The thesis describes the development of new and improved methods for analyzing degradation markers from organophosphorus Chemical Warfare Agents (CWAs). Paper I and II describes an innovative and significantly improved method for the enrichment, derivatization (trimethysilylation) and GC-MS analysis of a broad range of organophosphorus CWAs degradation markers, namely the alkylphosphonic acids and a zwitterionic compound. That was achieved using solid phase disc extraction in combination with solid phase derivatization. The new method overcomes most limitations observed with existing techniques: it offers almost 100 % recoveries, requires no elution or evaporation steps, facilitates miniaturization of the solid sorbent and reagent, is compatible with in-vial derivatization, and minimizes the chromatographic background due to the use of a highly selective anion exchange sorbent disc. Paper III describes the development of new fluorinated diazomethane derivatization reagents and their evaluation for rapid and high sensitivity screening and identification of nerve agent degradation markers. The reagents are water-tolerant to some extent, which simplifies the derivatization step. The best reagent identified was 3,5-bis(trifluoromethyl)benzyl diazomethane, which outperformed the other reagent isomers tested and also the established commercial alternative, pentafluorobenzylbromide, allowing for the rapid (5 min) and direct derivatization of a 25 μL aqueous sample in acetonitrile. The spectra of the formed derivatives (high-energy collision induced fragmentation MS/MS) were used to construct a database (Paper IV) that proved to be superior in terms of match factor and probability compared to EI data gathered for trimethylsilyl derivatives. The study also focused on efforts towards achieving detailed structure information on the alkyl chains of the compounds in question using diagnostic ion interpretation. The final paper (paper V) describes the first rapid direct derivatization method for analyzing nerve agent metabolites in urine at trace levels. The method is based on the derivative from the paper III and the unambiguous identification was proven using a combination of low resolution and high resolution negative ion chemical ionization selected ion monitoring techniques. Novel results presented in these papers include: the first in-situ derivatization of alkylphosphonic acids on an SPE disc; the first direct derivatization of nerve agent markers in water and biomedical samples; the first high sensitivity GC-MS screening for these markers; and the first highly reproducible high-energy isomer specific CID MS/MS library. Overall, the results presented in this thesis represent significant contributions to the analysis of nerve agent degradation products.

Positive-ion electrospray ionisation Fourier transform ion cyclotron resonance and ion trap mass spectrometry have been used to investigate the reactions of the flavonoids 3-hydroxyflavone, 5-hydroxyflavone, 5-methoxyflavoe, quercetin, quercitrin and rutin with monovalent Li+, Na+, K+ and Cs+, divalent Cu2+, Zn2+ and Pb2+ and trivalent La3+ and Eu3+ metal cations. The effect of capillary-skimmer potential difference and the ion residence time in the hexapole ion trap of the Fourier transform ion cyclotron resonance mass spectrometer are systematically investigated for the flavonoid-alkali and divalent metal ion experiment. It is observed that these variables impact significantly on the type of ions observed in the ESI experiments and hence the mass spectra. The binding selectivity of alkali metal ions towards 3-hydroxyflavone, 5-hydroxyflavone and 5-methoxyflavone are determined using the results from FTICR mass spectrometry experiments. The selectivity order follows the order Li+>Na+>K+ for individual flavonoids. Collision-induced dissociation experiments are carried out by Fourier transform ion cyclotron resonance and ion trap mass spectrometry to compare the fragmentation behaviour of metal-flavonoid complexes. Low energy collision-induced dissociation experiments of the [2L+M]+ for 3-hydroxyflavone, 5-hydroxyflavone and 5-methoxyflavone alkali metal complexes show the loss of ligand only. When the energy is increased only the lithiated dimer [2L+Li]+ for 5-methoxyflavone shows the loss of methyl radical along with the ligand. For quercitrin the predominant dissociation pathways are the loss of rhamnose for Li+, Na+ and K+ complexes although aglycone loss is also observed for the K+ complex. The favourable dissociation pathways for rutin are the loss of disaccharide, aglycone and rhamnose for the Na+ complex and the loss of disaccharide for the K+ complex. Collision-induced dissociation data are also used to determine the threshold dissociation energies for displacement of one flavonoid ligand from alkali metal flavonoid complexes. The threshold dissociation energies for loss of one ligand from [2L+M]+ of 5-methoxyflavone and quercitrin follow the order Li+ > Na+ > K+, rutin follows the order Na+ > K+ > Li+ , and 3-hydroxyflavone and 5-hydroxyflavone follow the order Li+ > Na+. For the same metal cation experiment, 5-methoxyflavone system has the highest dissociation energy compared to the 3-hydroxyflavone and 5-hydroxyflavone experiment. Preliminary DFT calculations show that the calculated dissociation energies follow the same trend as the experimental dissociation energies for the simple flavonoid alkali metal cation experiments. For 5-methoxyflavone-divalent metal cation (Zn2+, Cu2+ and Pb2+) complexes loss of methyl radical is the common process. CO loss is also observed for the Zn2+ complex whereas CHO and H2O losses are observed for Cu2+. For 3-hydroxyflavone and 5-hydroxyflavone divalent metal cation experiments loss of ligand is the dominant process. Zn2+ and Cu2+ complexes also show CO loss. La3+ and Er3+ with the same flavonoids show the ligand as the dominant product. For quercetin-divalent metal cation experiment, ligand loss is the dominant process. For quercitrin and rutin various dissociation products are observed where the dissociation occurs via the loss of the rhamnose and/or the disaccharide moieties. Similar dissociation patterns are also observed for La3+ and Er3+ complexes for quercitrin and rutin.

