Spectral trees as a robust annotation tool in LC–MS based metabolomics

The identification of large series of metabolites detectable by mass spectrometry (MS) in crude extracts is a challenging task. In order to test and apply the so-called multistage mass spectrometry (MS ⁿ ) spectral tree approach as tool in metabolite identification in complex sample extracts, we firstly performed liquid chromatography (LC) with online electrospray ionization (ESI)?CMS ⁿ , using crude extracts from both tomato fruit and Arabidopsis leaf. Secondly, the extracts were automatically fractionated by a NanoMate LC-fraction collector/injection robot (Advion) and selected LC-fractions were subsequently analyzed using nanospray-direct infusion to generate offline in-depth MS ⁿ spectral trees at high mass resolution. Characterization and subsequent annotation of metabolites was achieved by detailed analysis of the MS ⁿ spectral trees, thereby focusing on two major plant secondary metabolite classes: phenolics and glucosinolates. Following this approach, we were able to discriminate all selected flavonoid glycosides, based on their unique MS ⁿ fragmentation patterns in either negative or positive ionization mode. As a proof of principle, we report here 127 annotated metabolites in the tomato and Arabidopsis extracts, including 21 novel metabolites. Our results indicate that online LC?CMS ⁿ fragmentation in combination with databases of in-depth spectral trees generated offline can provide a fast and reliable characterization and annotation of metabolites present in complex crude extracts such as those from plants.     

Rapid isolation and identification of minor natural products by LC–MS,LC–SPE–NMR and ECD: Isoflavanones,biflavanones and bisdihydrocoumarins from Ormocarpum kirkii

The combination of the hyphenated techniques LC–MS and LC–SPE–NMR constitutes a powerful platform for the rapid isolation and identification of minor components from natural sources. Electronic circular dichroism (ECD) is a useful tool to determine the absolute configuration of small quantities of chiral molecules. In order to search for minor constituents present in an Ormocarpum kirkii extract, these techniques were applied for the separation and structure elucidation of a series of isoflavanones, biflavanones and biscoumarins. After optimization of chromatographic conditions and subsequent isolation, MS and 1D and 2D NMR data were collected. Experimental and calculated ECD spectra were used in conjunction with NMR data to confirm the absolute configuration of these compounds. Eight compounds were identified for the first time and six have been previously reported. The present approach offers a strategy for accelerating research on natural products.     

Identification of acylation products in SHAPE chemistry

SHAPE chemistry (selective 2′-hydroxyl acylation analyzed by primer extension) has been developed to specifically target flexible nucleotides (often unpaired nucleotides) independently to their purine or pyrimidine nature for RNA secondary structure determination. However, to the best of our knowledge, the structure of 2′-O-acylation products has never been confirmed by NMR or X-ray data. We have realized the acylation reactions between cNMP and NMIA under SHAPE chemistry conditions and identified the acylation products using standard NMR spectroscopy and LC–MS/MS experiments. For cAMP and cGMP, the major acylation product is the 2′-O-acylated compound (>99%). A trace amount of N-acylated cAMP has also been identified by LC–UV–MS². While for cCMP, the isolated acylation products are composed of 96% of 2′-O-acylated, 4% of N,O-diacylated, and trace amount of N-acylated compounds. In addition, the characterization of the major 2′-O-acylated compound by NMR showed slight differences in the conformation of the acylated sugar between the three cyclic nucleotides. This interesting result should be useful to explain some unexpected reactivity of the SHAPE chemistry.     

Microalgal transformation of progesterone by the terrestrial-isolated cyanobacterium Microchaete tenera

