This thesis explores the use of mass spectrometry to define the strengths, and understand solution phase speciation of phenolic oxime-based solvent extractants of the types used in the hydrometallurgical recovery of copper. Chapter 1 reviews briefly the current extraction technology for copper and focuses on hydrometallurgy and the use of phenolic oximes such as 5-nonylsalicylaldoxime. The modification of the latter to improve extraction efficiency is discussed, focussing on the introduction of X-substituents in the 3 position of the benzene ring. Modern mass spectrometry techniques are also discussed with a focus on their application to inorganic systems and their use in achieving the aims of this thesis, as defined above. The work described in chapter 2 involves the development of collision induced dissociation (CID) techniques to determine the relative gas phase stabilities of copper complex anions of the type [Cu(L)(L-H)]-, where LH is a 5-alkyl-3-X-2- hydroxybenzaldehyde oximes and X a range of substituents. The importance of interligand interactions in the outer-coordination sphere and their influence on gas phase anion stability, as defined by CID, is reported. The work described in Chapter 2 on CID is extended in chapter 3 and looks at the effect of charge, of ligand type, LH, and of the nature of the metal on the stability of ionic forms of [M(L)2] complexes, where LH is extended to include 5-alkyl-2- hydroxyphenylethanone oximes. The effects of substitution at the azomethine carbon atom and at the 3-position of the benzene ring and of variation of the nature of the metal on the ion dissociation mechanisms are shown to have a major influence on ion stability under CID conditions. In chapter 4 density functional theory calculations have been used to investigate the influences of substitution at the azomethine carbon atom and at the 3-position of the benzene ring and of variation of the nature of the metal on the gas phase structures of the neutral complexes, [M(L)2]. Gas phase deprotonation and dimerisation enthalpies of the ligands, LH, and enthalpies of formation of [M(L)2] complexes have been calculated and correlates with experimentally determined ligand extraction strength. The ligand type has been extended to include 3-X-2-hydroxybenzaldehyde hydrazones, which have previously been shown to have lower distribution coefficients for copper than the analogous 3-X-substituted oximes. The calculated gas phase formation enthalpies for [M(L)2] show a strong correlation with the strengths as extractants LH, measured as their pH0.5 values for metal uptake. Chapter 5 considers whether mass spectrometry can be used to define the solution equilibria when two different oxime-based ligands, LXH and LYH, compete for Cu(II) in a single phase solution. It has been established that shifts in the relative peak intensities of deprotonated ions derived from the Cu(II) complexes, [Cu(LX)2], [Cu(LY)2] and [Cu(LX)(LY)] reflect changes in the solution composition. The work described in chapter 6 extends the study of solution phase speciation using mass spectrometry. When the Cu(II) and proton concentrations of solutions were varied distinct changes in the resulting electrospray mass spectra were observed and the resulting species were identified using CID and high resolution mass spectrometry. A novel, [Cu3(L-H)3-μ3-O/OH]- species is determined to be a major component of solutions where Cu(II) concentrations are equal to/greater than the LH concentration. Various 3-X-2-hydroxybenzaldehyde oximes (X = CH2NR2) were synthesised. The incorporation of a protonatable arm in the 3-position enabled trinuclear complexes, [Cu3(L-H)3-μ3-OH], to be isolated and fully characterized, including two X-ray determined crystal structures.

