Data correction strategy for metabolomics analysis using gas chromatography–mass spectrometry

Kanani, Harin; Klapa, Maria I.

doi:10.1016/j.ymben.2006.08.001

Cited by 123 publications

(154 citation statements)

References 20 publications

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“…Specific details are provided in Supplemental Methods and Supplemental Data Set S1. After appropriate data correction, normalization, and filtering (Kanani et al, 2010;Kanani and Klapa, 2007), profiles of 55 metabolite derivatives were considered in the multivariate statistical analysis using the hierarchical clustering analysis, principal component analysis, and significance analysis for microarrays algorithms implemented in the "omic" data analysis software TM4 MeV (v4.8.1) software (Saeed et al, 2003(Saeed et al, , 2006. Further details on the metabolomic data normalization, filtering, and statistical analysis can be found in Supplemental Methods.…”

Section: Metabolomic Data Acquisition and Analysismentioning

confidence: 99%

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO₂ Source in Plants

et al. 2016

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Calcium oxalate crystals are widespread among animals and plants. In land plants, crystals often reach high amounts, up to 80% of dry biomass. They are formed within specific cells, and their accumulation constitutes a normal activity rather than a pathological symptom, as occurs in animals. Despite their ubiquity, our knowledge on the formation and the possible role(s) of these crystals remains limited. We show that the mesophyll crystals of pigweed (Amaranthus hybridus) exhibit diurnal volume changes with a gradual decrease during daytime and a total recovery during the night. Moreover, stable carbon isotope composition indicated that crystals are of nonatmospheric origin. Stomatal closure (under drought conditions or exogenous application of abscisic acid) was accompanied by crystal decomposition and by increased activity of oxalate oxidase that converts oxalate into CO 2 . Similar results were also observed under drought stress in Dianthus chinensis, Pelargonium peltatum, and Portulacaria afra. Moreover, in A. hybridus, despite closed stomata, the leaf metabolic profiles combined with chlorophyll fluorescence measurements indicated active photosynthetic metabolism. In combination, calcium oxalate crystals in leaves can act as a biochemical reservoir that collects nonatmospheric carbon, mainly during the night. During the day, crystal degradation provides subsidiary carbon for photosynthetic assimilation, especially under drought conditions. This new photosynthetic path, with the suggested name "alarm photosynthesis," seems to provide a number of adaptive advantages, such as water economy, limitation of carbon losses to the atmosphere, and a lower risk of photoinhibition, roles that justify its vast presence in plants.

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Section: Metabolomic Data Acquisition and Analysismentioning

confidence: 99%

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO₂ Source in Plants

et al. 2016

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“…The 40 pooled plasma samples were treated together with the samples from the OGTT, but left out in the following multivariate statistics calculations. Since the metabolome comprises a heterogeneous group of molecules, the impact on them by extraction, derivatisation and analysis differs substantially (Gullberg et al 2004;Kanani and Klapa 2007). Great care must therefore be taken to use the appropriate IS for normalisation.…”

Section: Data Treatment and Modellingmentioning

confidence: 99%

“…Amino acids were predominant among the analytes with the highest loadings along the predictive components. Drift of amino acids is frequently observed in GC/MS when all samples are derivatised at the same time, and is partially due to the slow progression of disilylation of primary amines (Kanani and Klapa 2007). Additional factors causing instrumental drift are septum bleeding and increased contamination of the injector liner, which gradually cause deterioration of the performance of GC (Anastassiades et al 2003).…”

Section: Orthogonal Projections To Latent Structuresmentioning

confidence: 99%

Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism

et al. 2009

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Gas chromatography/mass spectrometry-based metabolomics was applied to investigate dynamic changes in the plasma metabolome upon an oral glucose tolerance test (OGTT). The OGTT is a frequently used diagnostic test of glucose homeostasis and diabetes. Diabetes is diagnosed either when glucose levels C7.0 mM in the fasting state or C11.0 mM at 2 h after oral glucose intake. The accuracy of the OGTT would, however, most likely improve if additional variables could be identified. In the present study, plasma samples were drawn every 15 min for 2 h after an oral glucose load of 75 g preceded by an overnight fast in healthy individuals. Blood plasma levels of more than 200 putative metabolites were measured. Multivariate modelling was used to distinguish metabolic regulation due to the glucose challenge from that of other variability. Two data scaling methods were applied, yielding similar results when evaluated by appropriate diagnostic tools. Fatty acid levels were found to be strongly decreased during the OGTT. Also, the levels of amino acids were shown to decrease. However, technical and uninduced biological variations were found to affect the amino acid levels to a greater extent than the fatty acid levels, making the fatty acids more reliable as indicators of metabolic regulation. Levels of several metabolites correlated with the quadratic glucose profile and two were found having an inverse correlation. Raw data plots of all identified significantly altered metabolites confirmed the excellent performance of the multivariate models. Using this approach, a better understanding of the metabolic response to an OGTT can be achieved, paving the way for inclusion of other variables describing appropriate metabolic control.

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“…In many derivatization schemes, and specifically for TMS-based silylations, reactions are not stopped by adding quenching chemicals or fractionation schemes but may continue over hours. This fact has raised concerns that drifts over time need to be captured and corrected for [18]. Apart from the obvious necessity to completely randomize analytical sequences, it has been suggested to use technical replicates from pooled samples as baseline allowing comparisons even for unknown peaks and as a general measure to ensure minimal quality control [35].…”

Section: Quality Control and Methods Comparisonsmentioning

confidence: 99%

“…Most commonly, trimethylsilylation (TMS) is used to exchange acidic protons and thus increase volatility of (polar) metabolites [17] although some amino acids may require special attention with respect to the peak ratio corresponding to the different derivatization status of primary amine groups [18]. As alternative to the mild and universal silylation reaction, derivatization by ethylchloroformate, has been suggested for urine analysis [19] yielding quantitative precision better than 10% RSD for metabolites tested in standard addition series.…”

Section: Sample Preparation For Gc-ms Metabolite Profilingmentioning

confidence: 99%

Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry

Fiehn

2008

TrAC Trends in Analytical Chemistry

208

148

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Gas chromatography coupled to mass spectrometry (GC-MS) is one of the most frequently used tools for profiling primary metabolites. Instruments are mature enough to run large sequences of samples; novel advancements increase the breadth of compounds that can be analyzed, and improved algorithms and databases are employed to capture and utilize biologically relevant information. Around half the published reports on metabolite profiling by GC-MS focus on biological problems rather than on methodological advances. Applications span from comprehensive analysis of volatiles to assessment of metabolic fluxes for bioengineering. Method improvements emphasize extraction procedures, evaluations of quality control of GC-MS in comparison to other techniques and approaches to data processing. Two major challenges remain: rapid annotation of unknown peaks; and, integration of biological background knowledge aiding data interpretation.

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Data correction strategy for metabolomics analysis using gas chromatography–mass spectrometry

Cited by 123 publications

References 20 publications

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO₂ Source in Plants

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO₂ Source in Plants

Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism

Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry

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Data correction strategy for metabolomics analysis using gas chromatography–mass spectrometry

Cited by 123 publications

References 20 publications

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO2 Source in Plants

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO2 Source in Plants

Metabolomic analysis of a human oral glucose tolerance test reveals fatty acids as reliable indicators of regulated metabolism

Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry

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Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO₂ Source in Plants

Alarm Photosynthesis: Calcium Oxalate Crystals as an Internal CO₂ Source in Plants