AMDIS-Metab R data manipulation for the geographical and floral differentiation of selected honeys from Zambia and Botswana based on volatile chemical compositions using SPME–GC–MS

Sichilongo, Kwenga; Padiso, Tumelo; Turner, Queen

doi:10.1007/s00217-020-03523-x

Cited by 10 publications

(17 citation statements)

References 23 publications

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“…Using the IHC electrical conductivity values tabulated for the honeys from those origins as a guide, the Zambian and TLOK honey had similar values as blossom honey, while BOT, PELO, and RAMO honeys, from Botswana, had similar values as Honeydew honey. All the honey samples herewith have previously been shown to be polyfloral (Sichilongo et al., 2020) while the electrical conductivity values tabulated by the IHC are for monofloral honeys applicable to honeys from Europe, Asia, America, and Australia. The intersections were however expected.…”

Section: Resultsmentioning

confidence: 99%

Physicochemical characterization and adulteration detection of selected commercial and natural honeys from Zambia and Botswana

Padiso

Keiphetlhetswe

Chinyama

et al. 2021

J. Food Process. Preserv.

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Three commercial and three natural honeys from Zambia and Botswana were analyzed for selected physicochemical parameters using analytical methods prescribed by the International Honey Commission. The parameters were specific conductivity, moisture/ash contents, pH, acidity by titration to pH 8.3, sucrose, fructose, and glucose. Multivariate statistical evaluation of the physicochemical data using partial least squares was used to classify the honeys according to their geographical and floral origins. Sugars were analyzed using Fourier transform infrared spectroscopy (FTIR) in which validation of the methods employed gave limits of detection (LODs) that ranged between 3.4 and 8.8 g/100 honey and correlation coefficients that ranged between 0.9779 and 0.9865. The concentration ranges for the sugars were (g/100 g honey) sucrose (ND − 10.4), fructose (22.4–28.4), and glucose (29.3–49.2). Overall, none of the honeys examined showed signs of adulteration with the three sugars. These data are lacking in many African countries, which are emerging as honey production giants. Practical applications We report physicochemical properties of selected raw natural and commercial honeys from Zambia and Botswana using the International Honey Commission guidelines. This is a prelude to database creation to protect apiarists from fraud in honey trade in many African countries emerging as giant honey producers and is to the best of our knowledge the first such report in the Southern African Development Community region.

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Section: Resultsmentioning

confidence: 99%

Physicochemical characterization and adulteration detection of selected commercial and natural honeys from Zambia and Botswana

Padiso

Keiphetlhetswe

Chinyama

et al. 2021

J. Food Process. Preserv.

Self Cite

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“…Chemstation Version E0202 GC–MS sample raw data files were processed using the metabolomics workflow described by Sichilongo et al 11 and Aggio et al 12 In a nutshell, Automated Mass Spectral Deconvolution and Identification System (AMDIS), in combination with the NIST 14 Mass Spectral Library, 13,14 was used for automated deconvolution of the raw data files acquired by Chemstation. The data were further processed using Metab R on the R platform 15 for Windows to make it amenable for statistical evaluation.…”

Section: Methodsmentioning

confidence: 99%

“…46 LA is a geometric isomer of linoelaidic acid and is widely studied for different applications. [47][48][49][50] Other bioactive compounds observed in the species were farnesol (4), with confirmed quorum sensing disruption properties for Candida albicans [51][52][53] ; farnesyl acetate (5), implicated in the inhibition of DNA replication in both Chinese hamster ovary cells and human HeLa cells 54 ; lasiodiplodin (14), known to inhibit photophosphorylation and electron transport chain in thylakoids 55 ; and pyrogallol (11), with potential for antiproliferative effect on some human cancer cell lines and anti-inflammatory, antioxidant, and acetylcholine inhibition effects. [56][57][58] Farnesol (4) was mainly found in the n-hexane extracts of the leaves for both the maceration and Soxhlet extraction methods.…”

Section: Bioactive Constituents Of C Platypetalum Extractsmentioning

confidence: 95%

Untargeted GC–MS metabolomics to identify and classify bioactive compounds in Combretum platypetalum subsp. oatesii (Rolfe) Exell (Combretaceae)