Mining of datasets obtained from proteomics experiments was performed to investigate the dissociation pathways of protonated peptides activated in the gas phase under low energy collision-induced dissociation (CID). Intensity patterns in ion trap tandem mass spectra were exploited and different statistical approaches were employed to elucidate the dissociation mechanisms.Chapter 2 describes a study of 506 doubly-protonated tryptic peptides that shows the presence of an internal basic residue can increase the preferential fragmentation C-terminal to aspartic acid (Asp-Xxx) significantly. The degree of enhancement varies with the identity of the basic residues. The result corroborates a previously published mechanism based on studies from model peptides, and was incorporated into an existing peptide sequencing algorithm. A preliminary test on a separate dataset of 119 spectra shows that implementing rules to predict enhanced cleavages at Asp-Xxx improves the ability of the algorithm to identify the correct sequence from a list of candidates.Chapters 3-4 describe much more elaborate analyses on 28,330 peptides of different sequences and charge states. Extensive sorting based on prior knowledge was first performed to probe the correlation of fragmentation patterns with structural features. Pair-wise fragmentation maps reveal that the difference in basicity between Arg and Lys results in different dissociation patterns among singly-protonated tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of two or more protonated forms (proton partially-mobile) exist for Lys-ending peptides. Asp/Glu-Xxx dominates spectra from peptides that have a localized proton(s) and Xxx-Pro dominates those that have a mobile or partially mobile proton(s). When Pro is absent from peptides that have a mobile or partially mobile proton(s), cleavage at each peptide bond becomes more prominent. A fundamental dependence of gas phase peptide fragmentation on conformational constraints was found.A knowledge mining scheme was proposed in Chapter 5 to bypass the prior knowledge constraints and cluster the dissociation behaviors of 28,330 peptides into four distinct categories. The most influential factors in the fragmentation process are: the mobility of the proton(s), the presence and the location of Pro and Arg. Structural motifs responsible for each dissociation behavior are also elucidated.

Nowadays, polymer chemists undertake considerable efforts to achieve the preparation of new macromolecules and a perfect control over the macromolecular engineering, i.e. the mass parameters but also over the chain and end-group compositions, topology, etc… is definitively expected. In addition, more complex architectures, such as brush (co)polymers, jellyfish-like topologies…, are required to improve or drastically modify the physicochemical properties of the materials. As a direct consequence of the development of such complex molecular objects, sophisticated techniques are required for the in-depth characterization of the macromolecules, since the exact compositions and structures should be fully and unambiguously identified. Given the fact that the usual characterization tools such as Nuclear Magnetic Resonance (NMR) and Gel Permeation Chromatography (GPC) are extensively used, their abilities have been intensively developed to account for the increasing complexity and diversity of the targeted molecules. Nevertheless, all the usual techniques are averaging methodologies since they only provide pieces of information about the polymer mixture instead of affording data on the individual macromolecules. Since few decades, mass spectrometry (MS) has become as used as NMR and GPC for polymer characterization. In the context of large molecules analysis, MS undoubtedly underwent an impressive craze with the development of two modern ionization procedures, namely Electrospray Ionization (ESI) and Matrix-assisted Laser Desorption/Ionization (MALDI). Those ionization procedures permit the vaporization of macromolecules allowing the intact polymers to be analyzed without a too extensive level of degradation. ESI and MALDI are often considered as soft ionization methods since they offer the possibility to observe ions corresponding to the intact molecules. After their production in the ion source, ions corresponding to the polymer molecules can be mass analyzed by the mass spectrometer and important parameters such as the molecular weight distribution (Mn and Mw), polydispersity index (PDI), the nature of the monomer units and the end-groups can be derived from the measure of the mass-to-charge ratios of the produced ions. In the first part of the present thesis, we studied the MS behavior of different classes of polymers when submitted to ESI and MALDI ionizations. The investigations were devoted to the validation of MS as a truly reliable methodology for fragile polymers such as aliphatic polyesters for instance. In this context, a preliminary MS investigation on semi-telechelic polyethers revealed the importance of the source parameters for the characterization of polymers presenting fragile moieties. We also demonstrated the huge importance of the matrix molecule selection for the MALDI analyses of polymers. In particular, we introduced a new matrix for the MALDI measurements of electroconjugated polymers such as polythiophenes. After the study of the influence of the source parameters on the MS data, a complete study by single stage MS and double stage MS (MS/MS) on newly synthesized polylactides (PLA) was performed. The PLA samples were prepared following original procedures using carbene as catalyst. Finally, to achieve the MS study of PLA ions, we used ion mobility-mass spectrometry (IM-MS) experiments to obtained information on the tridimensional structure of the gas phase PLA ions. In particular, we put a special emphasis on the influence of the charge and size of the polymer chains on their gas-phase conformations. The conclusions derived from the MS/MS and IM-MS results were fully supported by theoretical calculations. In the second part of the thesis, the acquired MS experience was applied to the fine characterization of macromolecules presenting complex architectures obtained by two different polymerization procedures: (i) cobalt-mediated radical polymerization of inter alia acrylonitrile and vinyl acetate and (ii) ring-opening polymerization (ROP) of lactones using non-organometallic catalysts. In particular, mass spectrometry was used to tune the experimental conditions for the ROP of â-lactones using different phosphazenes as catalysts. As an ultimate conclusion, this work points to the very efficient synergy between polymer synthesis, mass spectrometry and theoretical calculations. We believe that this thesis paves the way for innumerable possibilities in the future.