A large number of microorganisms including various microalgal strains are able to convert steroid compounds into useful metabolites. In the present study, the ability of Microchaete tenera, a rice paddy field-isolated microalga, was investigated for biotransformation of progesterone. The incubation was carried out at 25°C under continuous illumination in the present of 0.25?g?L^?1 of progesterone. After 5?days incubation of the microalga in BG-11 liquid medium, the broth was extracted and the products were purified by the aid of chromatographic methods. Structure elucidation of the metabolites was performed by spectral data (¹³C NMR, ¹H NMR, FTIR, and MS) and physical constants (melting points and optical rotations). Eventually, four major steroids including 20β-hydroxypregn-4-en-3-one, 20α-hydroxypregn-4-en-3-one, 6β-hydroxypregn-4-en-3,20-dione and 6α-hydroxypregn-4-en-3,20-dione were the results of this biotransformation. The study also showed that the best concentration of starting material, temperature, photoregime, and the influence of CO₂ partial pressure on the production of bioconverted metabolites were 0.25?g?L^?1, 25°C, continuous light and 2.0?±?0.1% (v/v), respectively. Highest concentrations of all biotransformed metabolites were obtained in the 5th day.     

Metabolite profiling of polar steroid constituents in the Far Eastern starfish Aphelasterias japonica using LC–ESI MS/MS

Numerous polar steroids are characteristic metabolites of starfish which determine physiological activities of their extracts. The Far Eastern starfish Aphelasterias japonica is a rich source of different steroid glycosides and polyhydroxysteroids. For detailed analysis of complicated mixture of steroids from this species, isolated by solid-phase extraction, a liquid chromatography–electrospray tandem mass spectrometry (LC–ESI MS/MS) approach was selected and applied. The characteristic fragmentations in ESI MS/MS spectra of steroid glycosides allowed determining types of aglycones, presence of sulfate groups, sugar sequences as well as branching. In addition, main structural features of polyhydroxylated polar steroids including position of hydroxylation and level of sulfation were also established. Totally, 68 metabolites, comprising of 33 asterosaponins, 28 sulfated polyhydroxysteroid mono- and biosides and 7 sulfated polyhydroxysteroid compounds were found by this method. In addition to 15 previously isolated compounds from A. japonica, many new steroid glycosides including asterosaponins with unusual carbohydrate chains were discovered and characterized by their ESI product ion mass spectra. Some details of biosynthesis of polyhydroxylated steroids and their conjugated forms in the species studied such as a role of sulfation and order of introduction of hydroxyl group in A. japonica were proposed.     

Disclosure of new and recurrent microbial metabolites by mass spectrometric methods

The application of modern mass spectrometry methods (SI-CID-MS/MS; MS ⁿ ) in the disclosure of new and recurrent microbial metabolites is discussed. Spray ion (SI) sources coupled to different kinds of mass analyzers enable the determination of molecular weights and chemical formulas of given samples even in mixtures. Diagnostic fragment formation by collision-induced dissociation (CID-MS/MS) and MS ⁿ experiments using ion trap mass analyzers are shown as another indispensable source of structural information. Due to the development of benchtop-type mass spectrometers coupled to high-performance liquid chromatography (HPLC), MS can be practised in almost every laboratory as a powerful tool in natural product analysis. Examples are given for special MS applications in identification of bioactive metabolites from screening strains. Journal of Industrial Microbiology & Biotechnology (2001) 27, 136–143. Received 21 September 1999/ Accepted in revised form 19 January 2000     

Comparative metabolite profiling and fingerprinting of medicinal licorice roots using a multiplex approach of GC–MS,LC–MS and 1D NMR techniques

Glycyrrhiza glabra, commonly known as licorice, is a popular herbal supplement used for the treatment of chronic inflammatory conditions and possesses anticancer and antiviral activities. This species contains a plethora of phytochemicals including terpenoids, saponins, flavonoids, polyamines and polysaccharides. The full complement of bioactive compounds has yet to be elucidated, a step necessary in order to explain its medicinal use. There are over 30 species in the Glycyrrhiza genus world-wide, most of which have been little characterized in terms of phytochemical or pharmacological properties. Here, large scale multi-targeted metabolic profiling and fingerprinting techniques were utilized to help gain a broader insight into Glycyrrhiza species chemical composition. UV, MS and NMR spectra of extracted components were connected with NMR, MS, and multivariate analyses data from Glycyrrhiza glabra, Glycyrrhiza uralensis, Glycyrrhiza inflata and Glycyrrhiza echinata. Major peaks in ¹H NMR and MS spectra contributing to the discrimination among species were assigned as those of glycyrrhizin, 4-hydroxyphenyl acetic acid, and glycosidic conjugates of liquiritigenin/isoliquiritigenin. Primary metabolites profiling using GC–MS revealed the presence of cadaverine, an amino acid, exclusively found in G. inflata roots. Both LC–MS and NMR were found effective techniques in sample classification based on genetic and or geographical origin as revealed from derived PCA analysis.     

