Filip Lemière

Liquid chromatography–mass spectrometry in nucleoside, nucleotide and modified nucleotide characterization

Abstract Macromolecules such as deoxyribonucleic acid (DNA) and ribonucleic acid as well as their constituents play an important role in all kinds of biochemical reactions in nature. Hence their isolation and identification plays a major role in biochemical analysis. Mass spectrometry (MS) has gained an important position in this field because of the development of soft ionization techniques such as fast atom bombardment (FAB), liquid secondary mass spectrometry, thermospray ionization (TSP), the atmospheric pressure ionization techniques, electrospray ionization and atmospheric pressure chemical ionization and matrix assisted laser desorption. Because of their polar nature, mixtures of nucleosides, nucleotides and oligonucleotides are wel separated by liquid chromatography (LC) and electrophoretic techniques. Therefore it is not surprising to note that a lot of effort has been put into the development of LC–MS methods for the analysis of these compounds. In this review, covering the period 1990–1996, the LC–MS analysis of nucleobases, nucleosides, nucleotides, oligonucleotides and DNA adducts by TSP, continuous flow FAB and electrospray MS is discussed.

Development of an On-Line SPE-LC–ESI-MS Method for Urinary Nucleosides: Hyphenation of Aprotic Boronic Acid Chromatography with Hydrophilic Interaction LC–ESI-MS

The development of an on-line automated SPE-HPLC--ESI-MS method is described for targeted metabolomic analysis of urinary modified nucleoside levels. The setup comprises a boronate affinity column as a trapping device, a hydrophilic interaction chromatography (HILIC) separation and information-dependent MS detection modes. The system was optimized using standards and tested on biological samples, detecting a number of modified nucleosides. Other urinary biomarkers could also be analyzed by the system developed: for example, the urinary nucleobases were also available for analysis. A simultaneous creatinine-monitoring experiment was also demonstrated to be viable when utilizing the method, which is of benefit as creatinine is a urinary normalizing factor.

Detection of Estrogen DNA-Adducts in Human Breast Tumor Tissue and Healthy Tissue by Combined Nano LC-Nano ES Tandem Mass Spectrometry

For the first time estrogen DNA-adducts were identified in DNA human breast tumor tissue using nano-LC coupled to nano-Electrospray Tandem Mass Spectrometry. Normal breast tissue was analyzed analogously. The data obtained in the five breast tumor and five adjacent normal tissue samples were compared qualitatively, but no straightforward difference was observed. Prior to LC-MS analysis the DNA was enzymatically hydrolyzed to a nucleoside pool. The DNA-hydrolysates were directly injected onto a column switching system developed for on-line sample clean-up and subsequent analysis of the DNA-adducts. In four patients using Premarin, DNA-adducts of 4-hydroxy-equilenin (4OHEN) were detected. All except three samples contained DNA-adducts from 4-hydroxy-estradiol or 4-hydroxy-estrone. Also DNA isolated from eight alcohol fixed and paraffin embedded breast tumor tissue showed the presence of different estrogen DNA-adducts. Worthwhile mentioning is the presence of adducts responding to m/z 570 > m/z 454 transition. This is a well-known SRM-transition indicative for the presence of the 2′-deoxyguanosine (dGuo) adduct of Benzo[a]pyrene.

In-Source CID of Guanosine: Gas Phase Ion-Molecule Reactions

In-source collision induced dissociation was applied to access second generation ions of protonated guanosine. The in-source gas-phase behavior of [BH2]+-NH3 (m/z 135, C5H3N4O+) was investigated. Adduct formation and reactions with available solvent molecules (H2O and CH3OH) were demonstrated. Several addition/elimination sequences were observed for this particular ion and solvent molecules. Dissociation pathways for the newly formed ions were developed using a QqTOF mass spectrometer, permitting the assignment of elemental compositions of all product ions produced. Reaction schemes were suggested arising from the ring-opened intermediate of the protonated base moiety [BH2]+, obtained from fragmentation of guanosine. The mass spectral data revealed that the in-source CH3OH-reaction product underwent more complex fragmentations than the comparable ion following reaction with H2O. A rearrangement and a parallel radical dissociation pathway were discerned. Apart from the mass spectrometric evidence, the fragmentation schemes are supported by density functional theory calculations, in which the reaction of the ring-opened protonated guanine intermediate with CH3OH and a number of subsequent fragmentations were elaborated. Additionally, an in-source transition from the ring-opened intermediate of protonated guanine to the ring-opened intermediate of protonated xanthine was suggested. For comparison, a low-energy collision induced dissociation study of xanthosine was performed. Its dissociation pathways agreed with our assumption.

