Collision energy alteration during mass spectrometric acquisition is essential to ensure unbiased metabolomic analysis

Optimization Strategies for Mass Spectrometry-Based Untargeted Metabolomics Analysis of Small Polar Molecules in Human Plasma

The untargeted approach to mass spectrometry-based metabolomics has a wide potential to investigate health and disease states, identify new biomarkers for diseases, and elucidate metabolic pathways. All this holds great promise for many applications in biological and chemical research. However, the complexity of instrumental parameters on advanced hybrid mass spectrometers can make the optimization of the analytical method immensely challenging. Here, we report a strategy to optimize the selected settings of a hydrophilic interaction liquid chromatography-tandem mass spectrometry method for untargeted metabolomics studies of human plasma, as a sample matrix. Specifically, we evaluated the effects of the reconstitution solvent in the sample preparation procedure, the injection volume employed, and different mass spectrometry-related operating parameters including mass range, the number of data-dependent fragmentation scans, collision energy mode, duration of dynamic exclusion time, and mass resolution settings on the metabolomics data quality and output. This study highlights key instrumental variables influencing the detection of metabolites along with suggested settings for the IQ-X tribrid system and proposes a new methodological framework to ensure increased metabolome coverage.

Microwave assisted free radical degradation of Schisandra polysaccharides: Optimization, identification and application

In order to establish structural-fingerprinting of polysaccharides for improvement of quality assessment, a sample preparation method based on microwave assisted free radical degradation (MFRD) of plant polysaccharides was proposed to produce oligosaccharides and small M_w polysaccharides. As a case study of Schisandra chinensis and S. sphenanthera fruit polysaccharides (SCP and SSP), the MFRD condition (i.e., 100 °C, 30 s and 80 W) was confirmed to be optimal. The potential structures of the MFRD products of SCP and SSP were further discussed by combinations of HILIC-ESI^--QTOF-MS^E and HILIC-ESI^--Q-OT-IT-MS/MS. As followed, multivariable statistical analysis shows a clear separation of SCP and the SSP in PCA and OPLS-DA plots based HILIC-ESI^--QTOF-MS^E data. The VIP plot unveils several key Q-markers (e.g., peaks 3, 8, 9, 10, 15, 25, 26, 28, 29 and 30) with significant differences and stable emergences. Furthermore, a low-polymerization compositional fingerprinting was successfully constructed for SCP and SSP using a high-performance anion-exchange chromatography with pulsed amperometric detection. Compared to the conventional sample preparation methods, the MFRD took only a few thousandth of the time to accomplish degradations of plant polysaccharides. It significantly improves sample preparations and is generally applicable to various polysaccharide samples.

Analyzing Assay Specificity in Metabolomics Using Unique Ion Signature Simulations

Targeted, untargeted, and data-independent acquisition (DIA) metabolomics workflows are often hampered by ambiguous identification based on either MS1 information alone or relatively few MS2 fragment ions. While DIA methods have been popularized in proteomics, it is less clear whether they are suitable for metabolomics workflows due to their large precursor isolation windows and complex coisolation patterns. Here, we quantitatively investigate the conditions necessary for unique metabolite detection in complex backgrounds using precursor and fragment ion mass-to-charge (m/z) separation, comparing three benchmarked mass spectrometry (MS) methods [MS1, MRM (multiple reaction monitoring), and DIA]. Our simulations show that DIA outperformed MS1-only and MRM-based methods with regards to specificity by factors of ∼2.8-fold and ∼1.8-fold, respectively. Additionally, we show that our results are not dependent on the number of transitions used or the complexity of the background matrix. Finally, we show that collision energy is an important factor in unambiguous detection and that a single collision energy setting per compound cannot achieve optimal pairwise differentiation of compounds. Our analysis demonstrates the power of using both high-resolution precursor and high-resolution fragment ion m/z for unambiguous compound detection. This work also establishes DIA as an emerging MS acquisition method with high selectivity for metabolomics, outperforming both data-dependent acquisition (DDA) and MRM with regards to unique compound identification potential.

