Contemporary mass spectrometry (MS) instrumentation featuring electrospray ionisation (ESI) or matrix-assisted laser desorption/ionisation (MALDI) ion sources were used to characterise the polymer distributions generated in various free radical polymerisations, allowing insights to be gained into the reaction mechanisms operating in these systems. In studying atom transfer radical polymerisation (ATRP) mediated star polymerisations of methyl acrylate (MA), ESI was found to be more effective in obtaining a comprehensive list of the distinct products present in the samples under investigation when compared to the employed MALDI technique. Furthermore, these studies showed that terminal Br losses observed at relatively high monomer to polymer conversions could be accounted for via mechanisms involving the acetone derived radicals (CH3)2??OH, ??H3 and ??H2COCH3. Through the use of ESI, it was found that for bulk polymerisations of MA and aqueous media polymerisations of N-isopropylacrylamide (NIPAAm) initiated using 60Co ??-irradiation and mediated via reversible addition-fragmentation chain transfer (RAFT), hydrogen radicals formed via the radiolysis of RAFT agent and/or monomer, and in the case of the NIPAAm system, water, are capable of initiating the polymerisations. In the NIPAAm polymerisations under scrutiny, it was also observed that hydroxyl radicals generated via the radiolysis of water may contribute towards the initiation process, and that propagating chains can potentially become terminated via trithiocarbonate cleavage reactions. By using ESI instruments to characterise oligomer samples produced via the free radical polymerisations of vinyl phosphonates, it was observed that chain propagations are initiated via activated monomer radicals, which likely form as a result of transfer reactions involving initiator fragments and vinyl phosphonate monomer units. Transfer to monomer reactions were suggested to limit chain growth in these systems, and evidence was also found for scission reactions involving alkoxy moieties which are formed via intramolecular methine carbon abstraction reactions. Characterisation of the polymer distributions generated in R-group approach RAFT MA star polymerisations using an ESI instrument allowed formation processes operating in acrylate star living/controlled radical polymerisations (CRPs) to be ascertained. Initiator fragment derived linear chains, ideal stars, star-star couples, and terminated star products formed as a result of disproportionation and combination reactions were detected. Evidence for mid-chain radical (MCR) derived reaction pathways was also observed; specifically, for termination reactions involving intermolecularly formed MCRs on both star arms and linear chains, and for re-propagation of intermolecularly formed MCRs on star arms.

The principal aim of this study was to discover, through virtual screening, new nonimmunosuppressive inhibitors for the human immunophilin FKBP12, a target of the immunosuppressant drugs rapamycin and FK506. The enzyme acts as peptidyl-prolyl isomerase catalysing protein folding in the cell. Structurally similar isomerase domains are important for molecular recognition in multi-domain chaperone proteins. FKBP inhibitors have been shown to have protective effects against nerve damage and are therefore interesting targets for the treatment of neurodegenerative diseases. Virtual screening has been used to discover novel inhibitors for protein drug targets. Recent advances in computational power and the availability of large virtual libraries, such as the EDULISS database at Edinburgh University, have enhanced the appeal of this approach. X-ray structures of known protein-ligand complexes were examined to obtain an understanding of the key non-covalent interactions in the FKBP12 binding pocket. Virtual screening hits were selected using macromolecular docking and programs that employed a ligand-based approach. The bulk of the virtual screening in this study used Edinburgh University’s in-house program LIDAEUS. In the course of this study nearly three hundred compounds were screened in the laboratory using biophysical and biochemical binding assays. Thirty four compounds were found to have an affinity for FKBP12 of less than one hundred micromolar. To test virtual hits, it was necessary to select the most appropriate medium-throughput biophysical assay. The aim was to employ methods with sufficient sensitivity to detect compounds with affinity in the order of one hundred micromolar, coupled with the capacity to screen hundreds of compounds in a week. This study used a wide variety of biophysical techniques, these including: electrospray ionisation mass spectrometry, surface plasmon resonance and isothermal titration calorimetry. There was a particular emphasis on the quality of data from electrospray ionisation mass spectrometry. A correlation was found between the cone voltages that gave 50 % dissociation of the complex with the enthalpic contribution to the free energy of binding. From the careful examination of the differences in charge-state distributions between a pure protein and a protein-ligand mixture, it was possible to determine if a protein-ligand complex had been present in solution prior to dissociation during the electrospray process. This observation provides the basis for an assay that could be of general utility in detecting very weak inhibitors.

