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This work is the result of a research collaboration between the laboratory of Analytical Chemistry of Gembloux Agro-Bio Tech of l’Université de Liège (ULg) and the laboratory of Organic Pharmaceutical Chemistry of the Faculty of Pharmacy of l’Université Libre de Bruxelles (ULB). The main objective of this Master thesis was to verify the presence or absence of secondary metabolites of Alternaria fungus and more particularly those which are antagonistic to the metabolism of sphingolipids such as fumonisins, AAL toxins and australifungin in cereal samples contaminated with fungi using liquid chromatography coupled with mass spectrometry (LC-MS). The other objective of this work consisted of a more exhaustive search of the constituents extracted from the samples via LC-MS/MS chemometric tools. A metabolic approach was applied to be able to discriminate samples and look for metabolites that differentiate samples from each other. To do this, we started by an optimization of the chromatographic separations method on raw flour extracts. The introduction of an SPE clean-up was also done with a view to a "selective" improvement of the chromatographic profiles. The next step consisted in analyzing australifungin at m/z 409.2585 ± 0.1 [M + H]+ in the raw extracts. Analytical parameters (tR and MS spectrum) obtained from each samples were compared with those of the australifungin standard. On the other hand, the screening for mycotoxins (fumonisins, AAL toxins and others) in the raw and purified extracts was done in a mycotoxin specific database from Agilent Technologies. Finally, the last step of this work was dedicated to the metabolomic approach from raw and purified extracts. Data processing was carried out using the platform « workflow4metabolomics » and the metabolic fingerprints obtained from the different groups of samples were compared to each other. The effect of the SPE clean-up from raw extracts was also investigated. Issue d’une collaboration de recherche entre l’unité de Chimie Analytique de Gembloux Agro-Bio Tech de l’Université de Liège (ULg) et l’unité de Chimie Pharmaceutique Organique de la Faculté de Pharmacie de l’Université Libre de Bruxelles (ULB), ce travail de fin d’études avait pour objectif principal de vérifier la présence ou non des métabolites secondaires de moisissures d’Alternaria et plus particulièrement ceux qui sont antagonistes du métabolisme des sphingolipides tels que les fumonisines, les toxines AAL et l’australifungine dans des échantillons de céréale contaminés par des moisissures par chromatographique liquide couplée à la spectrométrie de masse à haute résolution et en tandem (LC-HRMS(/MS)). L’autre objectif de ce travail visait une recherche plus exhaustive des constituants extraits des échantillons avec des outils chimiométriques LC-MS/MS. Une approche métabolique qui permettrait de discriminer les échantillons et rechercher les métabolites qui font la différence entre échantillons. Pour ce faire, nous avons débuté par une optimisation de la méthode de séparation chromatographique des extraits bruts de farine. L’introduction d’un clean-up SPE a également été envisagée dans l’optique d’une amélioration « sélective » des profils chromatographiques. Dans un second temps, nous avons procédé à une analyse ciblée à m/z 409,2585 ± 0,1 [M+H]+ de l’autralifungine dans les extraits bruts en comparant les paramètres analytiques (tR et spectre de MS) des pics des échantillons avec ceux du standard d’australifungine. Par contre, la recherche des mycotoxines (fumonisines, toxines AAL et autres) a été réalisée sur les extraits purifiés en LC-MS dans une base de données spécifique de mycotoxines d’Agilent Technologies. Enfin, dans un troisième temps, nous avons appliqué une approche métabolomique à des extraits bruts et purifiés. Le traitement des données a été réalisé par la plateforme « workflow4metabolomics » et les empreintes métaboliques obtenues des différents groupes d’échantillons ont été comparées entre-elles. L’évaluation de l’effet de la purification « clean-up » SPE des extraits bruts a également été réalisée.