Center-of-Mass iso-Energetic Collision-Induced Decomposition in Tandem Triple Quadrupole Mass Spectrometry

Two scan modes of the triple quadrupole tandem mass spectrometer, namely Collision Induced Dissociation Precursor Ion scan and Neutral Loss scan, allow selectively pinpointing, in a complex mixture, compounds that feature specific chemical groups, which yield characteristic fragment ions or are lost as distinctive neutral fragments. This feature of the triple quadrupole tandem mass spectrometer allows the non-target screening of mixtures for classes of components. The effective (center-of-mass) energy to achieve specific fragmentation depends on the inter-quadrupole voltage (laboratory-frame collision energy) and on the masses of the precursor molecular ion and of the collision gas, through a non-linear relationship. Thus, in a class of homologous compounds, precursor ions activated at the same laboratory-frame collision energy face different center-of-mass collision energy, and therefore the same fragmentation channel operates with different degrees of efficiency. This article reports a linear equation to calculate the laboratory-frame collision energy necessary to operate Collision-Induced Dissociation at the same center-of-mass energy on closely related compounds with different molecular mass. A routine triple quadrupole tandem mass spectrometer can operate this novel feature (iso-energetic collision-induced dissociation scan; i-CID) to analyze mixtures of endogenous metabolites by Precursor Ion and Neutral Loss scans. The latter experiment also entails the hitherto unprecedented synchronized scanning of all three quadrupoles of the triple quadrupole tandem mass spectrometer. To exemplify the application of this technique, this article shows two proof-of-principle approaches to the determination of biological mixtures, one by Precursor Ion analysis on alpha amino acid derivatized with a popular chromophore, and the other on modified nucleosides with a Neutral Fragment Loss scan.

Untargeted metabolomics using liquid chromatography coupled with mass spectrometry for rapid discovery of metabolite biomarkers to reveal therapeutic effects of Psoralea corylifolia seeds against osteoporosis

Liquid chromatography coupled with mass spectrometry has been used as metabolomics profiling tool to discover and identify the metabolites in metabolic diseases. Osteoporosis (OP) syndrome is a chronic metabolic disease characterized by bone mass reduction and changes in bone microstructure. Psoralea corylifolia Linn. seeds (PCS) have a therapeutic effect on osteoporosis, but their action mechanism and therapeutic target are still unclear. This study aims to explore the metabolic changes of the urine profile in glucocorticoid-induced OP model rats and the therapeutic effect of PCS. High-throughput metabolomics based on the liquid chromatography coupled with mass spectrometry quadrupole time-of-flight mass spectrometry and multivariate data analysis were used to analyze the urine metabolites. The results showed that has an obvious separation between model and control groups. OPLS-DA was used to further analyze and discover substances that contributed to the separation. 42 potential biomarkers and 12 related metabolic pathways were identified in combination with network databases. After the intervention of PCS, 24 biomarkers were significantly regulated, mainly with glycone, serine and threonine metabolism, glutathione metabolism and purine metabolism and other metabolic pathways are related and discovered. This study has proved that PCS has therapeutic effect against OP by regulating that metabolic pathways disturbed in the OP. It provided a basis for the research and future development of new drugs for OP treatment.

Liquid chromatography coupled with mass spectrometry has been used as metabolomics profiling tool to discover and identify the metabolites in metabolic diseases.