No / When subjected to positive ion electrospray ionisation (ESI+) mass spectrometry (MS), indoles with a 3-alkyl substituent show a propensity to form novel [2M-H](+) 'covalently bound dimers'. This process, which appears to be initiated in the nebuliser of the instrument, is mechanistically interesting, analytically useful and potentially significant in organic synthesis. A selection of 2- and 3-substituted indoles have been synthesised and analysed by ESI-MS. The formation of the 'homo' and 'hetero' dimers of these compounds has been investigated using ESI+ mode. The mechanism of formation of the observed 'dimeric' species has been probed by synthesising authentic samples of the dimeric compounds. 'Dimeric' species corresponding to [2M-H](+) have been observed for all 3-substituted indoles studied, but not for indoles substituted in just the 2-position. By infusing equimolar mixtures of labelled and unlabelled indoles through the instrument, the expected approximately statistical mixture of homo- and heterodimeric species has been observed. Further experiments have established that this novel dimerisation occurs in the droplets formed in the nebuliser of the instrument. It has been shown that 3-substituted indoles form [2M-H](+) dimers in high abundance in the spray obtained from the nebiliser of an ESI+ instrument. The mechanism for the dimerisation does not involve the known 2M dimeric species that is readily formed in the solution-phase chemistry of indoles.

In this thesis, the application of electrospray ionisation mass spectrometry (ESI-MS) to the analysis of intact proteins is demonstrated. In papers I and II, the use of ESI-MS for the analysis of noncovalent protein-ligand complexes were discussed. In addition, the interfacing of liquid chromatography (LC) with ESI-MS and the development of an LC-ESI-MS method were demonstrated in paper III for the quality control of recombinant proteins. Furthermore, this method was applied in paper IV for the analysis of covalent glycosyl-enzyme intermediates. The monitoring of noncovalent complexes by ESI-MS is well established. However, the varying characteristic of ESI-MS data, especially in the analysis of noncovalent complexes can make the quantification of such complexes troublesome. In paper I, it was demonstrated how the variation in the position of the ESI-emitter and the initial droplet size of the electrosprayed droplets, together with different partitioning of a protein and its ligand in these droplets, can be the cause of such varying characteristics. Furthermore, it was shown that the partitioning can be of electrostatic and/or hydrophobic/hydrophilic origin. Thus it was demonstrated that if the ligand is more hydrophobic and thereby more surface active relative to the protein, decreasing the droplet size or increasing the distance between the electrospray emitter and the sampling orifice will lead to more efficient sampling of the droplet bulk where the ligand concentration is low. This results in a favoured sampling of free protein relative to the protein ligand complex. The opposite was shown to occur if the ligand is more hydrophilic than the protein. In paper II, Ribonuclease A (RNAse) was used as a model for enzymes acting on polymeric substrates with different chain lengths. Nano-ESI-MS was applied to monitor the noncovalent interactions between RNAse and different target ligands. Among the single building blocks of RNA, including ribose, the bases adenine, guanine, cytosine and uracil, and phosphate, only phosphate was observed to interact at multiple RNAse sites at a higher cone voltage. Furthermore, monobasic singlestranded deoxycytidylic acid oligomers (dCx) of different lengths (X=6, 9 and 12), and RNAse were analysed with nano-ESI-MS. The deoxycytidylic acid with 12 nucleotides was observed with the highest complex to free protein ratio, hence indicating the strongest interaction. Finally, collision induced dissociation of the noncovalent RNAseA-dC6 complex resulted in dissociation of covalently bound cytosine from the nucleotide backbone rather than break up of the noncovalent complex, illustrating the cooperative effect of multiple noncovalent interactions. In paper III an LC-ESI-MS method was presented capable of analysing proteins 10-100 kDa in size, from salt-containing liquid samples. The proteins included human protein fragments for the largescale production of antibodies and human protein targets for structural determination, expressed in E. coli. Also, glycosylated proteins expressed in Pichia pastoris were analysed. The method provides fast chromatography, is robust and makes use of cheap desalting/trap columns. In addition it was used with optimised reduction and alkylation protocols in order to minimize protein aggregation of denatured and incorrectly folded proteins containing cysteins, which otherwise form adducts by disulfide bond formation. Furthermore, the method was used in paper IV for the quantification of covalent proteinligand intermediates formed enzymatically between PttXET16-34, a xyloglucan endo-transglycosylase (XET) from hybrid aspen, and the synthetic substrates GalGXXXGGG and GalXXXGXXXG designed in order to function as donor substrates only. Thus covalent GalG-enzyme and GalGXXXG-enzyme complexes were detected. Moreover, establishing of a pseudo equilibrium for the formation of the covalent GalGXXXG-enzyme complex enabled quantification of the saccharide and enzyme constituents of this equilibrium and determination of the free energy of formation (∆G0). The high mass resolution of the TOF-MS allowed unambiguous assessment of the covalent nature of the glycosyl-enzyme complexes. Morover, the formation of noncovalent complexes between excess substrate and protein, which can deteriorate MS-signal and increase spectrum complexity, was efficiently avoided by the chromatographic step, which separated the saccharide content from the protein content. / QC 20100913

