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ABSTRACT: RATIONALE: Tandem mass spectrometry (MS/MS) dissociation pathways can vary markedly between compound classes and can result in challenging and time-consuming interpretation of the data. Compound, class and substructure specific fragmentation rules for protonated molecules require refinement to aid the structural elucidation process. METHODS: The application of a predictive science approach using density functional theory (DFT) calculations has been investigated to estimate the abundances of first-generation product ions observed using an ion trap mass spectrometer. This has been achieved by application of Boltzmann population theory to electrospray ionisation (ESI)-MS and MS/MS data. RESULTS: Tandem ESI-MS data for this preliminary study were used to investigate the internal stabilities of protonated species and their product ions. The calculated relative abundances of 11.3%, 96.5%, and 1.1% for the product ion (m/z 192) of three quinazoline structural isomers are compared with the experimental values of 16%, 90% and 0% observed in the first-generation product ion mass spectra. CONCLUSIONS: Close correlation between calculated and experimental data has been demonstrated for these initial data. Applying this approach and establishing fragmentation rules, based on structure specific and common fragmentation behaviour, would improve and expedite the structural elucidation process. Copyright © 2013 John Wiley & Sons, Ltd.
Rapid Communications in Mass Spectrometry 05/2013; 27(9):964-970. · 2.79 Impact Factor
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ABSTRACT: The large size of biological molecules such as proteins and oligonucleotides makes them inherently problematic to analyse and quantify directly by mass spectrometry. For these molecules, electrospray ionisation produces multiply charged species and associated alkali metal adducts which can reduce sensitivity and complicate quantification. Whereas time-of-flight mass analysers, often coupled to matrix-assisted laser desorption/ionisation, can have insufficient mass resolution to resolve these large molecules in the higher m/z range. This has led to the development of cleavable small molecule mass tag approaches for the indirect analysis of biomolecules such as proteins and oligonucleotides. Existing methodologies require the design and synthesis of a cleavable linker to join the biomolecule and the mass tag. Here, an alternative approach to small molecule mass tags is presented, which exploits the properties of the RNA molecule to afford self-reporting probes which can be easily synthesised using automated phosphoramidite chemistry. The sugar-phosphate backbone of RNA was used as a built-in enzyme cleavable linker and through the use of RNase digestion of bromine labelled oligonucleotides the observation of a range of small molecule mass tags by mass spectrometry is demonstrated. This study provides a proof-of-concept that RNase digestion can be used to produce labelled small molecule mass tags from oligonucleotide probes, thus eliminating the need for custom design and synthesis of a cleavable linker.
The Analyst 10/2012; · 4.23 Impact Factor
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Biological Mass Spectrometry 11/2011; 46(11):1182-5. · 3.41 Impact Factor
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ABSTRACT: The experimental investigation of site-specific intra-ionic hydrogen/deuterium (H/D) exchange in the low-energy collision-induced dissociation (CID) product ion spectra of protonated small molecules generated by electrospray ionisation (ESI) is presented. The observation of intra-ionic H/D exchange in such ions under low-energy CID conditions has hitherto been rarely reported. The data suggest that the intra-ionic H/D exchange takes place in a site-specific manner between the ionising deuteron, localised at either a tertiary amine or a tertiary amine-N-oxide, and a gamma-hydrogen relative to the nitrogen atom. Nuclear magnetic resonance (NMR) spectroscopy measurements showed that no H/D exchange takes place in solution, indicating that the reaction occurs in the gas phase. The compounds analysed in this study suggested that electron-withdrawing groups bonded to the carbon atom bearing the gamma-hydrogen can preclude exchange. The effect of the electron-withdrawing group appears dependent upon its electronegativity, with lower chi value groups still allowing exchange to take place. However, the limited dataset available in this study prevented robust conclusions being drawn regarding the effect of the electron-withdrawing group. The observation of site-specific intra-ionic H/D exchange has application in the area of structural elucidation, where it could be used to introduce an isotopic label into the carbon skeleton of a molecule containing specific structural features. This could increase the throughput, and minimise the cost, of such studies due to the obviation of the need to produce a deuterium-labelled analogue by synthetic means.