Unravelling the Metabolic Reconfiguration of the Post-Challenge Primed State in Sorghum bicolor Responding to Colletotrichum sublineolum Infection

Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of priming events is still limited. A non-targeted metabolomics approach was used to investigate metabolic changes in plant growth-promoting rhizobacteria (PGPR)-primed Sorghum bicolor seedlings infected with the anthracnose-causing fungal pathogen, Colletotrichum sublineolum, with a focus on the post-challenge primed state phase. At the 4-leaf growth stage, the plants were treated with a strain of Paenibacillus alvei at 10⁸ cfu mL⁻¹. Following a 24 h PGPR application, the plants were inoculated with a C. sublineolum spore suspension (10⁶ spores mL⁻¹), and the infection monitored over time: 1, 3, 5, 7 and 9 days post-inoculation. Non-infected plants served as negative controls. Intracellular metabolites from both inoculated and non-inoculated plants were extracted with 80% methanol-water. The extracts were chromatographically and spectrometrically analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to high-definition mass spectrometry. The acquired multidimensional data were processed to create data matrices for chemometric modelling. The computed models indicated time-related metabolic perturbations that reflect primed responses to the fungal infection. Evaluation of orthogonal projection to latent structure-discriminant analysis (OPLS-DA) loading shared and unique structures (SUS)-plots uncovered the differential stronger defence responses against the fungal infection observed in primed plants. These involved enhanced levels of amino acids (tyrosine, tryptophan), phytohormones (jasmonic acid and salicylic acid conjugates, and zeatin), and defence-related components of the lipidome. Furthermore, other defence responses in both naïve and primed plants were characterised by a complex mobilisation of phenolic compounds and de novo biosynthesis of the flavones, apigenin and luteolin and the 3-deoxyanthocyanidin phytoalexins, apigeninidin and luteolinidin, as well as some related conjugates.

Ion-neutral Clustering of Bile Acids in Electrospray Ionization Across UPLC Flow Regimes

Bile acid authentic standards were used as model compounds to quantitatively evaluate complex in-source phenomenon on a UPLC-ESI-TOF-MS operated in the negative mode. Three different diameter columns and a ceramic-based microfluidic separation device were utilized, allowing for detailed descriptions of bile acid behavior across a wide range of flow regimes and instantaneous concentrations. A custom processing algorithm based on correlation analysis was developed to group together all ion signals arising from a single compound; these grouped signals produce verified compound spectra for each bile acid at each on-column mass loading. Significant adduction was observed for all bile acids investigated under all flow regimes and across a wide range of bile acid concentrations. The distribution of bile acid containing clusters was found to depend on the specific bile acid species, solvent flow rate, and bile acid concentration. Relative abundancies of each cluster changed non-linearly with concentration. It was found that summing all MS level (low collisional energy) ions and ion-neutral adducts arising from a single compound improves linearity across the concentration range (0.125-5 ng on column) and increases the sensitivity of MS level quantification. The behavior of each cluster roughly follows simple equilibrium processes consistent with our understanding of electrospray ionization mechanisms and ion transport processes occurring in atmospheric pressure interfaces. Graphical Abstract ᅟ.

Leishmanicidal activity of the root bark of Erythrophleum Ivorense (Fabaceae) and identification of some of its compounds by ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS/MS)

ETHNOPHARMACOLOGICAL RELEVANCE

Leishmaniasis is one of the neglected tropical disease caused by a protozoan of the genus Leishmania transmitted by sandflies. High cost and lack of oral formulation of existing drugs, rapid developments of resistance by the parasite coupled with serious side effects require new treatments to augment or replace currently available therapies. The major merits of herbal medicine seem to demonstrate perceived efficacy, low incidence of serious adverse effects and low cost. Erythrophleum plants possess beneficial biological properties and, as such, characterization of the bioactive components of these plants is imperative. Previous work has shown an overwhelming presence of cassaine alkaloids in these plants. However, amongst these plants, the African based specie (Erythrophleum ivorense) is the least studied.

OBJECTIVE

In the current study, the in vitro anti-leishmanial activity of the crude extract, its fractions and isolated compounds were evaluated using direct counting assay of promastigotes of Leishmania donovani using amphotericin B as positive control.