No / Lipidomics aim to generate qualitative and quantitative information on different classes of lipids and their species, and when applied in conjunction with proteomic and genomic assays, facilitate the comprehensive study of lipid metabolism in cellular, organ or body systems. Advances in mass spectrometry have underpinned the expansion of lipidomic methodologies. Prostanoids are potent autacoids present in a plethora of cellular systems, known best for their intimate role in inflammation. Electrospray ionisation (ESI) allows the efficient ionisation of prostanoids in aqueous systems. ESI can be readily coupled to liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS)-based detection, thus allowing the development of a potent and selective LC/ESI-MS/MS quantitative assays. The protocol we describe in this chapter outlines the steps we follow to a) extract prostanoids from solid or liquid samples, b) semi-purify the metabolites using solid phase extraction c) set-up the HPLC separation using reverse phase chromatography and d) set up the MS/MS assay using a triple quadrupole mass spectrometer. The experimental details and notes presented here are based on the detailed protocols followed in our group

<p>The interest for miniaturisation in chemical and biological analysis has increased in recent years. In this work, the design, fabrication and characterisation of tools for microanalysis have been studied. The focus is set on polymer microchips for applications in chemical analysis. The work consists of three parts: design and fabrication of paraffin microactuators, design and fabrication of polymer microchips as interfaces in electrospray ionisation mass spectrometry (ESI-MS), and characterisation of conducting films for fused silica capillaries as interfaces in ESI-MS.</p><p>The principle of the paraffin actuators is based on the volume increase resulting from paraffin melting. Paraffin expansion is utilised to cause membrane deflection. The first plastic microactuator using paraffin as the actuator material was successfully demonstrated.</p><p>The microchips as interfaces in ESI-MS have been designed with the objective that the interface should be as much a part of the microchip as possible, and as to as large extent as possible, be fabricated in the same step as the microchannels. Sheathless electrospray from microchips was demonstrated for the first time. In addition a simplified fabrication process for ESI-MS interfaces in poly(dimethyl siloxane) (PDMS) was developed.</p><p>The degradation of conductive coatings for sheathless ESI-MS on fused silica capillaries was studied. It was shown that electrochemical experiments could successfully be used to simulate the electrospray conditions and predict the failure of different gold coatings.</p><p>It was concluded that a common issue in the fabrication of thermoplastic microchips is the crucial sealing of microchannels and cavities. From this point of view, PDMS is a more advantageous material in microfluidics.</p>

Phosphorus (P) regulates trophic status in most aquatic systems. However, only bioavailable P contributes to primary production. In most lakes and shallow seas, mineralisation of sediment P into its bioavailable form and its release to the water column is important for maintaining primary production. Sediment organic P forms a substantial proportion of this P to be mineralised and can originate from different sources on land (farmland, forests, etc.) or from primary production in the lake. These organic P forms can thus be expected to have differing composition, degradability and recyclable P content. Knowledge of the chemical structure of sediment organic P compounds is scarce, mainly due to lack of appropriate analytical techniques. The commonly used 31P-nuclear magnetic resonance (31P-NMR) technique, only identifies P binding groups, so a mass spectrometric (MS) analysis method was developed that allows individual sediment organic P compounds to be identified. EDTA as pre-extractant resulted in the highest P yield in subsequent NaOH extraction. Extracted organic P compound groups were identified using 31P-NMR. For identification of specific P compounds with MS, a sample preparation method prior to electrospray tandem mass spectrometry (ESI-MS/MS) analysis was developed. Liquid chromatography (LC) with porous graphitic carbon prior to ESI-MS/MS enhanced sensitivity and selectivity, enabling several of the ions detected to be identified as nucleotides. 31P-NMR analysis showed P monoesters to be the most stabile P compounds throughout a lake sediment profile. The developed LC-ESI-MS/MS analysis method revealed that some monoester-P (nucleotides) were labile, while other P compounds increased in concentration with Baltic Sea sediment depth and were therefore considered stabile. Differences in patterns of P compounds detected were also shown depending on catchment characteristics in relation to Baltic Sea sediment age. For cost-effective management of eutrophication, knowledge of the sources of degradable organic P forms, contributing to internal loading, is needed. This thesis showed the developed LC-ESI-MS/MS analysis method to be a powerful analytical tool for this purpose.

