Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation

Metabolomics: Going Deeper, Going Broader, Going Further

Metabolomics is a continuously dynamic field of research that is driven by demanding research questions and technological advances alike. In this review we highlight selected recent and ongoing developments in the area of mass spectrometry-based metabolomics. The field of view that can be seen through the metabolomics lens can be broadened by adoption of separation techniques such as hydrophilic interaction chromatography and ion mobility mass spectrometry (going broader). For a given biospecimen, deeper metabolomic analysis can be achieved by resolving smaller entities such as rare cell populations or even single cells using nano-LC and spatially resolved metabolomics or by extracting more useful information through improved metabolite identification in untargeted metabolomic experiments (going deeper). Integration of metabolomics with other (omics) data allows researchers to further advance in the understanding of the complex metabolic and regulatory networks in cells and model organisms (going further). Taken together, diverse fields of research from mechanistic studies to clinics to biotechnology applications profit from these technological developments.

Coupling between high-resolution mass spectrometry and focalized data-analysis methods provides the identification of new putative glycosidic non-anthocyanic flavonoids in grape

INTRODUCTION

The biochemical diversity of flavonoids is based on glycosylation, methylation, acylation, and many other modifications of the flavonoid backbone. Liquid chromatography coupled to high-resolution mass spectrometry demonstrated to be a powerful approach to gain new insights into the flavonoid composition of many plant species, including grapes.

OBJECTIVES

Among different metabolomic approaches, suspect screening analysis relies on the construction of a specific database and on ultra-high performance liquid chromatography/quadrupole time-of-flight (UHPLC/QTOF) analysis to find new compounds of oenological interest.

METHODS

A homemade database containing mass data information retrieved from the literature specific for plant flavonoid derivatives (GrapeFlavMet) was constructed. Tandem mass spectrometry analysis of V. vinifera and hybrid grape extracts was performed, and MS/MS fragmentation allowed to assign the putative flavonoid chemical structure to various identification levels, as established by the Metabolomics Standard Initiative.

RESULTS

By this approach, putative flavonoid derivatives with different glycosylation and acylation patterns were identified. They include three pentoside derivatives of tetrahydroxy-flavone, tetrahydroxy-flavanone and myricetin isomers, a putative dihydrorhamnetin hexoside derivative, three cinchonain isomers (phenylpropanoid-substituted flavan-3-ols with antidiabetic properties), and two syringetin isomer derivatives (acetyl- and p-coumaroyl-hexoside). Two acetyl-hexoside derivatives of dihydrorhamnetin and pentahydroxy-methoxy-flavanone, and three derivatives of tetrahydroxy-dimethoxy-flavanone (acetyl, p-coumaroyl, and caffeoyl-hexoside) were tentatively annotated.

CONCLUSIONS

Most of the compounds were identified in grape for the first time, while two putative syringetin derivatives previously proposed in the literature were confirmed. These findings deepen the current knowledge on grape flavonoids, suggesting more connections at the biochemical level.

Oxidation of 3'-methoxyflavone, 4'-methoxyflavone, and 3',4'-dimethoxyflavone and their derivatives having 5,7-dihydroxyl moieties by human cytochromes P450 1B1 and 2A13

Oxidation of 3'-methoxyflavone, 4'-methoxyflavone, and 3',4'-dimethoxyflavone and their derivatives containing 5,7-dihydroxyl groups by human cytochrome P450 (P450 or CYP) 1B1 and 2A13 was determined using LC-MS/MS systems.3'-Methoxyflavone and 4'-methoxyflavone were mainly O-demethylated to form 3'-hydroxyflavone and 4'-hydroxyflavone, respectively, and then 3',4'-dihydroxyflavone at higher rates with CYP1B1 than with CYP2A13. 4'-Methoxy-5,7-dihydroxyflavone (acacetin) was found to be demethylated by CYP1B1 and 2A13 to form 4',5,7-trihydroxyflavone (apigenin) at rates of 0.098^-1 and 0.42 min^-1, respectively. 3'-Methoxy-5,7-dihydroxyflavone was also demethylated by both P450s, with CYP2A13 being more active.3',4'-Dimethoxyflavone was a good substrate for CYP1B1 but not for CYP2A13 and was found to be mainly O-demethylated to form 3',4'-dihydroxyflavone (at a rate of 4.2 min^-1) and also several ring-oxygenated products having m/z 299 fragments. Molecular docking analysis supported the proper orientation for formation of these products by CYP1B1.Our present results showed that 3'- and 4'-methoxyflavone can be oxidised to their O-demethylated products and, to a lesser extent, to ring oxidation products by both P450s 1B1 and 2A13 and that 3',4'-dimethoxyflavone is a good substrate for CYP1B1 in forming both O-demethylated and ring-oxidation products. Introduction of a 57diOHF moiety into these methoxylated flavonoids caused decreased in oxidation by CYP1B1 and 2A13.

Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

Covering: up to the end of 2020Recently introduced computational metabolome mining tools have started to positively impact the chemical and biological interpretation of untargeted metabolomics analyses. We believe that these current advances make it possible to start decomposing complex metabolite mixtures into substructure and chemical class information, thereby supporting pivotal tasks in metabolomics analysis including metabolite annotation, the comparison of metabolic profiles, and network analyses. In this review, we highlight and explain key tools and emerging strategies covering 2015 up to the end of 2020. The majority of these tools aim at processing and analyzing liquid chromatography coupled to mass spectrometry fragmentation data. We start with defining what substructures are, how they relate to molecular fingerprints, and how recognizing them helps to decompose complex mixtures. We continue with chemical classes that are based on the presence or absence of particular molecular scaffolds and/or functional groups and are thus intrinsically related to substructures. We discuss novel tools to mine substructures, annotate chemical compound classes, and create mass spectral networks from metabolomics data and demonstrate them using two case studies. We also review and speculate about the opportunities that NMR spectroscopy-based metabolome mining of complex metabolite mixtures offers to discover substructures and chemical classes. Finally, we will describe the main benefits and limitations of the current tools and strategies that rely on them, and our vision on how this exciting field can develop toward repository-scale-sized metabolomics analyses. Complementary sources of structural information from genomics analyses and well-curated taxonomic records are also discussed. Many research fields such as natural products discovery, pharmacokinetic and drug metabolism studies, and environmental metabolomics increasingly rely on untargeted metabolomics to gain biochemical and biological insights. The here described technical advances will benefit all those metabolomics disciplines by transforming spectral data into knowledge that can answer biological questions.

