Electrochemical simulation of oxidation processes involving nucleic acids monitored with electrospray ionization–mass spectrometry

Oxidation is commonly involved in the alteration of nucleic acids giving rise to diverse effects including mutation, cell death, malignancy, and aging. We demonstrate that electrochemistry represents an efficient and fast method to mimic oxidative modification of nucleic acids occurring in biological systems. Oxidation reactions were performed in a thin-layer cell employing a conductive diamond electrode as the working electrode and were monitored with electrospray ionization–mass spectrometry. Mass voltammograms were acquired for guanosine, adenosine, cytidine, and uridine. The observed oxidation potentials increased in the order guanosine<<adenosine<cytidine<uridine. Oxidation products of guanosine were characterized using high-resolution (tandem) mass spectrometry performed with a quadrupole–quadrupole time-of-flight instrument. On the basis of these experiments, it was concluded that the initial electrode reaction involves a one-electron, one-proton step to give a free radical. The primary oxidation product represents the starting point for a number of follow-up reactions, including guanosine dimerization as well as further oxidation to 8-hydroxyguanosine. Similar results were obtained for guanosine monophosphate and the corresponding dinucleotide. Furthermore, the guanosine radical was identified as an important intermediate for the formation of a covalent adduct with acetaminophen. This observation sheds new light on the mechanism of adduct formation as it demonstrates that oxidative activation of both the nucleobase and the adduct-forming agent is necessary to observe a detectable amount of adduct species.     

Comparative direct infusion ion mobility mass spectrometry profiling of Thermus thermophilus wild-type and mutant ∆cruC carotenoid extracts

The major carotenoid species isolated from the thermophilic bacterium Thermus thermophilus HB27 have been identified as zeaxanthin–glucoside–fatty acid esters (thermozeaxanthins and thermobiszeaxanthins). Most of the genes of the proposed T. thermophilus carotenoid pathway could be found in the genome, but there is less clarity about the genes which encode the enzymes performing the final carotenoid glycosylation and acylation steps. To get a further insight into the biosynthesis of thermo(bis)zeaxanthins in T. thermophilus, we deleted the megaplasmid open reading frame TT_P0062 (termed cruC) by both exchanging it with a kanamycin resistance cassette (ΔcruC:kat) and by generating a markerless gene deletion strain (ΔcruC). A fast and efficient electrospray ionization–ion mobility–time-of-flight mass spectrometry method via direct infusion was developed to compare the carotenoid profiles of wild type and mutant T. thermophilus cell culture extracts. These comparisons revealed significant alterations in the carotenoid composition of the ΔcruC mutant, which was found to accumulate zeaxanthin. This is the first experimental evidence that the ORF encodes the glycosyltransferase enzyme necessary for the glycosylation of zeaxanthin in the final modification steps of the thermozeaxanthin biosynthesis in T. thermophilus HB27. Also, the proposed method for direct determination of carotenoid amounts and species in crude acetone extracts represents an improvement over existing methods in terms of speed and sensitivity and may be applicable in high-throughput analyses of other terpenoids as well as other important bacterial metabolites like fatty acids and their derivatives.

Ascorbic acid for homogenous redox buffering in electrospray ionization–mass spectrometry

Electrospray ionization (ESI) involves the dispersion of a liquid containing analytes of interest into a fine aerosol by applying a high potential difference to the sample solution with respect to a counter electrode. Thus, from the electrochemical point of view, the ESI source represents a two-electrode controlled-current electrochemical flow cell. The electroactive compounds part of the solvent sprayed may be altered by occurring electrolysis (oxidation in positive ion mode and reduction in negative ion mode). These reactions can be troublesome in the context of unknown identification and quantification. In the search for a simple, inexpensive, and efficient way to suppress electrochemical oxidation in positive ESI, the usability of ascorbic acid, hydroquinone, and glutathione for homogenous redox buffering was tested. Performance of the antioxidants was assessed by analyzing pharmaceutical compounds covering a broad range of functional groups prone to oxidation. Different emitter setups were applied for continuous infusion, flow injection, and liquid chromatography/mass spectrometry experiments. Best performance was obtained with ascorbic acid. In comparison to hydroquinone and glutathione, ascorbic acid offered superior antioxidant activity, a relatively inert oxidation product, and hardly any negative effect on the ionization efficiency of analytes. Furthermore, ascorbic acid suppressed the formation of sodiated forms and was able to induce charge state reduction. Only in the very special case of analyzing a compound isobaric to ascorbic acid, interference with the low-abundant [ascorbic acid+H](+) signal may become a point of attention.     

