Integration of LC/MS-based molecular networking and molecular docking allows in-depth annotation and prediction of the metabolome: A study of Salvia miltiorrhiza Bunge

Wang, Shiqi; Su, Yuekai; Li, Jingyu; Liu, Yongping; Mei, Xiangui; Wang, Jianhua

doi:10.1016/j.indcrop.2022.115298

Cited by 12 publications

(6 citation statements)

References 28 publications

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“…The binding energy between arabinan/AG-II and TLR4 were −31.4 and −30.5 kJ/mol, respectively (Table ). The binding energy <−5 kJ/mol indicated that the molecular docking result was good . Thus, it proved that both main chain and two side chains had a good docking effect with TLR4.…”

Section: Resultsmentioning

confidence: 99%

“…The binding energy <−5 kJ/mol indicated that the molecular docking result was good. 37 Thus, it proved that both main chain and two side chains had a good docking effect with TLR4. They all docked at the active part of TLR4 (Figure 7C1 (arabinan and AG-II) were similar and lower than that of the main chain.…”

Section: Molecular Docking Simulation Between Low/high Branched Pecti...mentioning

confidence: 91%

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Highly Branched Rhamnogalacturonan-I Type Pectin from Wolfberry: Purification, Characterization, and Structure-Prebiotic/Immunomodulatory Activity Relationship

Gu,

Lin,

Zhao

2024

J. Agric. Food Chem.

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Due to the difficulty in obtaining highly branched rhamnogalacturonan-I (RG-I) type pectin, the relationship between the extent of RG-I branching (EB) of pectin and prebiotic/immunomodulatory activity has not been systematically investigated. Moreover, it is only possible to establish a structure−activity relationship using pectin that is highly purified and accurately characterized. In this study, a homogeneous highly branched RG-I type pectin (LBP-P4, a final product) with dual proliferative effects on Bif idobacterium and macrophage was effectively purified for the first time using enzyme hydrolysis combined with ultrafiltration. The RG-I content and EB of LBP-P4 reached 97.32 and 77.12, respectively. Its two branches were composed of arabinan and arabinogalactan-II, containing → 5)-Araf-(1→, →3)-Araf-(1→, →3,6)-Galp-(1→ and →6)-Galp-(1→ residues). The structure−activity relationship analysis indicated that strong prebiotic/immunomodulatory activity of LBP-P4 was depended on its high EB, which was further confirmed by the molecular docking simulation between low/high branched pectin with β-1,6galactosidase, α-L-arabinanase, and Toll-like receptor 4 (TLR4).

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Section: Resultsmentioning

confidence: 99%

Section: Molecular Docking Simulation Between Low/high Branched Pecti...mentioning

confidence: 91%

Highly Branched Rhamnogalacturonan-I Type Pectin from Wolfberry: Purification, Characterization, and Structure-Prebiotic/Immunomodulatory Activity Relationship

Gu,

Lin,

Zhao

2024

J. Agric. Food Chem.

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“…SIRIUS provides a fragmentation tree to each relevant peak (feature), describing the fragmentation reaction from each molecule from the ESI. The CSI:FingerID feature can then be used to search in molecular structure databases from the internet for tentative identification of compounds 42 .…”

Section: Methodsmentioning

confidence: 99%

Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana

Subrahmaniam,

Lind Salomonsen,

Radutoiu

et al. 2023

Open Res Europe

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Background Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions. Methods Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions. Results Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software. Conclusions The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.

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“…The Q Exactive Plus Orbitrap Mass Spectrometer, for instance, boasts a resolution of 140,000 full width at half-maximum and a scanning accuracy of less than 1 ppm, making it suitable for analyzing complex mixtures. It has been extensively utilized in metabolomics 6 and proteomics research. 7 In 2011, it was confirmed that the composition fingerprints obtained by FT-ICR and Orbitrap analysis of crude oil samples were essentially the same.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Differential Markers among Crude Oil Samples Using UPLC-QE-MS/MS and Multivariate Statistical Analysis

Wang

Zuo

Gao³

et al. 2023

Energy Fuels

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In this study, we utilized ultra-high-performance liquid chromatography–Q Exactive plus Orbitrap mass spectrometry (to analyze the compounds in crude oil samples from two different reservoirs and proposed a novel analytical approach. The new method encompasses three-dimensional visualization of mass spectrometry (MS) data, various multivariate statistical analyses, and a combination of multivariate statistical and conventional analytical methods. The results revealed that the differential markers of the two groups of crude oil samples were primarily concentrated in N1, N1O1, and N1O1S1 compounds, with four-ring alkaline nitrogen-containing compounds such as benzacridines and highly condensed alkaline nitrogen-containing compounds serving as the best differential markers for distinguishing the two groups of crude oil samples. Furthermore, we discussed the application value of this method in petroleum-contaminated groundwater. This method demonstrates the potential and application value of multivariate statistical methods in the analysis of high-resolution MS data of crude oil.

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Integration of LC/MS-based molecular networking and molecular docking allows in-depth annotation and prediction of the metabolome: A study of Salvia miltiorrhiza Bunge

Cited by 12 publications

References 28 publications

Highly Branched Rhamnogalacturonan-I Type Pectin from Wolfberry: Purification, Characterization, and Structure-Prebiotic/Immunomodulatory Activity Relationship

Highly Branched Rhamnogalacturonan-I Type Pectin from Wolfberry: Purification, Characterization, and Structure-Prebiotic/Immunomodulatory Activity Relationship

Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana

Characterization of Differential Markers among Crude Oil Samples Using UPLC-QE-MS/MS and Multivariate Statistical Analysis

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