Biological Mass Spectrometry 04/2010; 45(4):347-57. · 3.41 Impact Factor
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ABSTRACT: A high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) approach to the characterization of dialkyl tertiary amine-N-oxides is presented. The methodology is based upon forming reconstructed ion current chromatograms (RICCs) of m/z values of product ions known to form through diagnostic losses from dialkyl tertiary amine-N-oxides. The diagnostic losses of N,N-dimethylhydroxylamine and N,N-diethylhydroxylamine were identified through the analysis of a structurally diverse library of compounds by ESI-low-energy collision-induced dissociation (CID)-MS/MS using quadrupole ion trap-mass spectrometry (QIT-MS) and quadrupole time-of-flight-mass spectrometry (QqTOF-MS). The library consisted of dialkyl tertiary amine-containing commercially available pharmaceuticals, along with a number of model, synthetic N-oxides. The loss of the nitrogen-containing group was observed in 89% of the low-energy CID product ion spectra acquired using various collision energies. Further, the resultant product ions, formed through the loss of the nitrogen-containing group, were shown to be unstable because of the observation of second-generation dissociation. These observations regarding gas-phase ion chemistry could be useful to developers of in silico programs for fragmentation prediction by allowing the creation of improved algorithms and models for predicting dissociation. Using the information derived from the library analysis, the characterization methodology was developed and demonstrated using tetracaine. The approach is rapid, MS/MS platform independent, utilizes existing technology, and could be automated. Further, it is definitive and overcomes the limitations of other tools for N-oxide identification by localizing the site of oxidation. Thus, it provides a useful addition to the existing approaches for metabolite identification.
Analytical Chemistry 02/2010; 82(6):2347-54. · 5.86 Impact Factor
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ABSTRACT: Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA.
Artificial DNA, PNA & XNA. 01/2010; 1(1):27-35.
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ABSTRACT: Diastereoisomeric mixtures of cis-uvariamicin I (15R,16R,19S,20S,36S and 15S,16S,19R,20R,36S) and cis-reticulatacin (17R,18R,21S,22S,36S and 17S,18S,21R,22R,36S) were synthesized to determine the stereochemistry of the natural products isolated from Annona muricata. It was not possible to resolve a mixture of the four synthetic isomers using chiral HPLC, but the mixed isomers could be distinguished using chiral HPLC EIMS with extracted fragment ion analysis. Comparison of synthetic standards with the natural isolate revealed that cis-uvariamicin I and cis-reticulatacin are present in nature as mixtures of threo-cis-threo diastereoisomers. It is suggested that the nomenclature for the natural products is amended as follows: (15R,16R,19S,20S,36S)-cis-uvariamicin I (cis-uvariamicin IA); (15S,16S,19R,20R,36S)-cis-uvariamicin I (cis-uvariamicin IB); (17R,18R,21S,22S,36S)-cis-reticulatacin (cis-reticulatacin A); (17S,18S,21R,22R,36S)-cis-reticulatacin (cis-reticulatacin B).
