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Metabolite Profiling Experiments

The GC-MS metabolite profiling experiments given below are made publicly available to get feedback from the community. The relative metabolite concentrations are normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol). Although these details are accessible within the GMD, they are not made available on the web site so far. For these details please refer to the publication. As it is our intention to increase the breadth GMD’s experiment repository in terms of organisms, organs and stresses, we actively work on cross experiment normalisation and thus, profile data and data representation might change in the future without any further notice. For maximal quality assessment, all experiments are described using the XEML framework (see tree below), while the GC-MS chromatograms are processed using the TagFinder software.
Mining for metabolic responses to long-term salt stress: a case study on Arabidopsis thaliana Col-0 (A) contact: kopka@mpimp-golm.mpg.de description: New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using diverse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and divergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress. start date: 2006-01-01 experiment Id: 10b38aaf-b977-4950-85b8-f4775f66658d links: metabolite profile  MapMan pathway  XEML experimental description  ISA-Tab export  TagList Metabolite raw export  TagList Metabolite norm export  TagList Analyte raw export  TagList Analyte norm export  TagList MST raw export
  • 6265if - A 6270
  • doi:10.1111/j.1399-3054.2007.00993.x
  • Sanchez, D. H., Siahpoosh, M. R., Roessner, U., Udvardi, M. and Kopka, J. (2008), Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiologia Plantarum, 132: 209–219. doi: 10.1111/j.1399-3054.2007.00993.x
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observation point: OP 4 observation time: 24.00:00:00 [days . hours : minutes : seconds]
TimeNameValueDurationUnit
initiationSalt0 mM
initiationgreen house studygreen house study  
initiationContainerPot  
initiationContainerPot size: 10 cm  
initiationTypePotting soil  
initiationTypeSoil type: Einheit (Type 0)  
initiationWateringPlants were watered with half-strength GS-90 plus 1/4 Hoagland solution.  
7 experimental conditions(s)
This tree schematises the experimental design of a single metabolite profiling experiment with the x-axis representing the time scale. Branches of the tree are used to describe the plant’s environmental condition. Recorded environmental conditions are either given to describe the general experimental setup and to support cross experiment comparisons, or to indicate the specific stress type. A “salt stress experiment” is described using different salt concentrations. Clicking the nodes of the tree, quantitative environmental conditions (e.g. temperature, salt concentrations, humidity, etc.) describing the plant’s environment can be inspected in the right table. Unfortunately, due to the limitations of the current html based visualisation, the scaling of the tree's branches is not proportional to the real length of time. Green tagged observation points (OP) represent sampling time points. Results in the data analysis (see heat map or MapMan links in table on top) correspond to these observation points. Please note that observation point names (OP1, OP2, etc.) do not relate to each other. Instead, use the description of the observation points to identify potential candidates for cross experiment profile comparison.
service last updated 13/08/2014 © 2008-2014 Golm Metabolome Database - All rights reserved
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