Mycotoxins – Alternaria Secondary Metabolites – Australifungin – Fumonisins – AAL toxins – Sphingolipids - Metabolomics – Liquid Chromatography / High Resolution Mass Spectrometry – SPE clean-up --- Mycotoxines - Métabolites secondaires d’Alternaria - Australifungine - Fumonisines - Toxines AAL - Sphingolipides - Métabolomique - Chromatographique liquide couplée à la spectrométrie de masse à haute résolution et en tandem – Clean-up SPE --- Sciences du vivant > Agriculture & agronomie

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The book deals with mycotoxins, their presence in various types of food, and how to prevent their presence in food . In addition to well-known molecules, such as aflatoxins or fumonisins, some contributors have dealt with emerging mycotoxins (e.g., alternaria toxins, botryodiplodin). Readers of the book can also find a new approach to reducing aflatoxins and fumonisins in food. In conclusion, the book presents both new mycotoxins and new information on old mycotoxins.

Humanities --- Social interaction --- Atlantic salmon --- zebrafish --- liquid chromatography high-resolution mass spectrometry --- mycotoxins --- phytoestrogens --- plant-based feed --- rice --- sterigmatocystin --- STC --- deoxynivalenol --- DON --- growing season --- azoxystrobin --- fungicide --- Fumonisins --- Fusarium spp. --- food contamination --- health issues --- secondary metabolites --- Aflatoxins --- binding --- food safety --- biocontrol --- food discipline --- ergot alkaloids --- ergochromes --- secalonic acid --- cereals --- tetrahydroxanthones --- Claviceps --- aflatoxin --- mycotoxin --- black soldier fly --- BSFL --- Hermetia illucens --- S9 fraction --- cytochrome P450 --- metabolic conversion --- enzyme induction --- Alternaria mycotoxins --- combinatory effects --- combined toxicity --- co-occurrence --- bioactive compounds --- fungi --- phaseolinone --- LC/MS --- soybean --- charcoal rot disease --- root infection mechanism --- Fusarium species --- toxigenic profile --- mycotoxin migration --- sweet pepper --- fungal disease --- fumonisin --- human exposure --- maize products --- botryodiplodin --- root toxicity --- Macrophomina phaseolina --- hydroponic culture --- AMF1 --- infant formulae --- estimated daily intake --- carcinogenic risk index --- Monterrey (Mexico) --- T-2 toxin --- HT-2 toxin --- deoxynivalenol (DON) --- enniatin B (EnnB) --- size sorting --- unprocessed cereals --- n/a

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The book deals with mycotoxins, their presence in various types of food, and how to prevent their presence in food . In addition to well-known molecules, such as aflatoxins or fumonisins, some contributors have dealt with emerging mycotoxins (e.g., alternaria toxins, botryodiplodin). Readers of the book can also find a new approach to reducing aflatoxins and fumonisins in food. In conclusion, the book presents both new mycotoxins and new information on old mycotoxins.