Microbiological production of omeprazole metabolites by Cunninghamella elegans

Incubation of Cunninghamella elegans ATCC 9245 and the anti ulcer drug omeprazole allowed putative fungal metabolites to be isolated in sufficient quantities for structural elucidation. Three metabolites produced by the fungi were isolated using semi-preparative HPLC and their structures identified by a combination of LC/MS(n) and NMR experiments. These isolates will be used as reference standards in the confirmatory analysis of mammalian metabolites of this drug.     

Amphidinol C,a major polyketide from an Irish strain of the dinoflagellate Amphidinium carterae

An Irish strain of the dinoflagellate Amphidinium carterae was previously shown to produce antibacterial amphidinol derivatives of unknown masses. Inspection of the major metabolites present in a bulk culture of this strain led to the isolation and structure elucidation of a new amphidinol derivative named amphidinol C featuring an unprecedented tetrahydropyran ring between the positions C-7 and C-11. The structure was determined using extensive analyses of NMR and MS data and comparison with data of analogues. The new ring was proposed to stem from a nucleophilic substitution of the sulphate present on the side chain of Amphidinol B. The major metabolites isolated were tested for their antibacterial and antifungal activities and Amphidinol C showed moderate fungicidal activity against yeast and filamentous fungi at 8–16 µg mL⁻¹.     

Analysis of sesterterpenoids from Aspergillus terreus using ESI‐QTOF and ESI‐IT

Introduction – Biosynthesis of terretonin was studied due to the interesting skeleton of this series of sesterterpenoids. Very recently, López‐Gresa reported two new sesterterpenoids (terretonins E and F) which are inhibitors of the mammalian mitochondrial respiratory chain. Mass spectrometry (MS), especially tandem mass spectrometry, has been one of the most important physicochemical methods for the identification of trace natural products due to it rapidity, sensitivity and low levels of sample consumption. The potential application prospect and unique skeleton prompted us to study structural characterisation using MS. Objective – To obtain sufficient information for rapid structural elucidation of this class of compounds using MS. Methodology – The elemental composition of the product ions was confirmed by low‐energy ESI‐CID‐QTOF‐MS/MS analyses. The fragmentation pathways were postulated on the basis of ESI‐QTOF‐MS/MS/MS and ESI‐IT‐MSⁿ spectra. Common features and major differences between ESI‐QTOF‐MS/MS and IT‐MSⁿ spectra were compared. For ESI‐QTOF‐MS/MS/MS experiments, capillary exit voltage was raised to induce in‐source dissociation. Ammonium acetate or acetic acid were added into solutions to improve the intensity of [M + H]⁺. The collision energy was optimised to achieve sufficient fragmentation. Some fragmentation pathways were unambiguously proposed by the variety of abundance of fragment ions at different collision energies even without MSⁿ spectra. Results – Fragmentation pathways of five representative sesterterpenoids were elucidated using ESI‐QTOF‐MS/MS/MS and ESI‐IT‐MSⁿ in both positive‐ and negative‐ion mode. The key group of characterising fragmentation profiles was ring B, and these fragmentation patterns are helpful to identify different types of sestertepenoids. Conclusion – Complementary information obtained from fragmentation experiments of [M + H]⁺ (or [M + NH₄]⁺) and [M ? H]^? precursor ions is especially valuable for rapid identification of this kind of sesterterpenoid.     

Twenty years of research into medicinal plants: Results and perspectives

Over the years 1981 to 2001 there has been a rapid evolution of research into medicinal plants. The major improvement has been the introduction of simple and predictive bioassays for bioactivity-guided isolation. Radical developments in separation methods have also taken place. Another important addition has been the development of hyphenated techniques involving HPLC: LC/UV, LC/MS, LC/MSⁿ and LC/NMR. These are indispensable nowadays for the early detection and identification of new compounds in crude plant extracts. Hyphenated techniques allow an efficient targeted isolation approach for the discovery of new lead compounds. Other areas of increasing importance include the investigation of toxic constituents of plants and phytomedicines, and the effects of genetic modifications on plant secondary metabolites. This revised version was published online in June 2006 with corrections to the Cover Date.     

Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC/ESI-MS/MS) Study for the Identification and Characterization of In Vivo Metabolites of Cisplatin in Rat Kidney Cancer Tissues: Online Hydrogen/Deuterium (H/D) Exchange Study

In vivo rat kidney tissue metabolites of an anticancer drug, cisplatin (cis-diamminedichloroplatinum [II]) (CP) which is used for the treatment of testicular, ovarian, bladder, cervical, esophageal, small cell lung, head and neck cancers, have been identified and characterized by using liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with on line hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, kidney tissues were collected after intravenous administration of CP to adult male Sprague-Dawley rats (n = 3 per group). The tissue samples were homogenized and extracted using newly optimized metabolite extraction procedure which involves liquid extraction with phosphate buffer containing ethyl acetate and protein precipitation with mixed solvents of methanol-water-chloroform followed by solid-phase clean-up procedure on Oasis HLB 3cc cartridges and then subjected to LC/ESI-HRMS analysis. A total of thirty one unknown in vivo metabolites have been identified and the structures of metabolites were elucidated using LC-MS/MS experiments combined with accurate mass measurements. Online HDX experiments have been used to further support the structural characterization of metabolites. The results showed that CP undergoes a series of ligand exchange biotransformation reactions with water and other nucleophiles like thio groups of methionine, cysteine, acetylcysteine, glutathione and thioether. This is the first research approach focused on the structure elucidation of biotransformation products of CP in rats, and the identification of metabolites provides essential information for further pharmacological and clinical studies of CP, and may also be useful to develop various effective new anticancer agents.     

Changes in the profile of flavonoid accumulation in Medicago truncatula leaves during infection with fungal pathogen Phoma medicaginis

Medicago truncatula is a model species for the study of the unique secondary metabolism in legumes. LC/MS/MS analysis was used to identify and profile flavonoid glycoconjugates and free aglycones in leaves of M. truncatula (ecotype R108-1) infected with the fungal pathogen Phoma medicaginis. Use of a high resolution analyzer with a collision induced dissociation tandem mass spectrometer (CID MS/MS) permitted structural elucidation of target secondary metabolites and four new acylated flavone glycosides have been identified. Changes in the phytoalexin medicarpin and its isoflavone precursors were quantitatively monitored at various time points after fungal spore application. Application of spores induced disease symptoms in the leaves of infected plants and resulted in an increase in the medicarpin precursors formononetin 7-O-glucoside and malonylated formononetin 7-O-glucoside between one and three days post-infection. Relative concentrations of medicarpin were highest five days post-infection. The rapid increase of these molecules was clearly positively correlated to the infection process as certain of them were absent in uninfected leaves, suggesting that the relative rate of their synthesis is tightly related with the infection process.     

One simple step in the identification of the cofactors signals, one giant leap for the solution structure determination of multiheme proteins

Multiheme proteins play major roles in various biological systems. Structural information on these systems in solution is crucial to understand their functional mechanisms. However, the presence of numerous proton-containing groups in the heme cofactors and the magnetic properties of the heme iron, in particular in the oxidised state, complicates significantly the assignment of the NMR signals. Consequently, the multiheme proteins superfamily is extremely under-represented in structural databases, which constitutes a severe bottleneck in the elucidation of their structural-functional relationships. In this work, we present a strategy that simplifies the assignment of the NMR signals in multiheme proteins and, concomitantly, their solution structure determination, using the triheme cytochrome PpcA from the bacterium Geobacter sulfurreducens as a model. Cost-effective isotopic labeling was used to double label (¹³C/¹⁵N) the protein in its polypeptide chain, with the correct folding and heme post-translational modifications. The combined analysis of ¹H-¹³C HSQC NMR spectra obtained for labeled and unlabeled samples of PpcA allowed a straight discrimination between the heme cofactors and the polypeptide chain signals and their confident assignment. The results presented here will be the foundations to assist solution structure determination of multiheme proteins, which are still very scarce in the literature.     