This dissertation presents an investigation into the structure of macromolecular protein assemblies by mass spectrometry. The experiments described within are designed to systematically assess the analytical utility of surface-induced dissociation (SID) tandem mass spectrometry in the characterization of multi-subunit protein complexes. This is accomplished by studying the effects of ion-surface collision on the fragmentation products of protein assemblies that vary by mass, number of subunits, and protein structural features. The dissociation energetics and mechanisms of protein complexes are considered by examining the influence of ion internal energy and sub-oligomeric protein structure on the dissociation process. Conditions are first established for the preservation of “native” protein quaternary structure and applied to previously characterized systems for proof-ofconcept. These conditions are subsequently extended to determine the molecular weight and subunit stoichiometry of several small heat shock proteins. Native mass spectrometry is then combined with limited proteolysis experiments to characterize the subunit interface of a unique small heat shock protein, Hsp18.5 from Arabidopsis thaliana, identifying regions of the protein essential for preservation of the native dimer. The dissociation of non-covalent protein assemblies is then explored on a quadrupole time-of-flight (Q-TOF) mass spectrometer, modified for the study of ion-surface collisions. This instrument allows ions to be dissociated through collisions with a surface or more conventional collisions with gas atoms. The dissociation of protein complexes is explored by both activation methods beginning with specific and non-specific dimers with masses less than 40 kDa. These studies are extended to larger assemblies with as many as 14 subunits weighing over 800 kDa, and are applied to both homo- and hetero-oligomeric protein complexes. Activation of a protein complex with “n” subunits through multiple collisions with inert gas atoms results in asymmetric dissociation into a highly charged monomer and complementary (n-1)-mer regardless of protein size or subunit architecture. This process is known to occur through an unfolding of the ejected subunit, and limits the amount of structural insight that can be gleaned from such studies. Collision at a surface however, results in more charge and mass symmetric fragmentation, and in some instances reflects the substructure of the protein assembly under investigation. The differences observed between the CID and SID of protein complexes is attributed to the rapid deposition of large amounts of internal energy deposited upon collision at a more massive target such as a surface. The ion activation time-frame and energy transfer efficiency are proposed to induce dissociation on a time-scale that precedes subunit unfolding providing access to dissociation pathways that are inaccessible by traditional means of activation. The systems studied here represent the largest ions fragmented via surface collisions within a mass spectrometer, and the fragmentation products observed by SID demonstrate its promise for expanding the role of mass spectrometry in the field of structural biology.