MATERIALS AND METHODS

The anti-leishmanial activity of E. ivorense extract was evaluated in vitro against the promastigote forms of Leishmania Donovani using a direct counting assay based on growth inhibition. Different crude extracts from ethyl acetate, pet-ether, and methanol as well as pure isolated compounds of E. ivorense: Erythroivorensin, Eriodictyol and Betulinic acid were screened. To know the possible components of the active methanolic extract, attempt was made to elucidate the extract using ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS/MS).

RESULTS

This afforded a weak pet-ether fraction, a moderately active ethyl acetate fraction and a significantly active methanol fraction (IC₅₀ = 2.97μg/mL) compared to Amphotericin B (IC₅₀ = 2.40±0.67μg/mL). The novel diterpene erythroivorensin, betulinic acid and the flavanone Eriodictyol, from the ethyl acetate fraction, showed weak activity. UPLC-QTOF-MS/MS was used to identify the cassaine diterpenoids from the active methanol fraction. Here, 10 compounds of this type were putatively identified from the ethanol crude extract.

CONCLUSION

The fragmentation mechanism of these metabolites is also proposed and are expected to serve as reference template for identification of these and related compounds in future. The presence of these compounds is an indication that they are an inherited and evolutionary component of plants belonging to the Erythrophleum genus. Our results further present another dimension where these compounds and their relative abundances can be used as chemo-taxonomical bio-markers of the genus. The present study also successfully demonstrated/re-affirmed the use of UPLC-QTOF-MS/MS as a robust technique for the characterization of natural products.

Synchronized Survey Scan Approach Allows for Efficient Discrimination of Isomeric and Isobaric Compounds during LC-MS/MS Analyses

Liquid chromatography-mass spectrometry- (LC-MS-) based multiple reaction monitoring (MRM) methods have been used to detect and quantify metabolites for years. These approaches rely on the monitoring of various fragmentation pathways of multiple precursors and the subsequent corresponding product ions. However, MRM methods are incapable of confidently discriminating between isomeric and isobaric molecules and, as such, the development of methods capable of overcoming this challenge has become imperative. Due to increasing scanning rates of recent MS instruments, it is now possible to operate MS instruments both in the static and dynamic modes. One such method is known as synchronized survey scan (SSS), which is capable of acquiring a product ion scan (PIS) during MRM analysis. The current study shows, for the first time, the use of SSS-based PIS approach as a feasible identification feature of MRM. To achieve the above, five positional isomers of dicaffeoylquinic acids (diCQAs) were studied with the aid of SSS-based PIS method. Here, the MRM transitions were automatically optimized using a 3,5-diCQA isomer by monitoring fragmentation transitions common to all five isomers. Using the mixture of these isomers, fragmentation spectra of the five isomers achieved with SSS-based PIS were used to identify each isomer based on previously published hierarchical fragmentation keys. The optimized method was also used to detect and distinguish between diCQA components found in Bidens pilosa and their isobaric counterparts found in Moringa oleifera plants. Thus, the method was shown to distinguish (by differences in fragmentation patterns) between diCQA and their isobars, caffeoylquinic acid (CQA) glycosides. In conclusion, SSS allowed the detection and discrimination of isomeric and isobaric compounds in a single chromatographic run by producing a PIS spectrum, triggered in the automatic MS/MS synchronized survey scan mode.

Deciphering the influence of column chemistry and mass spectrometry settings for the analyses of geometrical isomers of L-chicoric acid