Metabolomics and complementary techniques to investigate the plant phytochemical cosmos

Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.

A targeted prenylation analysis by a combination of IT-MS and HR-MS: Identification of prenyl number, configuration, and position in different subclasses of (iso)flavonoids

Prenylated (iso)flavonoids are potent bioactive compounds found in the Fabaceae family. Analysis and quantification of this type of phytochemicals is challenging due to their large structural diversity. In this study, the fragmentation of prenylated (iso)flavonoids was investigated using electrospray ionization ion trap mass spectrometry (ESI-IT-MSⁿ) with fragmentation by collision induced dissociation (CID) in combination and Orbitrap-MS (ESI-FT-MS²) with fragmentation by higher energy C-trap dissociation (HCD). With this combination of IT-MSⁿ and high resolution MS (FT-MSⁿ), it was possible to determine the fragmentation pathways and characteristic spectral features of different subclasses of prenylated (iso)flavonoid standards, as well as characteristic fragmentations and neutral losses of different prenyl configurations. Based on our findings, a decision guideline was developed to (i) identify (iso)flavonoid backbones, (ii) annotate prenyl number, (iii) configuration, and (iv) position of unknown prenylated (iso)flavonoids, in complex plant extracts. In this guideline, structural characteristics were identified based on: (i) UV absorbance of the compound, (ii) mass-to-charge (m/z) ratio of the parent compound; (iii) ratio of relative abundances between neutral losses 42 and 56 u in MSⁿ; (iv) retro-Diels-Alder (RDA) fragments, neutral losses 54 and 68 u, and the ratio [M+H-C₄H₈]⁺/[M+H]⁺. Using this guideline, 196 prenylated (iso)flavonoids were annotated in a Glycyrrhiza glabra root extract. In total, 75 skeletons were single prenylated, 104 were double prenylated, and for merely 17 skeletons prenyl number could not unambiguously be annotated. Our prenylation guideline allows rapid screening for identification of prenylated (iso)flavonoids, including prenyl number, configuration, and position, in complex plant extracts. This guideline supports research on these bioactive compounds in the areas of plant metabolomics and natural products.

Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.

Polyphenol Profiling of Chestnut Pericarp, Integument and Curing Water Extracts to Qualify These Food By-Products as a Source of Antioxidants

Plant polyphenols have beneficial antioxidant effects on human health; practices aimed at preserving their content in foods and/or reusing food by-products are encouraged. The impact of the traditional practice of the water curing procedure of chestnuts, which prevents insect/mould damage during storage, was studied to assess the release of polyphenols from the fruit. Metabolites extracted from pericarp and integument tissues or released in the medium from the water curing process were analyzed by matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and electrospray-quadrupole-time of flight-mass spectrometry (ESI-qTOF-MS). This identified: (i) condensed and hydrolyzable tannins made of (epi)catechin (procyanidins) and acid ellagic units in pericarp tissues; (ii) polyphenols made of gallocatechin and catechin units condensed with gallate (prodelphinidins) in integument counterparts; (iii) metabolites resembling those reported above in the wastewater from the chestnut curing process. Comparative experiments were also performed on aqueous media recovered from fruits treated with processes involving: (i) tap water; (ii) tap water containing an antifungal Lb. pentosus strain; (iii) wastewater from a previous curing treatment. These analyses indicated that the former treatment determines a 6–7-fold higher release of polyphenols in the curing water with respect to the other ones. This event has a negative impact on the luster of treated fruits but qualifies the corresponding wastes as a source of antioxidants. Such a phenomenon does not occur in wastewater from the other curing processes, where the release of polyphenols was reduced, thus preserving the chestnut’s appearance. Polyphenol profiling measurements demonstrated that bacterial presence in water hampered the release of pericarp metabolites. This study provides a rationale to traditional processing practices on fruit appearance and qualifies the corresponding wastes as a source of bioactive compounds for other nutraceutical applications.

Liquid chromatography-tandem mass spectrometry analysis of oxidation of 2'-, 3'-, 4'- and 6-hydroxyflavanones by human cytochrome P450 enzymes

2'-Hydroxyflavanone (2'OHFva), 3'OHFva, 4'OHFva, and 6OHFva, the major oxidative products of flavanone by human cytochrome P450 (P450, CYP) enzymes, were studied in regard to further oxidation by human CYP1A1, 1A2, 1B1.1, 1B1.3, and 2A6. The products formed were analyzed with LC-MS/MS and characterized by their positive ion fragmentations on mass spectrometry. Several di-hydroxylated flavanone (diOHFva) and di-hydroxylated flavone (diOHFvo) products, detected by analyzing parent ions at m/z 257 and 255, respectively, were found following incubation of these four hydroxylated flavanones with P450s. The m/z 257 products were produced at higher levels than the latter with four substrates examined. The structures of the m/z 257 products were characterized by LC-MS/MS product ion spectra, and the results suggest that 3'OHFva and 4'OHFva are further oxidized mainly at B-ring by P450s while 6OHFva oxidation was at A-ring. Different diOHFvo products (m/z 255) were also characterized by LC-MS/MS, and the results suggested that most of these diOHFvo products were formed through oxidation or desaturation of the diOHFva products (m/z 257) by P450s. Only when 4'OHFva (m/z 241) was used as a substrate, formation of 4'OHFvo (m/z 239) was detected, indicating that diOHFvo might also be formed through oxidation of 4'OHFvo by P450s. Finally, our results indicated that CYP1 family enzymes were more active than CYP2A6 in catalyzing the oxidation of these four hydroxylated flavanones, and these findings were supported by molecular docking studies of these chemicals with active sites of P450 enzymes.

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.