Locust phase polyphenism: Does epigenetic precede endocrine regulation?

The morphological, physiological and behavioural differences between solitarious and gregarious desert locusts are so pronounced that one could easily mistake the two phases as belonging to different species, if one has no knowledge of the phenomenon of phenotypic plasticity. A number of phase-specific features are hormonally controlled. Juvenile hormone promotes several solitarious features, the green cuticular colour being the most obvious one. The neuropeptide corazonin elicits the dark cuticular colour that is typical for the gregarious phase, as well as particular gregarious behavioural characteristics. However, it had to be concluded, for multiple reasons, that the endocrine system is not the primary phase-determining system. Our observation that longevity gets imprinted in very early life by crowding of the young hatchlings, and that it cannot be changed thereafter, made us consider the possibility that, perhaps, epigenetic control of gene expression might be, if not the missing, a primary phase-determining mechanism. Imprinting is likely to involve DNA methylation and histone modification. Analysis of a Schistocerca EST database of nervous tissue identified the presence of several candidate genes that may be involved in epigenetic control, including two DNA methyltransferases (Dnmts). Dnmt1 and Dnmt2 are phase-specifically expressed in certain tissues. In the metathoracic ganglion, important in the serotonin pathway for sensing mechanostimulation, their expression is clearly affected by crowding. Our data urge for reconsidering the role of the endocrine system as being sandwiched in between genetics and epigenetics, involving complementary modes of action.

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

The congruent development of computational technology, bioinformatics and analytical instrumentation makes proteomics ready for the next leap. Present-day state of the art proteomics grew from a descriptive method towards a full stake holder in systems biology. High throughput and genome wide studies are now made at the functional level. These include quantitative aspects, functional aspects with respect to protein interactions as well as post translational modifications and advanced computational methods that aid in predicting protein function and mapping these functionalities across the species border. In this review an overview is given of the current status of these aspects in plant studies with special attention to non-genomic model plants.

Herbal Medicines and Infectious Diseases: Characterization by LC‑SPE‑NMR of Some Medicinal Plant Extracts Used against Malaria

The extracts of two medicinal plants used in traditionalmedicine against malariawere characterized by means of an LC‑SPE‑NMR and LC‑MS platform. The structure of a series of major constituents from Bafodeya benna, as well as minor constituents from Ormocarpum kirkii, was determined. Bafodeya benna was found to contain (2R,3R)-taxifolin-3-O-α-L-rhamnoside or astilbin, and its isomers neoastilbin, neoisoastilbin, and isoastilbin, as well as quercetin-3-O-α-L-rhamnoside. From Ormocarpum kirkii, a series of known flavonoids and biflavonoids was obtained, as well as three new compounds, i.e., 7,7′′-di-O-β-D-glucosyl-(−)-chamaejasmin, 7-O-β-D-glucosyl-(I-3,II-3)-biliquiritigenin, and isovitexin-(I-3,II-3)-naringenin. The isolated constituents may explain, at least in part, the traditional use against malaria. LC‑SPE‑NMR, in combination with LC‑MS, is a powerful tool for the fast characterization of plant extracts, in order to define priorities at an early stage of a fractionation procedure. In addition, herbal medicinal products can completely be characterized, both with regard to their major as well as their minor constituents.

Identification of substances migrating from plastic baby bottles using a combination of low-resolution and high-resolution mass spectrometric analysers coupled to gas and liquid chromatography.