Peak assignment in multi-capillary column–ion mobility spectrometry using comparative studies with gas chromatography–mass spectrometry for VOC analysis

Over the past years, ion mobility spectrometry (IMS) as a well established method within the fields of military and security has gained more and more interest for biological and medical applications. This highly sensitive and rapid separation technique was crucially enhanced by a multi-capillary column (MCC), pre-separation for complex samples. In order to unambiguously identify compounds in a complex sample, like breath, by IMS, a reference database is mandatory. To obtain a first set of reference data, 16 selected volatile organic substances were examined by MCC-IMS and comparatively analyzed by the standard technique for breath research, thermal desorption–gas chromatography–mass spectrometry. Experimentally determined MCC and GC retention times of these 16 compounds were aligned and their relation was expressed in a mathematical function. Using this function, a prognosis of the GC retention time can be given very precisely according to a recorded MCC retention time and vice versa. Thus, unknown MCC-IMS peaks from biological samples can be assigned—after alignment via the estimated GC retention time—to analytes identified by GC/MS from equivalent accomplished data. One example of applying the peak assignment strategy to a real breath sample is shown in detail.     

Impurity profiling of acetylspiramycin by liquid chromatography–ion trap mass spectrometry

Investigation of acetylspiramycin (ASPM) and its related substances was carried out using a reversed-phase liquid chromatography/tandem mass spectrometry method. The identification of impurities in the ASPM complex was performed with a quadrupole ion trap mass spectrometer, with an electrospray ionization (ESI) source in the positive ion mode which provides MSⁿ capability. A total of 83 compounds were characterized in commercial samples, among which 31 impurities that had never been reported and 31 partially characterized impurities were deduced using the collision-induced dissociation (CID) spectra of major ASPM components as templates. Most of the major impurities arise from the starting materials and the synthesis process. This work provides very useful information for quality control of ASPM and evaluation of its synthesis process.     

Fast,sensitive and highly discriminant gas chromatography–mass spectrometry method for profiling analysis of fatty acids in serum

A method for the determination of fatty acids in serum based on GC–MS (micro-SIS detection mode) has been developed and the separation and cis/trans isomers have been identified. A prior two-step extraction/derivatization procedure accelerated by ultrasound allows individual determination of esterified (EFAs) and non-esterified fatty acids (NEFAs), and shortening of the derivatization steps to 5 min for EFAs and 15 min for NEFAs. The total analysis time for 39 fatty acids was 61 min. The minimum LOD and LOQ values were 0.002 and 0.006 μg/ml, respectively. The proposed method was validated for EFAs and NEFAs using two different methods and the results show no statistical differences between the proposed method and those used as reference. The proposed derivatization–extraction methodology is suitable for fatty-acid analysis of human serum, and can be applied to nutritional and epidemiological studies.     

A study of oxaliplatin–nucleobase interactions using ion trap electrospray mass spectrometry

Oxaliplatin is an important anti-cancer drug that has been approved for the treatment of colorectal cancer. It is known that oxaliplatin, like other Pt-based drugs, interacts with DNA to form cytotoxic Pt-DNA adducts that disrupt important biological processes such as DNA replication and protein synthesis. Linear ion trap electrospray ionisation mass spectrometry (ESI-MS) was employed to study the interaction of oxaliplatin with DNA nucleobases. It was shown that oxaliplatin formed adducts with all four DNA nucleobases when present individually and in combination in solution. Multiple-stage tandem mass spectrometry (MSⁿ) enabled the fragmentation pathways of each adduct to be established. In addition, proposed structures for each product ion were obtained from the MS data. When all four bases were present together with the drug at near-equal molar concentrations, adducts containing predominantly adenine and guanine were formed, confirming that the drug preferentially binds to these nucleobases. A large molar excess of drug was required to ensure the formation of cytosine and thymine adducts in the presence of adenine and guanine. Even with a large excess of oxaliplatin, only mono-adducts of these nucleobases were observed when all four nucleobases were present. Figure Schematic of a linear ion trap mass spectrometer being used to isolate the diadduct of guanine with oxaliplatin showing the characteristic isotope pattern due to ¹⁹⁴Pt, ¹⁹⁵Pt and ¹⁹⁶Pt.     