The interest for miniaturisation in chemical and biological analysis has increased in recent years. In this work, the design, fabrication and characterisation of tools for microanalysis have been studied. The focus is set on polymer microchips for applications in chemical analysis. The work consists of three parts: design and fabrication of paraffin microactuators, design and fabrication of polymer microchips as interfaces in electrospray ionisation mass spectrometry (ESI-MS), and characterisation of conducting films for fused silica capillaries as interfaces in ESI-MS. The principle of the paraffin actuators is based on the volume increase resulting from paraffin melting. Paraffin expansion is utilised to cause membrane deflection. The first plastic microactuator using paraffin as the actuator material was successfully demonstrated. The microchips as interfaces in ESI-MS have been designed with the objective that the interface should be as much a part of the microchip as possible, and as to as large extent as possible, be fabricated in the same step as the microchannels. Sheathless electrospray from microchips was demonstrated for the first time. In addition a simplified fabrication process for ESI-MS interfaces in poly(dimethyl siloxane) (PDMS) was developed. The degradation of conductive coatings for sheathless ESI-MS on fused silica capillaries was studied. It was shown that electrochemical experiments could successfully be used to simulate the electrospray conditions and predict the failure of different gold coatings. It was concluded that a common issue in the fabrication of thermoplastic microchips is the crucial sealing of microchannels and cavities. From this point of view, PDMS is a more advantageous material in microfluidics.

No / The Flinders Sensitive Line (FSL) rat is a genetic animal model of depression. Following recent findings that the brain fatty acid composition of FSL is characterised by increased arachidonic acid (AA), we used electrospray tandem mass spectrometry and 1H-NMR to examine lipid species in different brain areas. Cholesterol and sphingolipids were increased in the hypothalamus of the FSL rats. Furthermore, arachidonic acid-containing phosphatidylcholine species (AA-PC) were elevated with PC16:0/20:4, PC18:1/20:4 and PC18:0/20:4 (p<0.003) increased in the hypothalamus and striatum. In contrast, there was a decrease in some docosahexaenoic acid (DHA)-containing species, specifically PC18:1/22:6 (p<0.003) in the striatum and PE18:1/22:6 (p<0.004) in the prefrontal cortex. Since no significant differences were observed in the erythrocyte fatty acid concentrations, dietary or environmental causes for these observations are unlikely. The increase in AA-PC species which in this animal model may be associated with altered neuropathy target esterase activity, an enzyme involved in membrane PC homeostasis, may contribute to the depressive phenotype of the FSL rats.

No / Prostanoids modulate the activity of human pregnant myometrium and their functional role can be appreciated through characterisation of prostanoid receptors and tissue concentration of prostanoids. We have applied a lipidomic approach to elucidate the profile of prostanoids in human non-labouring and labouring myometrium. We have identified a total of nineteen prostanoids including prostacyclin, thromboxanes, prostaglandins and dihydro-prostaglandins. Prostacyclin was the predominant prostanoid in both non-labouring and labouring myometria, with PGD2 and PGF2¿ being the second most abundant. Although the total amount of prostanoids was increased in the labouring tissue, PGE2 and 13,14-dihydro-15-keto-PGE2 were the only prostanoids to increase significantly at early and late labour (p¿0.001). Our data suggest that PGF2¿ plays an important role in parturition, whilst the increase in PGE2 could occur to facilitate cervical dilation and relaxation of the lower myometrium during labour. Although the elevation in TXA2 was less marked than expected, in terms of translation to function even a relatively small increase in the level of this potent spasmogen may have significant effects.