This work presents a strategy for elucidation of unknown migrants from plastic food contact materials (baby bottles) using a combination of analytical techniques in an untargeted approach. First, gas chromatography (GC) coupled to mass spectrometry (MS) in electron ionisation mode was used to identify migrants through spectral library matching. When no acceptable match was obtained, a second analysis by GC-(electron ionisation) high resolution mass spectrometry time of flight (TOF) was applied to obtain accurate mass fragmentation spectra and isotopic patterns. Databases were then searched to find a possible elemental composition for the unknown compounds. Finally, a GC hybrid quadrupole-TOF-MS with an atmospheric pressure chemical ionisation source was used to obtain the molecular ion or the protonated molecule. Accurate mass data also provided additional information on the fragmentation behaviour as two acquisition functions with different collision energies were available (MS(E) approach). In the low-energy function, limited fragmentation took place, whereas for the high-energy function, fragmentation was enhanced. For less volatile unknowns, ultra-high pressure liquid chromatography-quadrupole-TOF-MS was additionally applied. Using a home-made database containing common migrating compounds and plastic additives, tentative identification was made for several positive findings based on accurate mass of the (de)protonated molecule, product ion fragments and characteristic isotopic ions. Six illustrative examples are shown to demonstrate the modus operandi and the difficulties encountered during identification. The combination of these techniques was proven to be a powerful tool for the elucidation of unknown migrating compounds from plastic baby bottles.

Analytical characterization of mannosylerythritol lipid biosurfactants produced by biosynthesis based on feedstock sources from the agrofood industry

Mannosylerythritol lipids (MELs) are currently one of the most promising biosurfactants because of their multifunctional applications and good biodegradability. Depending on the yeast strain and the feedstock used for the fermentation process, structural variations in the MELs obtained occur. Therefore, MELs produced by Pseudozyma aphidis DSMZ 70725 with a soybean oil feedstock were characterized by chromatography and mass spectrometry (MS). Column chromatography with silica provided fractionation of the different types of MEL. High-performance liquid chromatography combined with MS was employed for the analysis of the MEL fractions and crude mixtures. A characteristic MS pattern for the MELs was obtained and indications of the presence of new MEL homologues, showing the incorporation of longer and more unsaturated fatty acid chains than previously reported, were given. Gas chromatography–MS analysis confirmed the presence of such unsaturated fatty acid chains in the MELs, demonstrating the incorporation of fatty acids with lengths ranging from C8 to C14 and with up to two unsaturations per chain. The incorporation of C16 and C18 fatty acid chains requires further investigation. MS/MS data allowed the unambiguous identification of the fatty acids present in the MELs. The product ion spectra also revealed the presence of a new isomeric class of MELs, bearing an acetyl group on the erythritol moiety.

Evaluation of liquid chromatography—thermospray mass spectrometry in the determination of some phenylglycidyl ether-2′-deoxynucleoside adducts

Abstract The adducts formed between 2′-deoxyadenosine (dAdo), 2′-deoxycytidine (dCyd) and 2′-deoxyuridine (dUrd) and phenyl glycidyl ether (PGE) were analysed by HPLC and LC—thermospray (TSP)-MS. Good results were obtained on a 10 RP Select B column (12.5 cm × 4 mm I.D.) using 0.1 M NH4OAcCH3OH at a flow-rate of 0.8 ml/min. The mass spectra of the 2′-deoxynucleoside—PGE adducts, obtained under LC-TSP-MS conditions were all characterized by the presence of the protonated molecule [MH]+ and [BH + H]+ ions. The PGE-dCyd adduct underwent hydrolytic deamination to the corresponding PGE-dUrd adduct. There was an indication that this process of hydrolytic deamination also took place in the TSP interface. Localization of the alkylation site was possible in the PGE-dUrd adduct by the presence of an RDA rearrangement leading to a fragment ion at m/z 194. Preliminary sensitivity studies on PGE-dUrd showed a detection limit of 500 pg (signal-to-noise ratio = 2) in multiple ion monitoring at m/z 263 and 379.