Resolving the chemo-diversity of plant extract samples is an essential step for in-depth analyses of natural products which often exhibit promising biological activities. One of the challenges in this endeavor has been the confident differentiation of geometrical isomers. In this study, we investigated these aspects in chromatography (column chemistry and mobile phase composition) and mass spectrometry settings with regards to better differentiation of geometrical isomers. A standard of a hydroxycinnamic acid (HCA) derivative, L-chicoric acid (L-CA) - a di-acylated caffeoyltartaric acid ester found in a number of plant families - was used. Geometrical isomers of L-CA were formed by exposing the compound to ultraviolet (UV) radiation, to mimic the natural environment. The high performance liquid chromatography photo-diode array (HPLC-PDA) and ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS) platforms were used to analyze the trans and cis geometrical isomers of L-CA. The HPLC-PDA results confirmed the generation of two cis geometrical isomers following UV exposure of the authentic trans-L-CA standard. Furthermore, the HPLC-PDA analyses demonstrated that the changes in both column chemistry (reverse-phase: C₁₈, biphenyl, phenyl-hexyl and pentafluorophenyl propyl) and mobile phase composition (aqueous acetonitrile and aqueous methanol) affect the chromatographic elution profiles of the L-CA isomers. The MS results, on the other hand, revealed undisputed fragmentation differences between the geometrical isomers of L-CA. Thus, this study demonstrates that the identification of the L-CA isomers can be achieved more efficiently and confidently with good chromatography coupled to well-optimized mass spectrometry conditions, a requirement which has been proven impossible with other types of HCA derivatives. Moreover, differences in the binding modes of L-CA geometrical isomers to the HIV type 1 integrase enzyme were observed, suggesting a synergistic anti-HIV-1 activity of these isomers.

Stepped collisional energy MS(All) : an analytical approach for optimal MS/MS acquisition of complex mixture with diverse physicochemical properties

The analysis of complex mixtures is becoming increasingly important in various fields, such as nutrition, medicinal plants and metabolomics. The components contained in such complex mixtures are always characterized with diverse physiochemical properties that pose a major challenge during the optimization of various parameters using liquid chromatography-mass spectrometer (LC-MS). The parameter 'CE energy' that is normally set at a fixed value with a moderate range of CE spread during data-dependent acquisition (DDA) analysis, a prevalent approach for untargeted identification, often fails to generate sufficient MS/MS fragment ions for untargeted identification of components from complex mixtures. Here we developed a simple and generally applicable acquisition method named stepped MS(All) (sMS(All) ) in this study, aiming to obtain optimal MS/MS spectra for identification of chemically diverse compounds from complex mixtures. sMS(All) collects serial MS(All) scans acquired at low CE to gradually ramped-up high CE values in a cycle that conventional DDA scans cannot afford. The resultant MS/MS spectra of each compound were compared and evaluated among serial MS(All) scans, and the optimal spectra were used for identification. An untargeted data analysis strategy was then employed to analyze these optimal MS/MS spectra by searching common diagnostic ions and connecting the diagnostic ion families into a network via bridging components. This sMS(All) -based route enables identification of 71 natural products from a herbal preparation, whereas only 53 out of 71 compounds were identified using the classical DDA approach. Therefore, the sMS(All) -based approach is expected to find its wide applications for characterization of vastly diverse compounds with no priori knowledge from various complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.

Preferential alkali metal adduct formation by cis geometrical isomers of dicaffeoylquinic acids allows for efficient discrimination from their trans isomers during ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry

RATIONALE

Caffeoylquinic acid (CQA) derivatives are a group of structurally diverse phytochemicals that have attracted attention due to their many health benefits. The structural diversity of these molecules is due in part to the presence of regio- and geometrical isomerism. This structural diversity hampers the accurate annotation of these molecules in plant extracts. Mass spectrometry (MS) is successfully used to differentiate between the different regioisomers of the CQA derivatives; however, the accurate discrimination of the geometrical isomers of these molecules has proven to be an elusive task.

METHODS

UV-irradiated methanolic solutions of diCQA were analyzed using an ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UHPLC/QTOFMS) method in negative ionisation mode. An in-source collision-induced dissociation (ISCID) method was optimized by varying both the capillary and cone voltages to achieve differential fragmentation patterns between UV-generated geometrical isomers of the diCQAs during MS analyses.

RESULTS

Changes in the capillary voltage did not cause a significant difference to the fragmentation patterns of the four geometrical isomers, while changes in the cone voltage resulted in significant differences in the fragmentation patterns. The results also show, for the first time, the preferential formation of alkali metal (Li(+), Na(+) and K(+)) adducts by the cis geometrical isomers of diCQAs, compared to their trans counterparts.

