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The GMD web site use latest HTML5 features! This message indicates backward compatibility problems in GMD's mass spectra, chemical compound structure and metabolite profile visualizations. As your browser does not support the HTML5 <canvas> element, please consider to upgrade to a HTML5 ready web browser, including Microsoft Internet Explorer, Mozilla Firefox, Apple Safari, Google Chrome and Opera, to fully enjoy GMD's functionalities!

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.

Title
Factor(s)	Genus	Accessions	Replica Groups	Samples	Metabolites
metabolic changes during developmental senescence: a case study on Arabidopsis thaliana (single leaves)
Material, Time, Total Light	Arabidopsis	1	9	41	105
Mining for metabolic responses to long-term salt stress: a case study on Arabidopsis thaliana Col-0 (A)
Salt	Arabidopsis	1	5	30	68
Mining for metabolic responses to long-term salt stress: a case study on Arabidopsis thaliana Col-0 (B)
Salt	Arabidopsis	1	5	28	67
Mining for metabolic responses to long-term salt stress: a case study on Arabidopsis thaliana Col-0 (C)
Salt	Arabidopsis	1	5	30	67
Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (A)
Salt	Lotus	1	7	47	110
Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (B)
Salt	Lotus	1	7	46	107
Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (C)
Salt	Lotus	1	7	40	105
Metabolomic responses to long-term salt stress in related Lotus species (A)
Germplasm, Salt	Lotus	8	16	96	58
Metabolomic responses to long-term salt stress in related Lotus species (B)
Germplasm, Salt	Lotus	8	16	96	53
Metabolomic responses to long-term salt stress in related Lotus species (C)
Germplasm, Salt	Lotus	8	16	84	59
15 experiment(s)
Page of 2     Results per page: 5 10 25 50 100 500

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metabolic changes during developmental senescence: a case study on Arabidopsis thaliana (single leaves) contact: kopka@mpimp-golm.mpg.de description: Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence. start date: 1900-01-01 experiment Id: 542eb5ee-9f53-4ec0-bf81-92c67e95625f links: metabolite profile  MapMan pathway  XEML experimental description  ISA-Tab export         

• By: Watanabe, Mutsumi; Balazadeh, Salma; Tohge, Takayuki; et al.
• Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis
• doi: 10.1104/pp.113.217380
• PLANT PHYSIOLOGY Volume: 162 Issue: 3 Pages: 1290-1310 Published: JUL 2013
• submission to GMD: Alexander Erban / MPIMP

short day

OP 1

OP 4

OP 5

observation point: OP 1 observation time: 52.04:00:00 [days . hours : minutes : seconds]

Time	Name	Value	Duration	Unit
initiation	Total Light	150	08:00:00	µE/m^2/s
initiation	Total Light	0	16:00:00	µE/m^2/s
initiation	Temperature	20	08:00:00	°C
initiation	Temperature	16	16:00:00	°C
initiation	Type	Potting soil
initiation	Type	Soil Type GS-90 Einheitserde; Gebrueder Patzer
initiation	green house study	green house study
14d	growth chamber study	growth chamber study
8 experimental conditions(s)

ReplicaGroupLabel	GermPlasm	Material	Developmental Stage
rg1 52d04h central zone of the leaf lamina	Arabidopsis thaliana.Col-0	central zone of the leaf lamina	rosette growth stage
rg2 52d04h leaf base	Arabidopsis thaliana.Col-0	leaf base	rosette growth stage
rg3 52d04h leaf tip	Arabidopsis thaliana.Col-0	leaf tip	rosette growth stage
3 replica group(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.