Liquid–liquid extraction combined with differential isotope dimethylaminophenacyl labeling for improved metabolomic profiling of organic acids

A large fraction of the known human metabolome belong to organic acids. However, comprehensive profiling of the organic acid sub-metabolome is a major analytical challenge. In this work, we report an improved method for detecting organic acid metabolites. This method is based on the use of liquid–liquid extraction (LLE) to selectively extract the organic acids, followed by using differential isotope p-dimethylaminophenacyl (DmPA) labeling of the acid metabolites. The ¹²C-/¹³C-labeled samples are analyzed by liquid chromatography Fourier-transform ion cyclotron resonance mass spectrometry (LC–FTICR–MS). It is shown that this LLE DmPA labeling method offers superior performance over the method of direct DmPA labeling of biofluids such as human urine. LLE of organic acids reduces the interference of amine-containing metabolites that may also react with DmPA. It can also remove water in a biofluid that can reduce the labeling efficiency. Using human urine as an example, it is demonstrated that about 2500 peak pairs or putative metabolites could be detected in a 30-min gradient LC–MS run, which is about 3 times more than that detected in a sample prepared using direct DmPA labeling. About 95% of the 1000 or so matched metabolites to the Human Metabolome Database (HMDB) are organic acids. It is further shown that this method can be used to handle as small as 10 μL of urine. We believe that this method opens the possibility of generating a very comprehensive profile of the organic acid sub-metabolome that will be useful for comparative metabolomics applications for biological studies and disease biomarker discovery.     

Analysis of ancient Greco–Roman cosmetic materials using laser desorption ionization and electrospray ionization mass spectrometry

Microsamples of pink cosmetic powders from the Greco–Roman period were analyzed using two complementary analytical approaches for identification of the colouring agents (lake pigments originally manufactured from madder plants with an inert binder, usually a metallic salt) present in the samples. The first technique was a methanolic acidic extraction of the archaeological samples with an additional ethyl acetate extraction of the anthraquinone-type colouring agents which were identified using high performance liquid chromatography coupled to electrospray ionization with high resolution mass spectrometry (LC–ESI–HRMS), and the second was direct analysis of a microsample by laser desorption ionization–mass spectrometry (LDI–MS). The latter technique is well suited when the quantity of samples is very low. This soft ionization technique enables the detection of very small quantities of compounds using the combination of positive and negative-ion modes. It was also successfully applied for the direct analysis of some laboratory-made reference compounds. However, the presence of lead in one of these ancient samples induced a spectral suppression phenomenon. In this case and conditional on a sufficient quantity of available sample, the former method is better adapted for the characterization of these anthraquinone-type molecules. This study also confirmed that purpurin, munjistin, and pseudopurpurin are the principal colouring agents present in these ancient cosmetic powders constituted from madder plants. Presented at the Annual French National Symposium on Mass Spectrometry, Electrophoresis and Proteomics, 20–23 September 2007 in Pau, France.     

Reversed-phase high-performance liquid chromatography–electrospray mass spectrometry profiling of transgenic and non-transgenic maize for cultivar characterization