Mass spectrometry of negative ions is a convenient method for generating, isolating, and analyzing reactive intermediates that would otherwise be too short lived to detect. This ion approach is especially useful for studying the chemical properties of radicals. In this work, a negative charge-carrying group was attached to lignin model compounds and combined with collision-induced dissociation (CID) to generate and characterize radical species involved in the primary pyrolysis of lignin. The charge-tag served to increase the sensitivity of the model compounds using electrospray ionization mass spectrometry (ESI-MS) and promoted charge-remote fragmentations (CRF) upon being collisionally activated. The resulting product ions were comparable to the primary pyrolysis products of lignin; thus, CID-CRF proved to be an effective way of identifying the mechanisms by which lignin decomposes in the gas phase. <br><div><br></div><div>Additionally, this dissertation includes a review of nitrene anions. Nitrene anions are another class of reactive intermediates protected by an electron that provide a means for studying the corresponding neutral molecules via electron photodetachment spectroscopy and photoelectron spectroscopy. The added electron makes it possible for protected nitrene anions to be manipulated by external electric and magnetic fields of a mass spectrometer. Nitrene anions also display their own unique reactivities as reagents, which have been investigated using ion/molecule reactions. Mass spectrometry of negative ions has thereby provided information on the electronic states, reactivities, and thermochemical properties of nitrene intermediates.</div>