The Journal of Organic Chemistry 09/2009; 74(18):6924-8. · 4.45 Impact Factor
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ABSTRACT: S-oxidation is a common metabolic route for sulfur-containing compounds. Whilst investigating the dissociation of a series of chemically synthesised model S-oxide metabolites, two unexpected losses of 62 m/z units were observed in the collision-induced dissociation (CID) product ion spectrum of protonated 3-dimethylaminomethyl-4-(4-methanesulfinyl-3-methylphenoxy)benzenesulfonamide. A single loss was initially assigned using the low-resolution product ion spectrum, acquired by electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS), as methanethial, S-oxide via a charge-remote, four-centred rearrangement. This assignment was consistent with well-documented hydrogen rearrangements in the literature. Further, the loss was not observed for the parent compound. Thus, it was inferred that the site of metabolism was involved in the dissociation and the attractive nature of the four-centred rearrangement meant that the loss of methanethial, S-oxide was a logical assignment. However, deuterium-labelling experiments and accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS), showed that the nominal loss of 62 m/z units occurs via two distinct dissociation pathways. Neither of these losses was of methanethial, S-oxide as initially hypothesised from the low-resolution product ion spectrum of the protonated molecule. Mechanisms consistent with the experimental findings are postulated. An MS(3) spectrum of the fully exchanged, deuterated species supported the proposed mechanisms by suggesting that 3-dimethylaminomethyl-4-(4-methanesulfinyl-3-methylphenoxy)benzenesulfonamide has multiple sites of protonation in the gas phase. The planar structures of the posited product ions are likely to provide the driving force for the rearrangements. The relevance of the observations with regards to pharmaceutical drug metabolite identification is discussed.
Rapid Communications in Mass Spectrometry 08/2009; 23(13):2017-25. · 2.79 Impact Factor
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ABSTRACT: The effects of increasing concentrations of ammonium acetate additive in supercritical fluid chromatography were studied on silica, 2-ethyl-pyridine and endcapped 2-ethyl-pyridine stationary phases. The study involved the addition of increasing concentrations of the ammonium acetate either in the mobile phase modifier (methanol) or in the sample solvent. The effects of ammonium acetate on retention and peak shape of the analytes were evaluated. Compounds that exhibited satisfactory chromatographic behaviour in the absence of the additive were virtually unaffected by its presence in the mobile phase or sample solvent. Nevertheless, compounds that exhibited late elution and strongly tailing peak shapes when pure methanol was used showed dramatically improved chromatographic behaviour in the presence of the additive. Shorter retention was observed not only when the modifier was introduced in the mobile phase but also when it was in the sample solvent.
Journal of chromatography. A 08/2009; 1216(36):6441-50. · 4.19 Impact Factor
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ABSTRACT: Supercritical fluid chromatography (SFC) is fast becoming a technique of choice for the analysis of a wide range of compounds and has been found to be complementary to high-performance liquid chromatography (HPLC). The combination of SFC and mass spectrometry (MS) affords a very useful tool in the separation and analysis of compounds. In this study the ionisation of samples in the absence of an applied electrospray voltage has been observed when using SFC/MS, with some compounds showing increased sensitivity when all ionisation source high voltage (HV) is removed. In an attempt to understand the mechanism of ionisation, a series of test compounds were analysed using standard electrospray ionisation (ESI) and atmospheric pressure chemical ionisation (APCI) source configurations and also different API source designs. In both cases, data were acquired with the applied high voltage on (normal conditions) or with the high voltage off, i.e. no voltage spray (novo-spray). The standards were analysed with a range of pressure and modifier percentage conditions. To understand the nature of the ionisation process observed, this was compared with three established liquid-to-gas ionisation mechanisms. These were thermospray (TSP), charge residue model (CRM) of ESI and sonic spray ionisation (SSI). Experiments were undertaken in an attempt to explain this ionisation phenomenon and quantify any observed change in sensitivity. The most important point to note is that enhanced ionisation was observed under novo-spray conditions in a SFC/MS configuration, which in certain cases provides a lowering in the overall limit of detection (LOD).
