Design of Experiments in metabolomics-related studies: An overview

Jacyna, Julia; Kordalewska, Marta; Markuszewski, Michał J.

doi:10.1016/j.jpba.2018.11.027

Cited by 79 publications

(52 citation statements)

References 51 publications

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“…It is extremely important to design an experiment containing the correct controls, in order to be able to associate observed metabolite changes with the condition being investigated [7,8]. The main types of controls to consider including are: (a) Positive controls, where changes are expected.…”

Section: The Importance Of Controlsmentioning

confidence: 99%

From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data

Ivanišević

Want

2019

Metabolites

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Untargeted metabolomics (including lipidomics) is a holistic approach to biomarker discovery and mechanistic insights into disease onset and progression, and response to intervention. Each step of the analytical and statistical pipeline is crucial for the generation of high-quality, robust data. Metabolite identification remains the bottleneck in these studies; therefore, confidence in the data produced is paramount in order to maximize the biological output. Here, we outline the key steps of the metabolomics workflow and provide details on important parameters and considerations. Studies should be designed carefully to ensure appropriate statistical power and adequate controls. Subsequent sample handling and preparation should avoid the introduction of bias, which can significantly affect downstream data interpretation. It is not possible to cover the entire metabolome with a single platform; therefore, the analytical platform should reflect the biological sample under investigation and the question(s) under consideration. The large, complex datasets produced need to be pre-processed in order to extract meaningful information. Finally, the most time-consuming steps are metabolite identification, as well as metabolic pathway and network analysis. Here we discuss some widely used tools and the pitfalls of each step of the workflow, with the ultimate aim of guiding the reader towards the most efficient pipeline for their metabolomics studies.

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Section: The Importance Of Controlsmentioning

confidence: 99%

From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data

Ivanišević

Want

2019

Metabolites

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“…Metabolomics technique describes differences and similarities of biological materials by analyzing and comparing ingredients in organisms [19,20], which has been applied widely in the metabolites of diseases, herb species, and food types over recent years. Of various analytical techniques in metabolomics, UHPLC-Q-TOF/MS showed excellent sensitivity, high resolution, and practicality of databases that has been employed intensively in species discrimination and discovery of bioactive compounds from complex matrices [21].…”

Section: Introductionmentioning

confidence: 99%

Comparative investigation of phytochemicals among ten citrus herbs by ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time‐of‐flight mass spectrometry and evaluation of their antioxidant properties

Zhu

Zhou

et al. 2020

J of Separation Science

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The citrus herbs have proved their important medicinal and nutritional values as medicine–food dual‐purpose herbs, functional foods, or medical herbs in China. In this study, phytochemicals and antioxidant activity among ten typical citrus herbs (ethanol extracts) were investigated comprehensively. The major ingredients and their contents were analyzed by high‐resolution mass spectrometry, and the differences of typical fragment ions between flavanone‐7‐O‐rutinoside(s) and flavanone‐7‐O‐neohesperidoside(s) were discriminated properly in negative electrospray ionization mode. Total polyphenols, total flavonoids, 1,1‐diphenyl‐2‐picrylhydrazyl, 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulphonic acid), and ferric reducing antioxidant power tests were performed, which indicated their beneficial values and antioxidant effects. The medicine–food dual‐purpose herbs including Chenpi, Juluo, Daidaihua, Huajuhong, Xiangyuan, and Foshou exhibited antioxidant capacities significantly by decreasing intracellular reactive oxygen species intensity (P < 0.01), enhancing superoxide dismutase, catalase, and glutathione peroxidase activities (P < 0.01) in H2O2‐induced RIN‐m5F cells. Moreover, the functional foods Zhishi, Zhiqiao, and Qingpi showed moderate antioxidant bioactivity, while the medical herb Juhe showed weak antioxidant bioactivity, which were consistent with the multivariate analysis of their major flavonoids. The study provided a new sight for the chemical differentiation and practical application of citrus herbs as medicine–food dual‐purpose herbs, functional foods, or medical herbs.

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“…Furthermore, the simplex design for mixtures, is well known by the work of Scheffe 27 in 1963. According to several scientists [28][29][30][31][32][33] , mixture design is generally used to examine the formulations that are composed of many constituents to determine the best combination of all the components.…”

Section: Introductionmentioning

confidence: 99%

The use of experimental design methodology in the formulation of a new additive for the dispersion of elemental sulfur in triple superphosphate fertilizer

et al. 2020

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Yields improvement of the crop depends on many parameters witch each of them acts for a specific manner to boost the plant growth and allow the soil to be more efficient to any kind of plant. Our research is based on the implementation of elemental sulfur into the preparation of triple superphosphate fertilizer and its dispersion into the blend. By adding a small amount of it to the mixture, sulfur particles disperse uniformly by using additives in the phosphate fertilizer.This technique is successfully reached by integrating many additives obtained from different chemical industries to spread out the sulfur particle in the fertilizer.Several experiments were done by adopting the experimental design methodology (DOE) related to a screening mixture design to select the best surfactant used. So, nine commercial products with different chemical proprieties have been evaluated as a dispersant of elemental sulfur in triple superphosphate fertilizer. First, thanks to the screening mixture design, three products have been chosen for this formulation. Second, by using the mixture design method, new dispersants of elemental sulfur in triple superphosphate fertilizer have been reached. With this method, apart from it is being possible to obtain several dispersants, it is also possible to control the distribution and the average of the particle diameter of the elemental sulfur. Moreover, statistical validation tests confirm the achievement of the sulfur particle size of approximately 1000 µm.

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Design of Experiments in metabolomics-related studies: An overview

Cited by 79 publications

References 51 publications

From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data

From Samples to Insights into Metabolism: Uncovering Biologically Relevant Information in LC-HRMS Metabolomics Data

Comparative investigation of phytochemicals among ten citrus herbs by ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time‐of‐flight mass spectrometry and evaluation of their antioxidant properties

The use of experimental design methodology in the formulation of a new additive for the dispersion of elemental sulfur in triple superphosphate fertilizer

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