Oxidation of Flavone, 5-Hydroxyflavone, and 5,7-Dihydroxyflavone to Mono-, Di-, and Tri-Hydroxyflavones by Human Cytochrome P450 Enzymes

Biologically active plant flavonoids, including 5,7-dihydroxyflavone (57diOHF, chrysin), 4',5,7-trihydroxyflavone (4'57triOHF, apigenin), and 5,6,7-trihydroxyflavone (567triOHF, baicalein), have important pharmacological and toxicological significance, e.g., antiallergic, anti-inflammatory, antioxidative, antimicrobial, and antitumorgenic properties. In order to better understand the metabolism of these flavonoids in humans, we examined the oxidation of flavone, 5-hydroxyflavone (5OHF), and 57diOHF to various products by human cytochrome P450 (P450 or CYP) and liver microsomal enzymes. Individual human P450s and liver microsomes oxidized flavone to 6-hydroxyflavone, small amounts of 5OHF, and 11 other monohydroxylated products at different rates and also produced several dihydroxylated products (including 57diOHF and 7,8-dihydroxyflavone) from flavone. We also found that 5OHF was oxidized by several P450 enzymes and human liver microsomes to 57diOHF and further to 567triOHF, but the turnover rates in these reactions were low. Interestingly, both CYP1B1.1 and 1B1.3 converted 57diOHF to 567triOHF at turnover rates (on the basis of P450 contents) of >3.0 min^-1, and CYP1A1 and 1A2 produced 567triOHF at rates of 0.51 and 0.72 min^-1, respectively. CYP2A13 and 2A6 catalyzed the oxidation of 57diOHF to 4'57triOHF at rates of 0.7 and 0.1 min^-1, respectively. Our present results show that different P450s have individual roles in oxidizing these phytochemical flavonoids and that these reactions may cause changes in their biological and toxicological properties in mammals.

De novo structure determination of 3-((3-aminopropyl)amino)-4-hydroxybenzoic acid, a novel and abundant metabolite in Acinetobacter baylyi ADP1

INTRODUCTION

Metabolite identification remains a major bottleneck in the understanding of metabolism. Many metabolomics studies end up with unknown compounds, leaving a landscape of metabolites and metabolic pathways to be unraveled. Therefore, identifying novel compounds within a metabolome is an entry point into the 'dark side' of metabolism.

OBJECTIVES

This work aimed at elucidating the structure of a novel metabolite that was first detected in the soil bacterium Acinetobacter baylyi ADP1 (ADP1).

METHODS

We used high resolution multi-stage tandem mass spectrometry for characterizing the metabolite within the metabolome. We purified the molecule for 1D- and 2D-NMR (¹H, ¹³C, ¹H-¹H-COSY, ¹H-¹³C-HSQC, ¹H-¹³C-HMBC and ¹H-¹⁵N-HMBC) analyses. Synthetic standards were chemically prepared from MS and NMR data interpretation.

RESULTS

We determined the de novo structure of a previously unreported metabolite: 3-((3-aminopropyl)amino)-4-hydroxybenzoic acid. The proposed structure was validated by comparison to a synthetic standard. With a concentration in the millimolar range, this compound appears as a major metabolite in ADP1, which we anticipate to participate to an unsuspected metabolic pathway. This novel metabolite was also detected in another γ-proteobacterium.

CONCLUSION

Structure elucidation of this abundant and novel metabolite in ADP1 urges to decipher its biosynthetic pathway and cellular function.

Rapid characterization of chlorogenic acids in Duhaldea nervosa based on ultra-high-performance liquid chromatography-linear trap quadropole-Orbitrap-mass spectrometry and mass spectral trees similarity filter technique

Duhaldea nervosa (Wallich ex Candolle) A. Anderberg has been traditionally used as a food spice and also in folk medicine for treating traumatic injury and relieving rheumatism, especially accelerating the healing of a fracture. However, so far as we are aware, the chemical constituents have not been fully investigated. In this study, a practical method of mass spectral trees similarity filter, a data-mining technique, was developed and evaluated for the rapid detection and identification complicated constituents based on ultra-high-performance liquid chromatography-linear trap quadropole-Orbitrap-mass spectrometry. Finally, a total of 47 chlorogenic acids, including 19 monoacyl-quinic acids, 22 diacyl-quinic acids, and six triacyl-quinic acids, were unambiguously or tentatively identified based on their accurate mass measurement, chromatographic retention, MSⁿ spectra, and bibliography data. To our best knowledge, it is the first time to report the chlorogenic acids of D. nervosa, which would be beneficial for the further material basis and quality research. Meanwhile, this mass spectral trees similarity filter method could be envisioned to exhibit a wide application for the identification of complicated components from botanical extracts.

Untargeted metabolomic analysis of tomato pollen development and heat stress response

Pollen development metabolomics. Developing pollen is among the plant structures most sensitive to high temperatures, and a decrease in pollen viability is often associated with an alteration of metabolite content. Most of the metabolic studies of pollen have focused on a specific group of compounds, which limits the identification of physiologically important metabolites. To get a better insight into pollen development and the pollen heat stress response, we used a liquid chromatography-mass spectrometry platform to detect secondary metabolites in pollen of tomato (Solanum lycopersicum L.) at three developmental stages under control conditions and after a short heat stress at 38 °C. Under control conditions, the young microspores accumulated a large amount of alkaloids and polyamines, whereas the mature pollen strongly accumulated flavonoids. The heat stress treatment led to accumulation of flavonoids in the microspore. The biological role of the detected metabolites is discussed. This study provides the first untargeted metabolomic analysis of developing pollen under a changing environment that can serve as reference for further studies.