Rapid Communications in Mass Spectrometry 11/2008; 22(22):3673-82. · 2.79 Impact Factor
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ABSTRACT: A 50 m/z unit loss from protonated 4-benzenesulfinyl-3-methylphenylamine has been observed and investigated using electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS). It was hypothesised that the specific fragmentation was affected by the presence of an ortho methyl group in relation to the sulfoxide functionality, i.e. an ortho effect influences the preferred dissociation pathway. This was because the des-methyl homologue did not display a 50 m/z unit loss. This fragmentation was shown to be a two-step process with sequential losses of a hydroxyl radical and a thiol radical. Molecular modelling calculations showed that the most favourable site of protonation for 4-benzenesulfinyl-3-methylphenylamine was the sulfoxide oxygen, which would facilitate the loss of a hydroxyl radical. Subsequent deuterium-exchange experiments confirmed that the loss was a hydroxyl radical and afforded definitive assignment of the site of protonation. Furthermore, the involvement of a single exchangeable hydrogen atom in the overall 50 m/z unit loss was demonstrated. Thus, supportive evidence was provided for the involvement of the ortho methyl group in the second stage of the fragmentation, leading to the loss of the thiol radical. Accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS), verified the elemental formulae of the individual losses. The ion structure following the 50 m/z unit loss was proposed to be a protonated aminofluorene and was supported by comparing the product ion spectrum of commercially available protonated 2-aminofluorene with the MS4 data of protonated 4-benzenesulfinyl-3-methylphenylamine. Fragmentation mechanisms are proposed. The relevance of the loss with regards to pharmaceutical drug metabolite identification is discussed.
Rapid Communications in Mass Spectrometry 08/2008; 22(15):2355-65. · 2.79 Impact Factor
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ABSTRACT: Properties-retention studies were undertaken on a test library of sulfonamides using supercritical fluid chromatography with CO(2)-MeOH mobile phases (in the presence or absence of additive) and a 2-ethyl-pyridyl column. Taking a restricted range of retention ratios, k (1<k<10) and keeping the proportion of modifier in the mobile phase, phi, above 10%, it was shown that logk varies linearly with phi (R(2)>0.98). From these relationships, the different retention characteristics of the analytes were calculated. Literature studies of quantitative structure-retention relationships (QSRR) showed that these characteristics can be correlated with simple molecular descriptors to derive equations predicting the retention behaviour of new compounds. Measured retention characteristics were found to correlate with total dipole moment, mu, molecular surface area, A, and the electronic charge on the most negatively charged atom, delta(min). The correlation of chromatographic measurements with calculated molecular descriptors may allow the prediction of the retention behaviour for an unknown compound provided its properties are known.
Journal of Chromatography 05/2008; 1189(1-2):254-65. · 4.53 Impact Factor
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ABSTRACT: A mass spectrometric approach for rapid and simultaneous detection of several single nucleotide polymorphisms (SNPs) is reported. Oligonucleotide single base extension (SBE) primers, labelled at the 5'-end with photocleavable, quaternised and brominated peptidic mass tags, are extended by a mixture of the four dideoxynucleotides of which one is biotinylated. The 3'-biotinylated extension products are captured by streptavidin-coated solid phase magnetic beads, whilst non-biotinylated extension products and unreacted primers are washed away. Quaternised and brominated mass tags, cleaved from captured extension products during analysis by matrix-assisted laser desorption/ionisation-time-of-flight (MALDI-TOF) MS, are detected at pmol levels. This method is applied to the analysis of mitochondrial DNA polymorphisms for the purpose of human identification.
Organic & Biomolecular Chemistry 07/2007; 5(12):1878-85. · 3.70 Impact Factor
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Ilia Brondz,
Dag Ekeberg,
David S Bell,
Amy R Annino,
Jan Arild Hustad,
Robert Svendsen,
Vaso Vlachos,
Paul Oakley, G John Langley,
Thite Mohini,
Cazenave-Gassiot Amaury,
Felix Mikhalitsyn
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ABSTRACT: The drug primaquine diphosphate is used for causative treatment of malaria. Using HPLC-MS and GC-MS, this research group was previously able to show that the main contaminant of primaquine is the positional isomer quinocide [I. Brondz, D. Mantzilas, U. Klein, D. Ekeberg, E. Hvattum, M.N. Lebedeva, F.S. Mikhailitsyn, G.D. Soulimanov, J. Roe, J. Chromatogr. B: Anal. Technol. Biomed. Life Sci. 800 (2004) 211-223; I. Brondz, U. Klein, D. Ekeberg, D. Mantzilas, E. Hvattum, H. Schultz, F. S. Mikhailitsyn, Asian J. Chem. 17 (2005) 1678-1688]. Primaquine and quinocide are highly toxic substances which can have a number of side effects upon use in medical treatment. A standard for quinocide is not typically commercially available. In the present work, supercritical fluid chromatography-mass spectrometry (SFC-MS) with two different columns was used to achieve a shorter analysis time for the separation between the positional isomers quinocide and primaquine in primaquine diphosphate and to elucidate additional information about differences in their MS fragmentation. Unlike using HPLC-MS, it was possible to achieve the differential fragmentation of positional isomers at branching points using the SFC-MS technique. The desired short analysis time was achieved using SFC equipped with a Discovery HS F5 column and the differential fragmentation of positional isomers during SFC-MS provides information on the differences in the structure of these substances. Using a Chiralpak AD-H chiral column, it was possible to resolve the enantiomers in primaquine and separate quinocide from those enantiomers.