Umoh

Bojase

Masesane

et al. 2022

Phytochemical Analysis

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Introduction: Combretum platypetalum is used in traditional African healing practices against different infections. Unfortunately, no scientific knowledge of its phytochemical composition exists, except for the isolation of two compounds from the leaves.Scientific study has been limited to the leaves only, despite the applications of stems and roots in traditional medicine practice and natural product drug discovery programs. Objective: Omics was applied to identify and classify different volatile and semivolatile bioactive compounds in the leaf, stem, and root parts of C. platypetalum. The thermal stability of the plant constituents at 60-65 C extraction temperature by Soxhlet and maceration at room temperature on the type, class, and concentration of compounds in the leaf was further investigated. Method: A GC-MS untargeted metabolomics approach, automated deconvolution by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) for GC-MS data, preprocessing by Metab R, and multivariate statistical data analysis were employed in this study. Results: A total of 97 phytoconstituents, including 17 bioactive compounds belonging to the terpenoids, flavonoids, long-chain fatty acids, and other unclassified structural arrangements distributed across C. platypetalum, were identified for the first time. A correlation (r = 0.782; P = 0.000) between Soxhlet and maceration extraction methods relative to resolved chromatographic peak areas of metabolites was established. Conclusion: Findings corroborate the reported bio-investigation of its leaf extracts, its traditional uses, and previous findings from the Combretum genus. The results substantiate the possible applications of C. platypetalum in natural product drug discovery and provide a guide for future investigations.

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“…Metab R is for high-throughput of metabolomics data generated by GC-MS. MetabR was developed by the R Development Core Team in 2008. The package uses the R programming language for data correction, filtering and reshaping of datasets initially produced by AMDIS [32]. [32] combined the power of AMDIS, Metab R and MINITAB to classify the floral geographical origins of three randomly selected commercially produced and three unprocessed natural organic honeys from Zambia and Botswana using GC-MS untargeted metabolomics of volatile components.…”

Section: Metab Rpackagementioning

confidence: 99%

“…The package uses the R programming language for data correction, filtering and reshaping of datasets initially produced by AMDIS [32]. [32] combined the power of AMDIS, Metab R and MINITAB to classify the floral geographical origins of three randomly selected commercially produced and three unprocessed natural organic honeys from Zambia and Botswana using GC-MS untargeted metabolomics of volatile components. [32] used the Metab R package to recalculate peak intensities, display peak areas, remove false positives, normalize by internal standard, normalize by biomass as well as carry out the h test, that is, analysis of variance (ANOVA) and the t test on data generated by AMDIS for metabolomics, both targeted and non-targeted.…”

Section: Metab Rpackagementioning

confidence: 99%

Review of the use of R Programming for Data Analysis in Botswana Research

Ndaba¹

2022

Artificial Intelligence, Soft Computing and Applications

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R is widely used by researchers in the statistics field and academia. In Botswana, it is used in a few research for data analysis. The paper aims to synthesis research conducted in Botswana that has used R programming for data analysis and to demonstrate to data scientists, the R community in Botswana and internationally the gaps and applications in practice in research work using R in the context of Botswana. The paper followed the PRISMA methodology and the articles were taken from information technology databases. The findings show that research conducted in Botswana that use R programming were used in Health Care, Climatology, Conservation and Physical Geography, with R part as the most used R package across the research areas. It was also found that a lot of R packages are used in Health care for genomics, plotting, networking and classification was the common model used across research areas.

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AMDIS-Metab R data manipulation for the geographical and floral differentiation of selected honeys from Zambia and Botswana based on volatile chemical compositions using SPME–GC–MS

Cited by 10 publications

References 23 publications

Physicochemical characterization and adulteration detection of selected commercial and natural honeys from Zambia and Botswana

Physicochemical characterization and adulteration detection of selected commercial and natural honeys from Zambia and Botswana

Untargeted GC–MS metabolomics to identify and classify bioactive compounds in Combretum platypetalum subsp. oatesii (Rolfe) Exell (Combretaceae)

Review of the use of R Programming for Data Analysis in Botswana Research

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