CONCLUSIONS

Optimized QTOFMS-based methods may be used to differentiate the geometrical isomers of diCQAs. Finally, additives such as metal salts to induce adduct formation can be applied as an alternative method to differentiate closely related isomers which could have been difficult to differentiate under normal MS settings.

Secondary metabolite perturbations in Phaseolus vulgaris leaves due to gamma radiation

Oxidative stress is a condition in which the balance between the production and elimination of reactive oxygen species (ROS) is disturbed. However, plants have developed a very sophisticated mechanism to mitigate the effect of ROS by constantly adjusting the concentration thereof to acceptable levels. Electromagnetic radiation is one of the factors which results in oxidative stress. In the current study, ionizing gamma radiation generated from a Cobalt-60 source was used to induce oxidative stress in Phaseolus vulgaris seedlings. Plants were irradiated with several radiation doses, with 2 kGy found to be the optimal, non-lethal dose. Metabolite distribution patterns from irradiated and non-irradiated plants were analyzed using UHPLC-qTOF-MS and multivariate data models such as principal component analysis (PCA) and orthogonal projection to latent structures discriminate analysis (OPLS-DA). Metabolites such as hydroxycinnamic phenolic acids, flavonoids, terpenes, and a novel chalcone were found to be perturbed in P. vulgaris seedlings treated with the aforementioned conditions. The results suggest that there is a compensatory link between constitutive protectants and inducible responses to injury as well as defense against oxidative stress induced by ionizing radiation. The current study is also the first to illustrate the power of a metabolomics approach to decipher the effect of gamma radiation on crop plants.

Lipidomics: Novel insight into the biochemical mechanism of lipid metabolism and dysregulation-associated disease

The application of lipidomics, after genomics, proteomics and metabolomics, offered largely opportunities to illuminate the entire spectrum of lipidome based on a quantitative or semi-quantitative level in a biological system. When combined with advances in proteomics and metabolomics high-throughput platforms, lipidomics provided the opportunity for analyzing the unique roles of specific lipids in complex cellular processes. Abnormal lipid metabolism was demonstrated to be greatly implicated in many human lifestyle-related diseases. In this review, we focused on lipidomic applications in brain injury disease, cancer, metabolic disease, cardiovascular disease, respiratory disease and infectious disease to discover disease biomarkers and illustrate biochemical metabolic pathways. We also discussed the analytical techniques, future perspectives and potential problems of lipidomic applications. The application of lipidomics in disease biomarker discovery provides the opportunity for gaining novel insights into biochemical mechanism.

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.

The antihyperlipidemic effect of Fu-Ling-Pi is associated with abnormal fatty acid metabolism as assessed by UPLC-HDMS-based lipidomics

The surface layer of Poria cocos (SLPC), a traditional Chinese medicine, has been commonly used for diuretic and antihyperlipidemia in Asia.

Metabolomic insights into the bioconversion of isonitrosoacetophenone in Arabidopsis thaliana and its effects on defense-related pathways

Plants are constantly exposed to numerous biotic or abiotic stress factors throughout their life-cycle. Pathogens and pathogen-derived molecules are the best studied inducers of plant defense responses, but synthetic and naturally occurring molecules have also been used to induce various types of resistance in plants. Here, an oxime molecule, 2-isonitrosoacetophenone (INAP), related to the stress metabolite citaldoxime, was used to trigger metabolic changes in the metabolome of treated Arabidopsis thaliana plants as monitored by UHPLC-MS in conjunction with principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA). The chemometric methods revealed metabolites found to be significantly present in response to the treatment. These include bioconversion products (2-keto-2-phenylacetaldoxime-glycoside and l-mandelonitrile-glycoside) as well as those of which the levels are affected by the treatment (benzoic acid and derivatives, other phenylpropanoid-derived compounds and glucosinolates). Using in planta bacterial growth evaluations, INAP treatment was furthermore found to induce an anti-microbial environment in vivo.