Aristolactam derivatives from Fissistigma glaucescens

The phytochemical investigation of stems of Fissistigma glaucescens (Hance) Merr. led to the isolation of a new aristolactam derivative aristolactam AIb (1), together with eleven known aristolactam derivatives (2–12). Structure elucidation of these compounds were performed on the basis of NMR spectral data and MS. Compounds 2–7 were isolated from the F. glaucescens for the first time. The chemotaxonomic significance of the isolates was also discussed.     

Pterosin derivatives from Pteris morii Masamune

The phytochemical investigation of the aerial parts of Pteris morii Masamune led to the isolation of a new pterosin derivative pteririene A (1), together with seven pterosin sesquiterpenes (2–8). Structure elucidation of these compounds were performed on the basis of NMR spectral data and MS. All compounds were isolated from the P. morii for the first time. The chemotaxonomic significance of the isolates was also discussed.     

Determination of phenolic compounds and diterpenes in roots of Salvia miltiorrhiza and Salvia przewalskii by two LC–MS tools: Multi-stage and high resolution tandem mass spectrometry with assessment of antioxidant capacity

Comparative phytochemical analyses of hydroalcoholic (50% EtOH) extracts from roots of S. miltiorrhiza (SM) and S. przewalskii (SP) were performed using two complementary LC–MS systems: the first system HPLC-DAD-MSⁿ an ion trap mass spectrometer and the second system consisted high resolution MS/MS Orbitrap mass spectrometer. The individual compounds were identified using a previously published approach via comparison of the exact molecular masses, mass spectra and retention times to those of standard compounds, online available databases and literature data. Moreover, the determination of antioxidative activities of extracts by DPPH and FRAP methods was carried out. Analysis allowed to identify 39 chemical compounds in extracts from both species. Extract from root of SP differs from SM in the presence of several metabolites such as: przewalskinic acid and their derivatives, przewaquinone C, przewaquinonate A, glycosides of rosmarinic acid, methyltanshinonate, whereas tanshinones, salvianolic acids and lithospermic acids occurred in both species. Moreover, it was shown that hydroalcoholic extract from roots of SM exerted stronger antioxidant properties in a FRAP test (max. 323.92 μM Fe²⁺/L) and in DPPH test (max. 78.64 nM TE) in comparison with SP extract.     

Rapid screening of lignans from Phyllanthus myrtifolius and stilbenoids from Syagrus romanzoffiana by HPLC-SPE-NMR

Introduction – Application of on‐line solid‐phase extraction (SPE) as an interface between HPLC and NMR has gained great improvement in solving sensitivity problems and signal interferences by the eluents. Objective – Rapid analysis and characterisation by HPLC‐SPE‐NMR and LC/MS of the arylnaphthalene‐type lignans present in Phyllanthus myrtifolius and the minor stilbenoids present in the polyphenol‐rich fraction from the ethanol extract of the seeds of Syagrus romanzoffiana. Methodology – Pretreatment of fractions by liquid–liquid partitioning, followed by Sephadex LH‐20 fractionation, was found very useful to facilitate the focusing and analysis of the polyphenolic fraction. HPLC‐DAD‐SPE‐NMR (400 MHz and 600 MHz) analysis was carried out using an Agilent 1100 liquid chromatography, followed by a Prospekt 2 automated solid‐phase extraction unit, containing 96 HySphere‐Resin GP cartridges (10 × 2 mm, 10–12 µm), which was connected to a 120 or 60 µL LC probe. Results – Seven arylnaphthalene‐type lignans from the chloroform‐soluble fraction of P. myrtifolius and nine stilbenoids from a polyphenol‐rich butanol‐soluble fraction of the seeds of S. romanzoffiana were characterised. Conclusion – HPLC‐SPE‐NMR associated with HR‐ESI/MS, which consumed only analytical amounts of partially purified mixtures, was demonstrated to be a good tool for rapid screening of both known and new natural products. Copyright © 2011 John Wiley & Sons, Ltd.