Retention index thresholds for compound matching in GC–MS metabolite profiling

Strehmel, Nadine; Hummel, Jan; Erban, Alexander; Strassburg, Katrin; Kopka, Joachim

doi:10.1016/j.jchromb.2008.04.042

Cited by 161 publications

(135 citation statements)

References 35 publications

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“…de/; Kopka et al, 2005;Schauer et al, 2005;Hummel et al, 2010), dated 3/15/2011. At least four matching masses were required with a minimum match value of 750 and a maximum retention index deviation of 1.0 for the positive annotation of an analyte (Strehmel et al, 2008). From the annotated analytes, a data profile was calculated, where the intensities of each analyte were scaled to 100 over the different samples.…”

Section: Gc-ms: Polar Metabolitesmentioning

confidence: 99%

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

et al. 2014

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We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ‡8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.

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Section: Gc-ms: Polar Metabolitesmentioning

confidence: 99%

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

et al. 2014

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“…Metabolites were annotated manually using the Target Finder function in the TagFinder software using the Golm Metabolome Database (Kopka et al, 2005) (http://gmd.mpimp-golm.mpg.de). Criteria for manual metabolite identification were the presence of at least four specific mass fragments per compound, a match value >750, and a retention index deviation <1.0% (Strehmel et al, 2008).…”

Section: Measurements Of Metabolites By Gc-msmentioning

confidence: 99%

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model OrganismChlamydomonas reinhardtii

et al. 2014

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We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R 2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.

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“…Compounds were identified comparing RIs and mass spectra with the UPSC-SMC in-house database and with the public Golm Metabolome Database of the Max Planck Institute. For comparison with the Golm Metabolome Database, RIs measured on the 5% phenyl-95% dimethylpolysiloxane capillary column VAR5 (Golm Metabolome Database) were transferred to the DB-5 (10m) system of the UPSC-SMC (Strehmel et al, 2008;Hummel et al, 2010). Samples were normalized on the unit variance and no centering (UVN) scores of integrated areas for the internal standards (methyl stearate and salicylic acid-D4).…”

Section: Data Processing and Identificationmentioning

confidence: 99%

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

et al. 2016

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Plants have evolved adaptive mechanisms that allow them to tolerate a continuous range of abiotic and biotic stressors. Tropospheric ozone (O 3 ), a global anthropogenic pollutant, directly affects living organisms and ecosystems, including plant-herbivore interactions. In this study, we investigate the stress responses of Brassica nigra (wild black mustard) exposed consecutively to O 3 and the specialist herbivore Pieris brassicae. Transcriptomics and metabolomics data were evaluated using multivariate, correlation, and network analyses for the O 3 and herbivory responses. O 3 stress symptoms resembled those of senescence and phosphate starvation, while a sequential shift from O 3 to herbivory induced characteristic plant defense responses, including a decrease in central metabolism, induction of the jasmonic acid/ethylene pathways, and emission of volatiles. Omics network and pathway analyses predicted a link between glycerol and central energy metabolism that influences the osmotic stress response and stomatal closure. Further physiological measurements confirmed that while O 3 stress inhibited photosynthesis and carbon assimilation, sequential herbivory counteracted the initial responses induced by O 3 , resulting in a phenotype similar to that observed after herbivory alone. This study clarifies the consequences of multiple stress interactions on a plant metabolic system and also illustrates how omics data can be integrated to generate new hypotheses in ecology and plant physiology.

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Retention index thresholds for compound matching in GC–MS metabolite profiling

Cited by 161 publications

References 35 publications

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model OrganismChlamydomonas reinhardtii

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure

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