Influence of Quercetin and Its Methylglyoxal Adducts on the Formation of α-Dicarbonyl Compounds in a Lysine/Glucose Model System

Increasing evidence has identified α-dicarbonyl compounds, the reactive intermediates generated during Maillard reaction, as the potential factors to cause protein glycation and the development of chronic diseases. Therefore, there is an urgent need to decrease the levels of reactive dicarbonyl compounds in foods. In this study, we investigated the inhibitory effect of quercetin, a major dietary flavonoid, and its major mono- and di-MGO adducts on the formation of dicarbonyl compounds, such as methylglyoxal (MGO) and glyoxal (GO), in a lysine/glucose aqueous system, a model system to reflect the Maillard reaction in food process. Our result indicated that quercetin could efficiently inhibit the formation of MGO and GO in a time-dependent manner. Further mechanistic study was conducted by monitoring the formation of quercetin oxidation and conjugation products using LC-MS/MS. Quercetin MGO adducts, quercetin quinones, and the quinones of quercetin MGO adducts were detected in the system, indicating quercetin plays a dual role in inhibiting the formation of MGO and GO by scavenging free radicals generated in the system and trapping of MGO and GO to form MGO adducts. In addition, we prepared the mono- and di-MGO quercetin adducts and investigated their antioxidant activity and trapping capacity of MGO and GO. Our results indicated that both mono- and di-MGO quercetin adducts could scavenge the DPPH radical in a dose-dependent manner with >40% DPPH scavenged by the MGO adducts at 10 μM, and the di-MGO quercetin adduct could further trap MGO to generate tri-MGO adducts. Therefore, we demonstrate for the first time that quercetin MGO adducts retain the antioxidant activity and trapping capacity of reactive dicarbonyl species.

A Fragmentation Study on Four Unusual Secoiridoid Trimers, Swerilactones H-K, by Electrospray Tandem Mass Spectrometry

Swerilactones H-K (1-4) as four unprecedented secoiridoid trimers represent a new type of natural product, which has attracted much interest of natural chemists due to their novel skeletons and promising bioactivity. In order to well understand their MS fragmentation behaviors, they were investigated by electrospray ionization ion-trap time-of-flight multistage product ion mass spectrometry (ESI-IT-TOF-MS ⁿ ) for the first time. The protonated molecules ([M+H]⁺) of swerilactones J and K, and deprotonated molecules ([M-H]^-) of swerilactones H, J and K were readily observed in the conventional single-stage mass spectra (MS); however only the [M+Cl]^- ion for swerilactone I was obtained in negative mode. Based on the MS ⁿ study, the fragmentation pathways of swerilactones H and I in negative mode, and swerilactones J and K in both positive and negative modes were proposed. The neutral losses of H₂O, CO, CO₂ and C₂H₄O moieties are the particular elimination from the precursor ions due to the presence of hydroxyl, δ-lactone and 1-O-ethyl moieties in their structures, of which the retro-Diels-Alder cleavage was the most particular dissociation. The fragment ions at m/z 341 and 291 in negative mode can be considered as the diagnostic ions for secoiridoid trimers. This investigation will provide valuable information for their fast characterization from complicated natural mixtures and extensive understanding their structural architectures.

Target and non-target identification of chemical components in Lamiophlomis rotata by liquid chromatography/quadrupole time-of-flight mass spectrometry using a three-step protocol

RATIONALE

As a herbal plant used in traditional Chinese medicine, Lamiophlomis rotata (Benth.) Kudo mainly displays its pharmacological effect by promoting blood circulation and hemostasis, dispelling wind, and acting as an analgesic. To identify the components contained in L. rotata, global detection and structural elucidation of both target and non-target components in the medicinal material was performed.

METHODS

L. rotata was ultrasonically extracted with methanol. Separation and analysis were achieved using liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/QTOF-MS). A three-step protocol which included (1) potential components screening, (2) collection of qualitative information, and (3) database searching and structural elucidation was used for target and non-target identification.

RESULTS

A total of 42 components were tentatively identified, which included 12 iridoids (2 aglycones and 10 glucosides), 11 flavonoids (4 aglycones and 7 glucosides), and 13 phenylethanoid glycosides. Moreover, components of L. rotata extract belonging to the three main structural categories could be well separated in a 3D point plot according to their retention times, mass defects and degrees of unsaturation, facilitating the structural classification and identification in the subsequent studies.

CONCLUSIONS

The results provide a reasonable picture of the components contained in L. rotata extract and promote the further pharmacodynamic and/or pharmacokinetic characterization of this medical material, meanwhile demonstrating the utility of a universal methodology for the systematical study of herbal medicines. Copyright © 2016 John Wiley & Sons, Ltd.

Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives

A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules.

An Integrated Approach for Studying Exposure, Metabolism, and Disposition of Multiple Component Herbal Medicines Using High-Resolution Mass Spectrometry and Multiple Data Processing Tools

A typical prescription of traditional Chinese medicine (TCM) contains up to a few hundred prototype components. Studying their absorption, metabolism, distribution, and elimination (ADME) presents great challenges. The objective of this study was to develop a practical approach for investigating ADME of individual prototypes in TCM. An active fraction of Xiao-Xu-Ming decoction (AF-XXMD) as a model TCM prescription was orally administered to rats. AF-XXMD-related components in plasma, urine, bile, and feces were detected using high-resolution mass spectrometry and background subtraction, an untargeted data-mining tool. Components were then structurally characterized on the basis of MS(n) spectral data. Connection of detected AF-XXMD metabolites to their precursor species, either prototypes or upstream metabolites, were determined on the basis of mass spectral similarity and the matching of biotransformation reactions. As a result, 247 AF-XXMD-related components were detected and structurally characterized in rats, 134 of which were metabolites. Among 198 AF-XXMD prototypes dosed, 65 were fully or partially absorbed and 13 prototypes and 34 metabolites were found in the circulation. Glucuronidation, isomerization, and deglycosylation followed by biliary and urinary excretions and direct elimination of prototypes via kidney and liver were the major clearance pathways of AF-XXMD prototypes. As an example, the ADME profile of H56, the single major AF-XXMD component in rat plasma, was elucidated on the basis of profiles of H56-related components in plasma and excreta. The results demonstrate that the new analytical approach is a useful tool for rapid and comprehensive detection and characterization of TCM components in biologic matrix in a TCM ADME study.

