal variation: Multivariate analysis of spectroscopic data
Open this publication in new window or tab >>Improving interpretation by orthogonal variation: Multivariate analysis of spectroscopic data
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The desire to use the tools and concepts of chemometrics when studying problems in the life sciences, especially biology and medicine, has prompted chemometricians to shift their focus away from their field‘s traditional emphasis on model predictivity and towards the more contemporary objective of optimizing information exchange via model interpretation. The complex data structures that are captured by modern advanced analytical instruments open up new possibilities for extracting information from complex data sets. This in turn imposes higher demands on the quality of data and the modeling techniques used.

The introduction of the concept of orthogonal variation in the late 1990‘s led to a shift of focus within chemometrics; the information gained from analysis of orthogonal structures complements that obtained from the predictive structures that were the discipline‘s previous focus. OPLS, which was introduced in the beginning of 2000‘s, refined this view by formalizing the model structure and the separation of orthogonal variations. Orthogonal variation stems from experimental/analytical issues such as time trends, process drift, storage, sample handling, and instrumental differences, or from inherent properties of the sample such as age, gender, genetics, and environmental influence.

The usefulness and versatility of OPLS has been demonstrated in over 500 citations, mainly in the fields of metabolomics and transcriptomics but also in NIR, UV and FTIR spectroscopy. In all cases, the predictive precision of OPLS is identical to that of PLS, but OPLS is superior when it comes to the interpretation of both predictive and orthogonal variation. Thus, OPLS models the same data structures but provides increased scope for interpretation, making it more suitable for contemporary applications in the life sciences.

This thesis discusses four different research projects, including analyses of NIR, FTIR and NMR spectroscopic data. The discussion includes comparisons of OPLS and PLS models of complex datasets in which experimental variation conceals and confounds relevant information. The PLS and OPLS methods are discussed in detail. In addition, the thesis describes new OPLS-based methods developed to accommodate hyperspectral images for supervised modeling. Proper handling of orthogonal structures revealed the weaknesses in the analytical chains examined. In all of the studies described, the orthogonal structures were used to validate the quality of the generated models as well as gaining new knowledge. These aspects are crucial in order to enhance the information exchange from both past and future studies.

Place, publisher, year, edition, pages
Umeå: Kemiska institutionen, Umeå universitet, 2011. 62 p.
OPLS, PLS, Multivariate Analysis, Orthogonal variation, Chemometrics, hyperspectral images, FTIR, NIR, spectroscopy
National Category
Chemical Sciences
urn:nbn:se:umu:diva-43476 (URN)978-91-7459-207-8 (ISBN)
Public defence
2011-06-01, KBC-huset, KB3A9, Umeå universitet, Umeå, 10:00 (English)
Available from: 2011-05-11 Created: 2011-05-02 Last updated: 2011-05-30Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Gorzsás, AndrásStenlund, HansPersson, PerTrygg, Johan
By organisation
Department of Chemistry
In the same journal
The Plant Journal

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 233 hits
ReferencesLink to record
Permanent link

Direct link