Humanities --- Social interaction --- Atlantic salmon --- zebrafish --- liquid chromatography high-resolution mass spectrometry --- mycotoxins --- phytoestrogens --- plant-based feed --- rice --- sterigmatocystin --- STC --- deoxynivalenol --- DON --- growing season --- azoxystrobin --- fungicide --- Fumonisins --- Fusarium spp. --- food contamination --- health issues --- secondary metabolites --- Aflatoxins --- binding --- food safety --- biocontrol --- food discipline --- ergot alkaloids --- ergochromes --- secalonic acid --- cereals --- tetrahydroxanthones --- Claviceps --- aflatoxin --- mycotoxin --- black soldier fly --- BSFL --- Hermetia illucens --- S9 fraction --- cytochrome P450 --- metabolic conversion --- enzyme induction --- Alternaria mycotoxins --- combinatory effects --- combined toxicity --- co-occurrence --- bioactive compounds --- fungi --- phaseolinone --- LC/MS --- soybean --- charcoal rot disease --- root infection mechanism --- Fusarium species --- toxigenic profile --- mycotoxin migration --- sweet pepper --- fungal disease --- fumonisin --- human exposure --- maize products --- botryodiplodin --- root toxicity --- Macrophomina phaseolina --- hydroponic culture --- AMF1 --- infant formulae --- estimated daily intake --- carcinogenic risk index --- Monterrey (Mexico) --- T-2 toxin --- HT-2 toxin --- deoxynivalenol (DON) --- enniatin B (EnnB) --- size sorting --- unprocessed cereals --- Atlantic salmon --- zebrafish --- liquid chromatography high-resolution mass spectrometry --- mycotoxins --- phytoestrogens --- plant-based feed --- rice --- sterigmatocystin --- STC --- deoxynivalenol --- DON --- growing season --- azoxystrobin --- fungicide --- Fumonisins --- Fusarium spp. --- food contamination --- health issues --- secondary metabolites --- Aflatoxins --- binding --- food safety --- biocontrol --- food discipline --- ergot alkaloids --- ergochromes --- secalonic acid --- cereals --- tetrahydroxanthones --- Claviceps --- aflatoxin --- mycotoxin --- black soldier fly --- BSFL --- Hermetia illucens --- S9 fraction --- cytochrome P450 --- metabolic conversion --- enzyme induction --- Alternaria mycotoxins --- combinatory effects --- combined toxicity --- co-occurrence --- bioactive compounds --- fungi --- phaseolinone --- LC/MS --- soybean --- charcoal rot disease --- root infection mechanism --- Fusarium species --- toxigenic profile --- mycotoxin migration --- sweet pepper --- fungal disease --- fumonisin --- human exposure --- maize products --- botryodiplodin --- root toxicity --- Macrophomina phaseolina --- hydroponic culture --- AMF1 --- infant formulae --- estimated daily intake --- carcinogenic risk index --- Monterrey (Mexico) --- T-2 toxin --- HT-2 toxin --- deoxynivalenol (DON) --- enniatin B (EnnB) --- size sorting --- unprocessed cereals

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Metabolomics data analysis strategies are central to transforming raw metabolomics data files into meaningful biochemical interpretations that answer biological questions or generate novel hypotheses. This book contains a variety of papers from a Special Issue around the theme “Best Practices in Metabolomics Data Analysis”. Reviews and strategies for the whole metabolomics pipeline are included, whereas key areas such as metabolite annotation and identification, compound and spectral databases and repositories, and statistical analysis are highlighted in various papers. Altogether, this book contains valuable information for researchers just starting in their metabolomics career as well as those that are more experienced and look for additional knowledge and best practice to complement key parts of their metabolomics workflows.

Research & information: general --- metabolic networks --- mass spectral libraries --- metabolite annotation --- metabolomics data mapping --- nontarget analysis --- liquid chromatography mass spectrometry --- compound identification --- tandem mass spectral library --- forensics --- wastewater --- gut microbiome --- meta-omics --- metagenomics --- metabolomics --- metabolic reconstructions --- genome-scale metabolic modeling --- constraint-based modeling --- flux balance --- host–microbiome --- metabolism --- global metabolomics --- LC-MS --- spectra processing --- pathway analysis --- enrichment analysis --- mass spectrometry --- liquid chromatography --- MS spectral prediction --- metabolite identification --- structure-based chemical classification --- rule-based fragmentation --- combinatorial fragmentation --- time series --- PLS --- NPLS --- variable selection --- bootstrapped-VIP --- data repository --- computational metabolomics --- reanalysis --- lipidomics --- data processing --- triplot --- multivariate risk modeling --- environmental factors --- disease risk --- chemical classification --- in silico workflows --- metabolome mining --- molecular families --- networking --- substructures --- mass spectrometry imaging --- metabolomics imaging --- biostatistics --- ion selection algorithms --- liquid chromatography high-resolution mass spectrometry --- data-independent acquisition --- all ion fragmentation --- targeted analysis --- untargeted analysis --- R programming --- full-scan MS/MS processing --- R-MetaboList 2 --- liquid chromatography–mass spectrometry (LC/MS) --- fragmentation (MS/MS) --- data-dependent acquisition (DDA) --- simulator --- in silico --- untargeted metabolomics --- liquid chromatography–mass spectrometry (LC-MS) --- experimental design --- sample preparation --- univariate and multivariate statistics --- metabolic pathway and network analysis --- LC–MS --- metabolic profiling --- computational statistical --- unsupervised learning --- supervised learning