Many anticancer therapies are based on the interaction of small molecule drugs with nucleic acids, particularly DNA. Electrospray ionization tandem mass spectrometry has established itself as an irreplaceable tool for the characterization of DNA adducts produced by alkylating agents, carcinogens, and antitumor drugs, in addition to the characterization of nucleic acid post-transcriptional modifications. ESI-MS was used to assess the non-covalent binding of a novel series of intercalating anthrapyrazoles to duplexes containing different sequences. Relative binding affinities paralleled the shift in melting point of the DNA duplexes measured from a previous study. Upon collisionally induced dissociation of the duplex/anthrapyrazole complexes, different binding strengths were discerned based on the fragmentation patterns. In addition, the interactions of a new series of sulfur-containing acridine ligands, some that functioned as alklyating mustards, with duplex DNA were also evaluated. Non-covalent and covalent binding of each ligand was determined, and the site of adduction (G > A) was revealed for the covalent modifications. The distribution of cross-linked products and mono-adducts by psoralen analogs was also monitored by both LC-UV and IRMPD-MS methods. Reactions at 5’-TA sites were favored over 5’-AT sites. The sites of interstrand cross-linking were determined by fragmentation of the duplex/psoralen complexes by infrared multiphoton dissociation (IRMPD). Ultraviolet photodissociation (UVPD) at 193 nm caused efficient charge reduction of deprotonated oligodeoxynucleotides via electron detachment. Subsequent CID of the charge-reduced oligodeoxynucleotides formed upon electron detachment, in a net process called electron photodetachment dissociation (EPD), resulted in a diverse array of abundant sequence ions which allowed the modification site(s) of three modified oligodeoxynucleotides to be pinpointed to a more specific location than by conventional CID. Electron transfer dissociation (ETD) caused efficient charge reduction of multi-protonated oligonucleotides. Subsequent CAD of the charge-reduced oligonucleotides formed upon electron transfer, in a net process termed electron transfer collision activated dissociation (ETcaD), resulted in rich backbone fragmentation, with a marked decrease in the abundance of base loss ions and internal fragments. ETcaD of an oligonucleotide duplex resulted in specific backbone cleavages, with conservation of weaker non-covalent bonds. In addition, IRMPD and UVPD were used to activate charge-reduced oligonucleotides formed upon electron transfer. ET-IRMPD afforded tunable characterization of the modified DNA and RNA, allowing for modified bases to be directly analyzed. ET-UVPD promoted higher energy backbone fragmentation pathways and created the most diverse MS/MS spectra. The numerous products generated by the hybrid MS/MS techniques (ETcaD, ET-IRMPD, and ET-UVPD) resulted in specific and extensive backbone cleavages which allowed for the modification sites of multiple oligonucleotides to be pinpointed. / text

La compréhension de l'irradiation à l'échelle du nanomètre dans les systèmes biomoléculaires nécessite l'observation de caractéristiques nouvelles auxquelles les développements techniques actuels nous permettent d'accéder. Ce travail se situe au coeur de la construction du nouveau dispositif DIAM Dispositif d’Irradiation d’Agrégats de Molécules biologiques développé à l’Institut de Physique Nucléaire de Lyon. Le développement d’une source d’agrégats associée à un spectromètre de masse à double focalisation a permis l’obtention des premiers faisceaux d’agrégats moléculaires protonés sélectionnés en masse. De plus, un système de détection innovant a été développé et validé dans des expériences de dissociations d’agrégats d’eau protonés par collision sur un gaz. Les résultats obtenus contribuent à la connaissance de la stabilité et de la structure des petits agrégats d’eau protonés et des agrégats mixtes d’eau et de pyridine protonés / Nanoscale characterization of irradiation in biomolecular systems requires observation of novel features which are now achievable with the recent technical progress. This work is a central part in the development of DIAM which is a new experimental set-up devoted to irradiation of biomolecular clusters at the Institut de Physique Nucléaire de Lyon. The development of the cluster source and of a double focusing mass spectrometer leads to the production of intense beams of mass selected protonated molecular clusters. Combined with this mass selected cluster beams an innovative detection technique is demonstrated in collision induced dissociation experiments. The results contribute to the knowledge of the stability and the structure of the small protonated water clusters and mixed clusters of water and pyridine