A reversed-phase high-performance liquid chromatography–electrospray mass spectrometry (RP-HPLC–ESI-MS (ion trap)) method is developed, for the first time, for profiling transgenic and non-transgenic maize with the aim of cultivar characterization. To optimize chromatographic conditions the following parameters were studied: column, gradient, and ion-pairing reagent. Moreover, the influence in the MS signal of the variation of the capillary voltage and the accumulated ions in the trap was also studied. The developed method was applied to the profiling of different protein fractions (albumin, globulin, prolamin, and glutelin) isolated from Bt transgenic and non-transgenic maize cultivars. Moreover, different maize samples, namely, maize cultivars from different geographical origins (USA, Canada, France, and Spain), transgenic maize samples with certified GMO content, and three transgenic Bt maize cultivars with their isogenic non-transgenic counterparts (Aristis Bt vs. Aristis, PR33P67 vs. PR33P66, and DKC6575 vs. Tietar) were profiled by the developed method. Mass spectra obtained for certain peaks in the maize cultivars studied resulted, in some occasions, useful for cultivar characterization and differentiation. The comparison of UV and MS profiles and mass spectra corresponding to the protein fractions with those of the whole seeds enabled the assignment of some peaks.     

Development of versatile isotopic labeling reagents for profiling the amine submetabolome by liquid chromatography–mass spectrometry

Metabolomic profiling involves relative quantification of metabolites in comparative samples and identification of the significant metabolites that differentiate different groups (e.g., diseased vs. controls). Chemical isotope labeling (CIL) liquid chromatography–mass spectrometry (LC–MS) is an enabling technique that can provide improved metabolome coverage and metabolite quantification. However, chemical identification of labeled metabolites can still be a challenge. In this work, a new set of isotopic labeling reagents offering versatile properties to enhance both detection and identification are described. They were prepared by a glycine molecule (or its isotopic counterpart) and an aromatic acid with varying structures through a simple three-step synthesis route. In addition to relatively low costs of synthesizing the reagents, this reaction route allows adjusting reagent property in accordance with the desired application objective. To date, two isotopic reagents, 4-dimethylaminobenzoylamido acetic acid N-hydroxylsuccinimide ester (DBAA-NHS) and 4-methoxybenzoylamido acetic acid N-hydroxylsuccinimide ester (MBAA-NHS), for labeling the amine-containing metabolites (i.e., amine submetabolome) have been synthesized. The labeling conditions and the related LC–MS method have been optimized. We demonstrate that DBAA labeling can increase the metabolite detectability because of the presence of an electrospray ionization (ESI)-active dimethylaminobenzoyl group. On the other hand, MBAA labeled metabolites can be fragmented in MS/MS and pseudo MS³ experiments to provide structural information on metabolites of interest. Thus, these reagents can be tailored to quantitative profiling of the amine submetabolome as well as metabolite identification in metabolomics applications.     

Microchip capillary electrophoresis–electrospray ionization–mass spectrometry of intact proteins using uncoated Ormocomp microchips

We present rapid (<5 min) and efficient intact protein analysis by mass spectrometry (MS) using fully microfabricated and monolithically integrated capillary electrophoresis–electrospray ionization (CE–ESI) microchips. The microchips are fabricated fully of commercial inorganic–organic hybrid material, Ormocomp, by UV-embossing and adhesive Ormocomp–Ormocomp bonding (CE microchannels). A sheath-flow ESI interface is monolithically integrated with the UV-embossed separation channels by cutting a rectangular emitter tip in the end with a dicing saw. As a result, electrospray was produced from the corner of chip with good reproducibility between parallel tips (stability within 3.8–9.2% RSD). Thanks to its inherent biocompatibility and stable (negative) surface charge, Ormocomp microchips enable efficient intact protein analysis with up to ∼10⁴ theoretical separation plates per meter without any chemical or physical surface modification before analysis. The same microchip setup is also feasible for rapid peptide sequencing and mass fingerprinting and shows excellent migration time repeatability from run to run for both peptides (5.6–5.9% RSD, n = 4) and intact proteins (1.3–7.5% RSD, n = 3). Thus, the Ormocomp microchips provide a versatile new tool for MS-based proteomics. Particularly, the feasibility of the Ormocomp chips for rapid analysis of intact proteins with such a simple setup is a valuable increment to the current technology.     