Spatially Resolved Plant Metabolomics: Some Potentials and Limitations of Laser-Ablation Electrospray Ionization Mass Spectrometry Metabolite Imaging

Laser-ablation electrospray ionization (LAESI)-mass spectrometry imaging has been applied to contrasting plant organs to assess its potential as a procedure for performing in vivo metabolomics in plants. In a proof-of-concept experiment, purple/white segmented Phalaenopsis spp. petals were first analyzed using standard liquid chromatography-mass spectrometry analyses of separate extracts made specifically from the purple and white regions. Discriminatory compounds were defined and putatively annotated. LAESI analyses were then performed on living tissues, and these metabolites were then relocalized within the LAESI-generated data sets of similar tissues. Maps were made to illustrate their locations across the petals. Results revealed that, as expected, anthocyanins always mapped to the purple regions. Certain other (nonvisible) polyphenols were observed to colocalize with the anthocyanins, whereas others were found specifically within the white tissues. In a contrasting example, control and Cladosporium fulvum-infected tomato (Solanum lycopersicum) leaves were subjected to the same procedures, and it could be observed that the alkaloid tomatine has clear heterogeneous distribution across the tomato leaf lamina. Furthermore, LAESI analyses revealed perturbations in alkaloid content following pathogen infection. These results show the clear potential of LAESI-based imaging approaches as a convenient and rapid way to perform metabolomics analyses on living tissues. However, a range of limitations and factors have also been identified that must be taken into consideration when interpreting LAESI-derived data. Such aspects deserve further evaluation before this approach can be applied in a routine manner.

Characterization of lemon (Citrus limon) polar extract by liquid chromatography-tandem mass spectrometry in high resolution mode

Eighty four metabolites (32 flavonoids, 15 amino acids, nine carboxylic acids, six coumarins, six sugars, five phenolic acids and 11 unclassified compounds) have been tentatively identified in a polar extract from lemon, without reference standards, based on their liquid chromatography-quadrupole-time-of-flight MS/MS spectra and the comparison with databases. Despite information in databases for some families of plant compounds is poor, tentative identification based on MS/MS information (mass of the precursor ion and their fragments, together with neutral mass loss) was possible with the help of known fragmentation patterns for the given families of compounds. Both positive and negative ionization modes and at least two collision energies were always applied to obtain as much information as possible from each molecular entity, thus helping for identification. As the tentatively identified metabolites are the same regardless of the organism they belong, their fragmentation patterns are useful for identification with independence of the sample nature.

Identification of the chemical constituents of Chinese medicine Yi-Xin-Shu capsule by molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation

The incomplete identification of the chemical components of traditional Chinese medicinal formula has been one of the bottlenecks in the modernization of traditional Chinese medicine. Tandem mass spectrometry has been widely used for the identification of chemical substances. Current automatic tandem mass spectrometry acquisition, where precursor ions were selected according to their signal intensity, encounters a drawback in chemical substances identification when samples contain many overlapping signals. Compounds in minor or trace amounts could not be identified because most tandem mass spectrometry information was lost. Herein, a molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation method for complex Chinese medicine chemical constituent analysis was developed. The precursor ions were selected according to their two-dimensional characteristics of retention times and mass-to-charge ratio ranges from herbal compounds, so that all precursor ions from herbal compounds were included and more minor chemical constituents in Chinese medicine were identified. Compared to the conventional automatic tandem mass spectrometry setups, the approach is novel and can overcome the drawback for chemical substances identification. As an example, 276 compounds from the Chinese Medicine of Yi-Xin-Shu capsule were identified.

Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation

Mass spectrometry is a powerful tool in natural product structure elucidation, but our ability to directly correlate fragmentation spectra to these structures lags far behind similar efforts in peptide sequencing and proteomics. Often, manual data interpretation is required and our knowledge of the expected fragmentation patterns for many scaffolds is limited, further complicating analysis. Here, we summarize advances in natural product structure elucidation based upon the application of collision induced dissociation fragmentation mechanisms.

Enhanced acylcarnitine annotation in high-resolution mass spectrometry data: fragmentation analysis for the classification and annotation of acylcarnitines

Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software¹. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context of untargeted metabolomics experiments is a valuable tool to enhance the annotation of small metabolites.

Ion tree-based structure elucidation of acetophenone dimers (AtA) from Acronychia pedunculata and their identification in extracts by liquid chromatography electrospray ionization LTQ-Orbitrap mass spectrometry

Acronychia-type acetophenones (AtA) is a chemical group of compounds of important structural and biological interest, abundant in Acronychia species. However, there are no data available for their characterization using mass spectrometry. In the current work, AtA have been investigated by multistage high resolution mass spectrometry and both electrospray ionization and atmospheric pressure chemical ionization, in positive and negative mode, were utilized for their structure elucidation and identification. The analysis of AtA using a linear ion trap-Orbitrap analyzer enabled the structural determination of key fragment ions and cleavages, which can be used for the structural characterization thereof. A systematic nomenclature based on protonated and deprotonated fragment ions under collision-induced dissociation conditions and decision trees for the structural determination of AtA are proposed. Furthermore, taking advantage of the characteristic fragmentation patterns, a selective Ultra High Performance Liquid Chromatography Electrospray Ionization multistage Mass Spectrometry (UHPLC-ESI(-)-MS(n)) method was developed and successfully applied for the dereplication of known AtA and the identification of potentially new ones in Acronychia extracts. Despite the structure similarity and the presence of isomers, accurate characterization of known and unknown AtA derivatives was possible.

Mass spectrometric profiling of flavonoid glycoconjugates possessing isomeric aglycones

In fields such as food and nutrition science or plant physiology, interest in untargeted profiling of flavonoids continues to expand. The group of flavonoids encompasses several thousands of chemically distinguishable compounds, among which are a number of isobaric compounds with the same elemental composition. Thus, the mass spectrometric identification of these compounds is challenging, especially when reference standards are not available to support their identification. Many different types of isomers of flavonoid glycoconjugates are known, i.e. compounds that differ in their glycosylation position, glycan sequence or type of interglycosidic linkage. This work focuses on the mass spectrometric identification of flavonoid glycoconjugate isomers possessing the same glycan mass and differing only in their aglycone core. A non-targeted HPLC-ESI-MS/MS profiling method using a triple quadrupole MS is presented herein, which utilizes in-source fragmentation and a pseudo-MS(3) approach for the selective analysis of flavonoid glycoconjugates with isomeric/isobaric aglycones. A selective MRM-based identification of the in-source formed isobaric aglycone fragments was established. Additionally, utilizing the precursor scanning capability of the employed triple quadrupole instrument, the developed method enabled the determination of the molecular weight of the studied intact flavonoid glycoconjugate. The versatility of the method was proven with various types of flavonoid aglycones, i.e. anthocyanins, flavonols, flavones, flavanones and isoflavones, along with their representative glycoconjugates. The developed method was also successfully applied to a commercially available sour cherry sample, in which 16 different glycoconjugates of pelargonidin, genistein, cyanidin, kaempferol and quercetin could be tentatively identified, including a number of compounds containing isomeric/isobaric aglycones.

