TagFinder for the quantitative analysis of gas chromatography—mass spectrometry (GC-MS)-based metabolite profiling experiments

Luedemann, Alexander; Strassburg, Katrin; Erban, Alexander; Kopka, Joachim

doi:10.1093/bioinformatics/btn023

Cited by 508 publications

(410 citation statements)

References 51 publications

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“…Samples were analyzed using GC-TOF-MS (ChromaTOF software, Pegasus driver 1$61; LECO). The chromatograms and mass spectra were evaluated using TagFinder software (Luedemann et al, 2008) and NIST05 software (http://www.nist.gov/srd/mslist.cfm). Metabolite identification was manually supervised using the mass spectral and retention index collection of the Golm Metabolome Database (Kopka et al, 2005;Hummel et al, 2010).…”

Section: Measurement Of Primary Metabolism By Gc-time Of Flight-ms Anmentioning

confidence: 99%

Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis

et al. 2013

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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 stressinduced 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.

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Section: Measurement Of Primary Metabolism By Gc-time Of Flight-ms Anmentioning

confidence: 99%

Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis

et al. 2013

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“…Chromatograms and mass spectra were evaluated by Chroma TOF Ò 4.2 (Leco, St. Joseph, MI) and TagFinder 4.0 [31] for quantification and annotation of the peaks using the MPI Golm Metabolome Database (GMD, http://gmd.mpimp-golm.mpg.de/, [32]). The amounts of metabolites were determined as relative metabolite abundances, calculated by normalization of signal intensity to that of ribitol, which was added as an internal standard and then by dry weight of the material.…”

Section: Metabolome Analysismentioning

confidence: 99%

Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis

Gechev¹,

Benina²,

Obata

et al. 2012

Cell. Mol. Life Sci.

169

262

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“…Aliquots (150 mL) of the polar (upper) phase were evaporated to dryness using a centrifugal concentrator, and metabolites were subsequently derivatized and analyzed using an established GC-TOF-MS protocol (Lisec et al, 2006). GC-TOF-MS chromatograms were evaluated using TagFinder (Luedemann et al, 2008). Analytes were manually identified using the TargetFinder plug-in of the TagFinder software and a reference library of ambient and 13 C-or 15 N-labeled mass spectra and retention indices from the Golm Metabolome Database (http://gmd.mpimp-golm.mpg.…”

Section: Extraction Of Metabolites and Gc-tof-ms Metabolitementioning

confidence: 99%

Regulation of Primary Metabolism in Response to Low Oxygen Availability as Revealed by Carbon and Nitrogen Isotope Redistribution

et al. 2015

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Based on enzyme activity assays and metabolic responses to waterlogging of the legume Lotus japonicus, it was previously suggested that, during hypoxia, the tricarboxylic acid cycle switches to a noncyclic operation mode. Hypotheses were postulated to explain the alternative metabolic pathways involved, but as yet, a direct analysis of the relative redistribution of label through the corresponding pathways was not made. Here, we describe the use of stable isotope-labeling experiments for studying metabolism under hypoxia using wild-type roots of the crop legume soybean (Glycine max). [ 13 C]Pyruvate labeling was performed to compare metabolism through the tricarboxylic acid cycle, fermentation, alanine metabolism, and the g-aminobutyric acid shunt, while [ 13 C]glutamate and [ 15 N]ammonium labeling were performed to address the metabolism via glutamate to succinate. Following these labelings, the time course for the redistribution of the 13 C/ 15 N label throughout the metabolic network was evaluated with gas chromatography-time of flight-mass spectrometry. Our combined labeling data suggest the inhibition of the tricarboxylic acid cycle enzyme succinate dehydrogenase, also known as complex II of the mitochondrial electron transport chain, providing support for the bifurcation of the cycle and the down-regulation of the rate of respiration measured during hypoxic stress. Moreover, up-regulation of the g-aminobutyric acid shunt and alanine metabolism explained the accumulation of succinate and alanine during hypoxia.

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TagFinder for the quantitative analysis of gas chromatography—mass spectrometry (GC-MS)-based metabolite profiling experiments

Abstract: Exemplary TagFinder workspaces and test data sets are made available upon request to the contact authors. TagFinder is made freely available for academic use from http://www-en.mpimp-golm.mpg.de/03-research/researchGroups/01-dept1/Root_Metabolism/smp/TagFinder/index.html.

Cited by 508 publications

References 51 publications

Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis

Comprehensive Dissection of Spatiotemporal Metabolic Shifts in Primary, Secondary, and Lipid Metabolism during Developmental Senescence in Arabidopsis

Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis

Regulation of Primary Metabolism in Response to Low Oxygen Availability as Revealed by Carbon and Nitrogen Isotope Redistribution

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