Application of Langmuir–Blodgett technology for the analysis of saturated fatty acids using the MALDI-TOF mass spectrometry

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Alkaloid profiling of the Chinese herbal medicine Fuzi by combination of matrix-assisted laser desorption ionization mass spectrometry with liquid chromatography–mass spectrometry

A matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) method was developed for the high throughput and robust qualitative profiling of alkaloids in Fuzi—the processed lateral roots of the Chinese herbal medicine Aconitum carmichaeli Debx (A. carmichaeli). After optimization, powdered roots – without any further sample preparation – could be used to screen for the presence of Aconitum alkaloids. Furthermore, the semi-quantitative potential of MALDI-MS was confirmed using liquid chromatography–mass spectrometry (LC–MS) as reference. In total over sixty alkaloids were detected by LC–MS and fifteen of them were tentatively identified. Both MALDI-MS and LC–MS analysis revealed significant variation in alkaloid content in different (commercial) samples. LC–MS analysis of three toxic alkaloids in 14 batches of Fuzi resulted in a variation of their concentrations expressed as RSDs of 138%, 99% and 221% for aconitine, hypaconitine and mesaconitine, respectively. The variation in concentrations (expressed as RSD) of about the ninety constituents detected were classified as follows: 13 constituents showed an RSD of 77–100%, 46 with an RSD of 100–150%, 21 with an RSD of 150–200% and 9 constituents with an RSD in concentration of 200–235%. These results demonstrate a strong difference in chemical composition of the various Fuzi and illustrate the necessity of adequate QA/QC procedures for both safety and efficiency of herbal medicine. The described analytical procedures for alkaloid profiling could play a role in these procedures.     

Site-specifically cleavage of oxidized insulin B chain with Zn（Ⅱ） ion studied by electrospray ionization mass spectrometry

The electrospray ionization mass spectrometry and tandem mass spectrometry investigation showed that the binding sites of Zn^2＋ with oxidized insulin B chain are His 5, His 10, and Arg 22, which lead to the selective cleavages of the peptide bonds at Ash 3- Gin 4, His 5-Leu 6, Gly 8-Ser 9, and Glu 21-Arg 22 of oxidized insulin B chain.     

Direct molecular haplotyping of multiple polymorphisms within exon 4 of the human catechol-O-methyltransferase gene by liquid chromatography–electrospray ionization time-of-flight mass spectrometry

The applicability of ion-pair reversed-phase high-performance liquid chromatography hyphenated to electrospray ionization time-of-flight mass spectrometry (ICEMS) for the haplotyping of five SNPs (rs769223, rs4818, rs4986871, rs8192488, rs4680) located within exon 4 of the human catechol-O-methyltransferase (COMT, EC 2.1.1.6) gene is demonstrated. Two differently sized products of polymerase chain reaction—a 71-bp amplicon partially covering the sequence of a 124-bp amplicon—were used to determine unequivocally the allelic states of the single nucleotide polymorphisms linked on both chromosomes. The two amplicons were co-loaded onto the chromatographic column and simultaneously analyzed within a single gradient run. Using the described strategy, 101 individuals representing an Austrian population sample were typed. The obtained haplotype frequencies will serve as reference values in future association studies to examine the impact of the COMT gene on neuropsychiatric disorders. Additionally, two newly discovered polymorphic sites within the sequence of the COMT gene are described (a synonymous C>T mutation at the third position of the amino acid codon 99 in the soluble COMT protein or 149 in the membrane-bound COMT protein; a non-synonymous G>A substitution at the second position of the amino acid codon 95 in the soluble COMT protein or 145 in the membrane-bound-COMT protein).     

Investigation of noncovalent complexes between β-cyclodextrin and polyamide acids containing N-methylpyrrole and N-methylimidazole by electrospray ionization mass spectrometry

Electrospray ionization (ESI) mass spectrometry was utilized to investigate noncovalent complexes between beta-cyclodextrin (beta-CD) and five novel polyamide acids containing N-methylpyrrole and N-methylimidazole. The 1:1 binding mode was specified by examining the binding stoichiometry from ESI mass spectra. It found that polyamide acids with beta-CD have binding affinities in the order: ImImImbetaCOOH > ImPyImbetaCOOH > ImPyPybetaCOOH > PyPyPybetaCOOH > NO(2)PyPyPybetaCOOH. The method gives, simultaneously, the binding constants between beta-CD and polyamide acids based on a novel linear equation.