Identification of the chemical components of Saussurea involucrata by high-resolution mass spectrometry and the mass spectral trees similarity filter technique

RATIONALE

Saussurea involucrata is a rare traditional Chinese medicine (TCM) that displays anti-fatigue, anti-inflammatory and anti-tumor effects. In this paper, the different chemical components of Saussurea involucrata were characterized and identified over a wide dynamic range by high-performance liquid chromatography coupled with high-resolution hybrid mass spectrometry (HPLC/HRMS/MS(n)) and the mass spectral trees similarity filter (MTSF) technique.

METHODS

The aerial parts of Saussurea involucrata were extracted with 75% ethanol. The partial extract was separated on a chromatography column to concentrate the low-concentration compounds. Mass data were acquired using full-scan mass analysis (resolving power 50,000) with data-dependent incorporation of dynamic exclusion analysis. The identified compounds were used as templates to construct a database of mass spectral trees. Data for the unknown compounds were matched with those templates and matching candidate structures were obtained.

RESULTS

The detected compounds were characterized based on matching to candidate structures by the MTSF technique and were further identified by their accurate mass weight, multiple-stage analysis and fragmentation patterns and through comparison with literature data. A total of 38 compounds were identified including 19 flavones, 11 phenylpropanoids and 8 sphingolipids. Among them, 7 flavonoids, 8 phenylpropanoids and 8 sphingolipids were identified for the first time in Saussurea involucrata.

CONCLUSIONS

HPLC/HRMS/MS(n) combined with MTSF was successfully used to discover and identify the chemical compounds in Saussurea involucrata. The results indicated that this combined technique was extremely useful for the rapid detection and identification of the chemical components in TCMs.

High resolution mass spectrometry based techniques at the crossroads of metabolic pathways

The metabolome is the set of small molecular mass compounds found in biological media, and metabolomics, which refers to as the analysis of metabolome in a given biological condition, deals with the large scale detection and quantification of metabolites in biological media. It is a data driven and multidisciplinary approach combining analytical chemistry for data acquisition, and biostatistics, informatics and biochemistry for mining and interpretation of these data. Since the middle of the 2000s, high resolution mass spectrometry is widely used in metabolomics, mainly because the detection and identification of metabolites are improved compared to low resolution instruments. As the field of HRMS is quickly and permanently evolving, the aim of this work is to review its use in different aspects of metabolomics, including data acquisition, metabolite annotation, identification and quantification. At last, we would like to show that, thanks to their versatility, HRMS instruments are the most appropriate to achieve optimal metabolome coverage, at the border of other omics fields such as lipidomics and glycomics.

Metabolomic-based strategies for anti-parasite drug discovery

Metabolomics-based studies are proving of great utility in the analysis of modes of action (MOAs) and resistance mechanisms of drugs in parasitic protozoa. They have helped to determine the MOA of eflornithine, half of the gold standard combination therapy in use against human African trypanosomiasis (HAT), as well as the mechanism of resistance to this drug. In Leishmania, metabolomics has also given insight into the MOA of miltefosine, an alkylphospholipid. Several studies on antimony resistance in Leishmania have been conducted, analyzing the metabolic content of resistant lines, offering clues as to the MOA of this class of drugs. A study of chloroquine resistance in Plasmodium falciparum combined metabolomics techniques with other genetic and proteomic techniques to offer new insight into the role of the PfCRT protein. The MOA and mechanism of resistance to a group of halogenated pyrimidines in Trypanosoma brucei have also recently been elucidated. Effective as metabolomics techniques are, care must be taken in the design and implementation of these experiments, to ensure the resulting data are meaningful. This review outlines the steps required to conduct a metabolomics experiment as well as provide an overview of metabolomics-based drug research in protozoa to date.

Mass spectrometric behavior of phenolic acids standards and their analysis in the plant samples with LC/ESI/MS system

Liquid chromatography coupled to mass spectrometry (MS) with electrospray ionization (ESI) is one of analytical techniques to obtain accurate results of low molecular weight aromatic compounds in biological samples of different origin. The interpretations of mass spectra of these aromatic compounds in the negative spectra registered in the full scan MS mode may be uneasy due to presence of deprotonated molecules [M-H](-) from different co-eluting entities, fragment ions created after the break-up of precursor ions and also ions representing modified molecules clusters. Thus, the first aim of this study was to evaluate general parameters during analysis performed in the full scan MS or MS/MS mode. Secondly, to set general fragmentation rules for aromatic compounds and entities in a complex biological matrix. We established that different groups of low molecular weight phenolic acids form unique adduct ions and additionally registration LC/MS/MS spectra with two different collision energies may allow for differentiating isomeric or isobaric molecules. These findings together with some general fragmentation rules can facilitate identifications of aromatic acids as we outlined in the sample of cold-pressed rose-hip oil and lupine leaves extract.

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa

The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed.

Strategies for differentiation of isobaric flavonoids using liquid chromatography coupled to electrospray ionization mass spectrometry

Flavonoids are a class of secondary plant metabolites existing in great variety in nature. Due to this variety, identification can be difficult, especially as overlapping compounds in both chromatographic separations and mass spectrometric detection are common. Methods for distinguishing isobaric flavonoids using MS(2) and MS(3) have been developed. Chromatographic separation of various plant extracts was done with RP-HPLC and detected with positive ESI-MS operated in information-dependent acquisition (IDA) mode. Two methods for the determination of flavonoid identity and substitution pattern, both featuring IDA criteria, were used together with the HPLC equipment. A third method where the collision energy was ramped utilized direct infusion. With the developed strategies, it is possible to differentiate between many isobaric flavonoids. Various classes of flavonoids were found in all of the plant extracts, in the red onion extract 45 components were detected and for 29 of them the aglycone was characterized, while the substituents were tentatively identified for 31 of them. For the strawberry extract, those numbers were 66, 30 and 60, and for the cherry extract 99, 56 and 71. The great variety of flavonoids, several of them isobaric, found in each of the extracts highlights the need for reliable methods for flavonoid characterization. Methods capable of differentiating between most of the isobars analyzed have been developed.