Proteomic studies aim to identify, quantify and characterise the full complement of proteins in a cell or organism under a defined set of conditions, and are important to our understanding of cellular mechanisms. However, such studies represent a major analytical challenge. A typical proteome analysis involves enzyme-mediated digestion of complex protein mixtures to yield an even more complex mixture of peptides. Combined reverse-phase liquid chromatography and tandem mass spectrometry is then traditionally utilised to ascertain sequence information from the characteristic peptide sequences. Analytical data derived for the peptides are employed as search terms in database searching of protein sequences derived from gene sequences. The extreme complexity of the peptide mixtures analysed means that additional novel approaches are required to fully interrogate the vast number of tandem mass spectra generated, assigning peptide identity and thereby helping to address demanding biological questions. The research reported here aims to further our understanding of both gas phase peptide/peptide fragment ion structure and peptide fragmentation behaviour using a combination of tandem mass spectrometry and ion mobility measurement.To facilitate the determination of peptide ion collision cross section, a novel standard, QCAL-IM, produced using the QconCAT strategy, has been developed to enable calibration of drift time in Travelling Wave Ion Mobility instruments. The standard facilitates empirical determination of the rotationally averaged collision cross section of any peptide/peptide fragment ion that lies within the calibration range encompassed. QCAL-IM was subsequently utilised to determine the collision cross section of a range of peptide ions produced by Lys-C and Lys-N proteolysis of ‘standard’ proteins. Data produced allowed the effect upon gas phase ion conformation through changing the location of the basic residue lysine within a peptide sequence to be assessed.The fragmentation behaviour of peptide ions produced by a variety of digestion regimes during both collision-induced dissociation (CID) and electron transfer dissociation (ETD) has also been extensively studied. The proteases trypsin and Lys-C are those typically utilised during proteomic studies and peptides produced by each have either the basic residues arginine or lysine at their carboxy-terminus. Secondary enzymatic treatment with the exoprotease carboxypeptidase B cleaves these basic residues from the C-terminus. Tandem mass spectrometric analysis of both tryptic/Lys-C peptides and their CBPB truncated analogue highlights that the dominant fragment ion series observed during both CID and ETD is determined, at least in part, by the location of such basic residues.Finally, studies were undertaken to investigate the factors which may promote/inhibit scrambling of peptide fragment ion sequence, which has recently been shown to take place during CID. The effect of modifying the gas phase basicity of the N-terminal amino acid residue is studied through a combination of derivatisation and synthesis of alternative peptide sequences. Increasing the gas phase basicity is shown to inhibit the observed sequence scrambling while promoting concomitant rearrangement/retention of a carboxyl oxygen at the C-terminus to give enhanced formation of bn+H2O product ion species.

Mass spectrometry with electrospray ionization is an excellent method for structural analysis of coordination compounds with outstanding sensitivity and selectivity. However, it fails to detect some low-polar rhenium complexes. This master thesis describes derivatization method of non-ionizable rhenium complexes with 1,2-dihydroxybenzene and 2,3- dihydroxytoluenene. Fragmentation mechanisms and structure of prepared complexes was studied using high resolution mass spectrometry and collision-induced dissociation (CID). Furthermore, density functional theory (DFT) computational method was used for prediction of bond cleavage based on bond lengthening.

Mass spectrometry (MS) has become a widely used technique for the characterization of a wide range of substances in diverse fields. The selection of appropriate ionization techniques, source parameters, charge carriers based on the analyte’s polarity is essential in MS as only the ions are detected. When using a soft ionization technique, single stage-MS at best provides only chemical composition; thus, tandem MS is needed to determine structural information and dissociation pathways. This dissertation focuses on the characterization of various small molecules and ions using different ionization techniques, charge carriers, and collision-induced dissociation (CID). In Chapter II, commercially available ionic liquid (IL) cations, specifically imidazolium-based IL cations with different side-chain chemistries, were characterized by CID-MS. The imidazolium-based IL cations have diverse dissociations pathways depending on the nature of the side chain (aliphatic or aromatic) or the functional groups (allyl, vinyl, alcohol, methoxy, nitro) present on the side chain. Additionally, it was observed that some IL cations undergo thermal degradation under normal operating temperatures of electrospray ~275 °C. A variety of experimental and complementary computational chemistry results are presented. In Chapter III, cis-3-hydroxyproline (c3hPro) and cis-4-hydroxyproline (c4hPro) isomers were differentiated upon lithiation using CID-MS. The CID-MS of [c4hPro+Li]+ produces three primary fragmentation pathways, namely the neutral losses of H2O, CO, and CO2; whereas CID-MS of [c3hPro+Li]+ produces only loss of CO2 in this same region. These observations may have analytical utility, and in this work, the experimental observations were explored with thermodynamic and transition state calculations to better understand the processes. In Chapter IV, the accurate mass of synthetic monomers including PAH perfluorocycloalkene monomers and their precursors were measured and reported with a publication-quality mass accuracy using atmospheric pressure chemical ionization (APCI)-MS. Additionally, the effect of solution flow rate, ionization mode, source parameters (such as vaporization temperature, dry gas temperature and dry gas flow rate, nebulizer gas pressure), acidification, and different solvent systems on APCI-MS signal intensity were studied.

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