The Effect of Temperature on Pressurised Hot Water Extraction of Pharmacologically Important Metabolites as Analysed by UPLC-qTOF-MS and PCA

Metabolite extraction methods have been shown to be a critical consideration for pharmacometabolomics studies and, as such, optimization and development of new extraction methods are crucial. In the current study, an organic solvent-free method, namely, pressurised hot water extraction (PHWE), was used to extract pharmacologically important metabolites from dried Moringa oleifera leaves. Here, the temperature of the extraction solvent (pure water) was altered while keeping other factors constant using a homemade PHWE system. Samples extracted at different temperatures (50, 100, and 150°C) were assayed for antioxidant activities and the effect of the temperature on the extraction process was evaluated. The samples were further analysed by mass spectrometry to elucidate their metabolite compositions. Principal component analysis (PCA) evaluation of the UPLC-MS data showed distinctive differential metabolite patterns. Here, temperature changes during PHWE were shown to affect the levels of metabolites with known pharmacological activities, such as chlorogenic acids and flavonoids. Our overall findings suggest that, if not well optimised, the extraction temperature could compromise the "pharmacological potency" of the extracts. The use of MS in combination with PCA was furthermore shown to be an excellent approach to evaluate the quality and content of pharmacologically important extracts.

Multivariate statistical models of metabolomic data reveals different metabolite distribution patterns in isonitrosoacetophenone-elicited Nicotiana tabacum and Sorghum bicolor cells

Isonitrosoacetophenone (INAP, 2-keto-2-phenyl-acetaldoxime) is a novel inducer of plant defense. Oxime functional groups are rare in natural products, but can serve as substrates depending on existing secondary pathways. Changes in the metabolomes of sorghum and tobacco cells treated with INAP were investigated and chemometric tools and multivariate statistical analysis were used to investigate the changes in metabolite distribution patterns resulting from INAP elicitation. Liquid chromatography combined with mass spectrometry (UHPLC-MS) supplied unique chemical fingerprints that were generated in response to specific metabolomic events. Principal component analysis (PCA) together with hierarchical cluster analysis (HCA) and Metabolic Trees were used for data visualization. Orthogonal projections to latent structures discriminant analysis (OPLS-DA) and shared and unique structure (SUS) plots were exploited in parallel to reveal the changes in the metabolomes. PCA indicated that the cells responded differentially to INAP through changes in the metabolite profiles. Furthermore, HCA and Metabolic Trees showed that INAP induced metabolic perturbations in both cell lines and that homeostasis was re-established over time. OPLS-DA-based shared and unique structure (SUS) plots confirmed the results and revealed differences in the metabolites distribution patterns between tobacco and sorghum cells. Chemometric analyses of metabolomic data offers insight into changes in metabolism in response to chemical elicitation. Although similar, the response in sorghum cells was found to be more consistent and well-coordinated when compared to tobacco cells, indicative of the differences in secondary metabolism between cyanogenic and non-cyanogenic plants for oxime metabolism.

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

Metabolism represents the 'sharp end' of systems biology, because changes in metabolite concentrations are necessarily amplified relative to changes in the transcriptome, proteome and enzyme activities, which can be modulated by drugs. To understand such behaviour, we therefore need (and increasingly have) reliable consensus (community) models of the human metabolic network that include the important transporters. Small molecule 'drug' transporters are in fact metabolite transporters, because drugs bear structural similarities to metabolites known from the network reconstructions and from measurements of the metabolome. Recon2 represents the present state-of-the-art human metabolic network reconstruction; it can predict inter alia: (i) the effects of inborn errors of metabolism; (ii) which metabolites are exometabolites, and (iii) how metabolism varies between tissues and cellular compartments. However, even these qualitative network models are not yet complete. As our understanding improves so do we recognise more clearly the need for a systems (poly)pharmacology.