The food metabolome: a window over dietary exposure

The food metabolome is defined as the part of the human metabolome directly derived from the digestion and biotransformation of foods and their constituents. With >25,000 compounds known in various foods, the food metabolome is extremely complex, with a composition varying widely according to the diet. By its very nature it represents a considerable and still largely unexploited source of novel dietary biomarkers that could be used to measure dietary exposures with a high level of detail and precision. Most dietary biomarkers currently have been identified on the basis of our knowledge of food compositions by using hypothesis-driven approaches. However, the rapid development of metabolomics resulting from the development of highly sensitive modern analytic instruments, the availability of metabolite databases, and progress in (bio)informatics has made agnostic approaches more attractive as shown by the recent identification of novel biomarkers of intakes for fruit, vegetables, beverages, meats, or complex diets. Moreover, examples also show how the scrutiny of the food metabolome can lead to the discovery of bioactive molecules and dietary factors associated with diseases. However, researchers still face hurdles, which slow progress and need to be resolved to bring this emerging field of research to maturity. These limits were discussed during the First International Workshop on the Food Metabolome held in Glasgow. Key recommendations made during the workshop included more coordination of efforts; development of new databases, software tools, and chemical libraries for the food metabolome; and shared repositories of metabolomic data. Once achieved, major progress can be expected toward a better understanding of the complex interactions between diet and human health.

In silico prediction and automatic LC-MS(n) annotation of green tea metabolites in urine

The colonic breakdown and human biotransformation of small molecules present in food can give rise to a large variety of potentially bioactive metabolites in the human body. However, the absence of reference data for many of these components limits their identification in complex biological samples, such as plasma and urine. We present an in silico workflow for automatic chemical annotation of metabolite profiling data from liquid chromatography coupled with multistage accurate mass spectrometry (LC-MS(n)), which we used to systematically screen for the presence of tea-derived metabolites in human urine samples after green tea consumption. Reaction rules for intestinal degradation and human biotransformation were systematically applied to chemical structures of 75 green tea components, resulting in a virtual library of 27,245 potential metabolites. All matching precursor ions in the urine LC-MS(n) data sets, as well as the corresponding fragment ions, were automatically annotated by in silico generated (sub)structures. The results were evaluated based on 74 previously identified urinary metabolites and lead to the putative identification of 26 additional green tea-derived metabolites. A total of 77% of all annotated metabolites were not present in the Pubchem database, demonstrating the benefit of in silico metabolite prediction for the automatic annotation of yet unknown metabolites in LC-MS(n) data from nutritional metabolite profiling experiments.

Structural analysis and profiling of phenolic secondary metabolites of Mexican lupine species using LC-MS techniques

Flavonoid glycoconjugates from roots and leaves of eight North America lupine species (Lupinus elegans, Lupinus exaltatus, Lupinus hintonii, Lupinus mexicanus, Lupinus montanus, Lupinus rotundiflorus, Lupinus stipulatus, Lupinus sp.), three Mediterranean species (Lupinus albus, Lupinus angustifolius, Lupinus luteus) and one species from South America domesticated in Europe (Lupinus mutabilis) were analyzed using two LC/MS systems: low-resolution ion trap instrument and high-resolution quadrupole-time-of-flight spectrometer. As a result of the LC/MS profiling using the CID/MS(n) experiments structures of 175 flavonoid glycoconjugates found in 12 lupine species were identified at three confidence levels according to the Metabolomic Standard Initiative, mainly at level 2 and 3, some of them were classified to the level 1. Among the flavonoid derivatives recognized in the plant extracts were isomeric or isobaric compounds, differing in the degree of hydroxylation of the aglycones and the presence of glycosidic, acyl or alkyl groups in the molecules. The elemental composition of the glycoconjugate molecules was established from the exact m/z values of the protonated/deprotonated molecules ([M+H](+)/[M-H](-)) measured with the accuracy better than 5 ppm. Information concerning structures of the aglycones, the type of sugar moieties (hexose, deoxyhexose or pentose) and, in some cases, their placement on the aglycones as well as the acyl substituents of the flavonoid glycoconjugates was achieved in experiments, in which collision-induced dissociation was applied. Flavonoid aglycones present in the studied O-glycoconjugates were unambiguously identified after the comparison of the pseudo-MS(3) spectra with the spectra registered for the standards. Isomers of flavonoid glycoconjugates, in which one or two sugar moieties were attached to 4'- or 7-hydroxyl groups or directly to the C-6 or C-8 of the aglycones, could be distinguished on the basis of the MS(2) spectra. However, the collision energy applied in the CID experiments had to be optimized for each group of the compounds and there were no universal settings that allowed the acquisition of structural information for all the compounds present in the sample. Information obtained from the flavonoid conjugate profiling was used for the chemotaxonomic comparison of the studied lupine species. A clear-cut discrimination of the Mediterranean and North American lupines was obtained as a result of this analysis.

Identification of regioisomers of methylated kaempferol and quercetin by ultra high performance liquid chromatography quadrupole time-of-flight (UHPLC-QTOF) tandem mass spectrometry combined with diagnostic fragmentation pattern analysis

The O-methylation of active flavonoids can enhance their antiallergic, anticancerous, and cardioprotective effects depending on the methylation position. Thus, it is biologically and pharmacologically important to differentiate methylated flavonoid regioisomers. In this study, we examined the regioisomers of methylated kaempferol and quercetin using ultra high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry. The methyl groups on the flavonoids can generally be cleaved as methyl radicals in a position-independent manner. We found that methyl groups can be cleaved as methane. If there are protons adjacent the methoxy on the flavonol rings, intra-molecule proton transfer can occur via collision-induced dissociation, and one molecule of methane can then be eliminated. The remaining charged fragment ([M+H-CH4](+)) reflects the adjacent structure and is specific to the methoxy position. Furthermore, the retro Diels-Alder (RDA) fragmentation of methylated flavonols can generate fragments with the methoxy at the original methylated ring. Combining the position-specific [M+H-CH4](+) fragment with the RDA fragments provides a diagnostic pattern for rapidly identifying methylated regioisomeric flavonols. Along with their retention behaviour, we have successfully identified ten regioisomers of methylated kaempferol and quercetin, which include six compounds previously reported in plants and shown to be biologically active. The developed approach is sensitive, rapid, reliable, and requires few standard compounds. It is highly efficient for characterising the specificity of novel flavonoid O-methyltransferases and can help direct enzymatic or chemical syntheses during the early stages of drug discovery. This method also has potential for use in identifying other methylated isomeric flavonoids.