Journal of Pharmaceutical and Biomedical Analysis 03/2007; 43(3):937-44. · 2.97 Impact Factor
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ABSTRACT: The effective use of pencil as a matrix for matrix-assisted laser desorption/ionisation (MALDI) for the study of actinides has previously been demonstrated (Black et al., Rapid Commun. Mass Spectrom. 2006; 20: 1053). Here, the scope of the types of molecules amenable to analysis by this method has been extended, establishing that approximately 90% of a library containing 50 diverse small molecules can be successfully analysed by this technique. Further, the role played by the bulk materials present in the different pencil leads has been investigated and a simple one-step deposition of matrix and calibration materials has been achieved through the fabrication of different calibration pencils (Cali-Pens).
Rapid Communications in Mass Spectrometry 02/2007; 21(2):180-90. · 2.79 Impact Factor
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Annalen der Chemie und Pharmacie 01/2007; 2007(8):1345 - 1356. · 3.10 Impact Factor
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Rapid Communications in Mass Spectrometry 02/2004; 18(3):363-6. · 2.79 Impact Factor
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ABSTRACT: The use of a second electrospray nebuliser has proved to be highly successful for exact mass measurement during high-performance liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry (HPLC/FTICRMS). Much improved accuracy and precision of mass measurement were afforded by the introduction of the internal calibration solution, thus overcoming space charge issues due to the lack of control over relative ion abundances of the species eluting from the HPLC column. Further, issues of suppression of ionisation, observed when using a T-piece method, are addressed and this simple system has significant benefits over other more elaborate approaches providing data that compares very favourably with these other approaches. The technique is robust, flexible and transferable and can be used in conjunction with HPLC, infusion or flow injection analysis (FIA) to provide constant internal calibration signals to allow routine, accurate and precise mass measurements to be recorded.
Rapid Communications in Mass Spectrometry 02/2004; 18(24):3035-40. · 2.79 Impact Factor
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ABSTRACT: Sulphonamides are antibacterial compounds used extensively in farming and veterinary practice. Residues are commonly found in meat and milk. The growing concern about antibiotic resistance of bacteria led to a lowering of the legal concentration limits of sulphonamides in food. A range of analytical methods, employing tandem mass spectrometry (MS/MS) and selected reaction monitoring (SRM), have been developed to allow screening at the limit of detection (LOD) levels. Interest was drawn to the fragment ions produced by the sulphonamides, some involving complex rearrangements that have not previously been looked at. Here we report an investigation into the fragmentation pattern of sulphonamides under electrospray (ES) MS/MS conditions using ion trap and Fourier transform ion cyclotron resonance (FTICR) mass spectrometers. Structures are proposed for the main fragment ions observed for a range of sulphonamides, the effects of the functional groups in the dissociation pathway of the compounds are investigated, and the mechanisms leading to the main fragment ions are explored.
Rapid Communications in Mass Spectrometry 02/2003; 17(21):2373-9. · 2.79 Impact Factor
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ABSTRACT: Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation.
Rapid Communications in Mass Spectrometry 02/2003; 17(11):1163-8. · 2.79 Impact Factor