System-wide hypersensitive response-associated transcriptome and metabolome reprogramming in tomato

The hypersensitive response (HR) is considered to be the hallmark of the resistance response of plants to pathogens. To study HR-associated transcriptome and metabolome reprogramming in tomato (Solanum lycopersicum), we used plants that express both a resistance gene to Cladosporium fulvum and the matching avirulence gene of this pathogen. In these plants, massive reprogramming occurred, and we found that the HR and associated processes are highly energy demanding. Ubiquitin-dependent protein degradation, hydrolysis of sugars, and lipid catabolism are used as alternative sources of amino acids, energy, and carbon skeletons, respectively. We observed strong accumulation of secondary metabolites, such as hydroxycinnamic acid amides. Coregulated expression of WRKY transcription factors and genes known to be involved in the HR, in addition to a strong enrichment of the W-box WRKY-binding motif in the promoter sequences of the coregulated genes, point to WRKYs as the most prominent orchestrators of the HR. Our study has revealed several novel HR-related genes, and reverse genetics tools will allow us to understand the role of each individual component in the HR.

Detoxification of α-tomatine by Cladosporium fulvum is required for full virulence on tomato

· α-Tomatine is an antifungal glycoalkaloid that provides basal defense to tomato (Solanum lycopersicum). However, tomato pathogens overcome this basal defense barrier by the secretion of tomatinases that degrade α-tomatine into the less fungitoxic compounds β-tomatine and tomatidine. Although pathogenic on tomato, it has been reported that the biotrophic fungus Cladosporium fulvum is unable to detoxify α-tomatine. · Here, we present a functional analysis of the glycosyl hydrolase (GH10), CfTom1, which is orthologous to fungal tomatinases. · We show that C. fulvum hydrolyzes α-tomatine into tomatidine in vitro and during the infection of tomato, which is fully attributed to the activity of CfTom1, as shown by the heterologous expression of this enzyme in tomato. Accordingly, ∆cftom1 mutants of C. fulvum are more sensitive to α-tomatine and are less virulent than the wild-type fungus on tomato. · Although α-tomatine is thought to be localized in the vacuole, we show that it is also present in the apoplast, where it is hydrolyzed by CfTom1 on infection. The accumulation of tomatidine during infection appears to be toxic to tomato cells and does not suppress defense responses, as suggested previously. Altogether, our results show that CfTom1 is responsible for the detoxification of α-tomatine by C. fulvum, and is required for full virulence of this fungus on tomato.

Unravelling ionization and fragmentation pathways of carotenoids using orbitrap technology: a first step towards identification of unknowns

Vegetables are a major source of carotenoids and carotenoids are identified as potentially important natural antioxidants that may aid in the prevention of several human chronic degenerative diseases. Characterization of carotenoids in organic biological matrices is a crucial step in any research valorization trajectory. This study reports for the first time the use of high mass resolution and exact mass orbitrap technology for the elucidation of carotenoid fragmentation pathways. This contributes to the generation of new tools for identifying unknown carotenoids based on fragmentation patterns. Two different chromatographic methods making use of different mobile phases resulted in the generation of different ion species because of the large influence of the mobile phase solvent composition on ionization. It was shown that depending on the molecular ion species that are generated (protonated ions or radical molecular ions), different fragments are formed when applying higher energy collisional dissociation. Fragmentation and the abundance of fragments provide valuable structural information on the type of functional groups, the polyene backbone and the location of double bonds in ring structures of carotenoids. Furthermore, coherence between specific substructures in the molecules and characteristic fragmentation patterns was observed allowing the assignment of fragmentation patterns for carotenoid substructures that can theoretically be extrapolated to carotenoids with similar (sub)structures. Differentiation between isomeric carotenoids by compound specific fragments could however not be made for all the isomeric groups under study. As a wide variety of isomeric forms of carotenoids exist in nature, the combination of good chromatographic separation with high resolution mass spectrometry and other complementary qualitative structure elucidation techniques such as a photo diode array detector and/or nuclear magnetic resonance spectroscopy are indispensable for unambiguous identification of unknown carotenoids.

Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea

Liquid chromatography coupled with multistage accurate mass spectrometry (LC-MS(n)) can generate comprehensive spectral information of metabolites in crude extracts. To support structural characterization of the many metabolites present in such complex samples, we present a novel method ( http://www.emetabolomics.org/magma ) to automatically process and annotate the LC-MS(n) data sets on the basis of candidate molecules from chemical databases, such as PubChem or the Human Metabolite Database. Multistage MS(n) spectral data is automatically annotated with hierarchical trees of in silico generated substructures of candidate molecules to explain the observed fragment ions and alternative candidates are ranked on the basis of the calculated matching score. We tested this method on an untargeted LC-MS(n) (n ≤ 3) data set of a green tea extract, generated on an LC-LTQ/Orbitrap hybrid MS system. For the 623 spectral trees obtained in a single LC-MS(n) run, a total of 116,240 candidate molecules with monoisotopic masses matching within 5 ppm mass accuracy were retrieved from the PubChem database, ranging from 4 to 1327 candidates per molecular ion. The matching scores were used to rank the candidate molecules for each LC-MS(n) component. The median and third quartile fractional ranks for 85 previously identified tea compounds were 3.5 and 7.5, respectively. The substructure annotations and rankings provided detailed structural information of the detected components, beyond annotation with elemental formula only. Twenty-four additional components were putatively identified by expert interpretation of the automatically annotated data set, illustrating the potential to support systematic and untargeted metabolite identification.