Research presented in this dissertation falls into two parts: fragmentation mechanisms of peptide and fragmentation mechanism of amino acid derivatives. The study of peptide fragmentation may help to improve protein identification by incorporating the rules governing this process into search algorithms. This study elucidates the chemical 'rules' governing peptide dissociation. It is believed that these 'rules' can be incorporated into searching algorithms to achieve better protein identification. The present study focuses on the effects of different amino acids on fragmentation. Amino acids with a wide range of different chemical and physical properties are investigated, including amino acids with hydrophilic side chains, amino acids with aliphatic side chains and amino acids without side chains. It can be concluded from the present studies that the different amino acid properties have great influence on the peptide fragmentation and spectrum appearance.The study of fragmentation mechanisms of amino acid derivatives is another focus of this dissertation. Based on the fragmentation mechanism study, a quantification method was developed. The method can distinguish glutamine with 15N-label at N-terminal amine vs the side chain even if they have same molecular weight. Ammonia metabolism was successfully monitored by feeding mosquitoes with isotope-labeled compounds and subsequently measuring the amount of the labeled amino acids. This method demonstrates the power of mass spectrometry in metabolism studies.

Quadrupole ion trap(QIT) mass spectrometry has become one of the most widelyused tools in the analysis of the structure of small molecules. The motion of the ionsstored in the quadrupole ion trap is extremely important. This ion motion within thequadrupole ion trap is controlled by several factors including the m/z ratio and thecollisional cross section of the ion. Investigation of ion motion within the QIT has thepotential to elucidate a new way to separate ions based on these factors. DC tomographyexperiments allow for the trajectory of the ion motion to be measured withoutmodifications to the ion trap. The ability to use DC tomography for separation ofisomeric ions on a commercial GC/MS system was investigated.Investigation of the mass range within the ion trap is necessary for the analysis ofa wide range of molecules. The ability of the quadrupole ion trap to perform MS/MSanalyses can provide insight into the structural information of many compounds.However, there exists a low mass cut-off (LMC) within the quadrupole ion trap and thusinformation about the low m/z fragments from a parent ion is lost. Schwartz and coworkerspresented a new technique labeled pulsed q dissociation (PQD) at the 53rdAnnual ASMS Conference in San Antonio TX in 2005. PQD eliminates the LMC byperforming CID at a qz of 0.4 but, then immediately lowering the q level before the massscan in a linear ion trap. By operating the quadrupole ion trap in this same manner, lowm/z product ions can be detected. This technique and elucidation of the energetic processcontained within PQD were explored further using a modified commercial quadrupoleion trap and the results discussed in this work.

This dissertation mainly focuses on analytical method development for characterization of proteins, glycoproteins and glycans using the recently developed ion mobility spectrometry (IMS) techniques and various electron activated dissociation (ExD) tandem mass spectrometry methods. IMS and ExD have become important techniques in structure analysis of biomolecules. IMS is a gas-phase separation method orthogonal to liquid chromatography (LC) fractionation. ExD is capable of producing a large number of structurally informative fragment ions for elucidation of structural details, complementary to collision-induced dissociation (CID). We first applied the selected accumulation-trapped IMS (SA-TIMS)-electronic excitation dissociation (EED) method to analyze various mixtures of glycan isomers. Glycan linkage isomers with linear or branched structure were successfully separated and subsequently identified. Theoretical modeling was also performed to gain a better understanding of isomer separation. The calculated collisional cross section (CCS) values match well with the experimentally measured ones, and suggested that the choice of metal charge carrier and charge state is critical for successful IMS separation of isomeric glycans. In addition, a SA-TIMS-electron capture dissociation (ECD) approach was employed to study gas-phase protein conformation, as the ECD fragmentation pattern is influenced by both the charge distribution and the presence of various non-covalent interactions. We demonstrated that different conformations of protein ions in a single charge state could produce distinct fragmentation pattern, presumably because of their differences in tertiary structures and/or proton locations. The second part describes characterization of glycoproteins using LC-hot ECD. To improve the cleavage coverage of glycopeptides, hot ECD, a fragmentation method utilizing the irradiation of high-energy electrons, was optimized for both middle-down and bottom-up analyses of glycopeptides, including peptides with multiple glycosylation sites. Hot ECD was shown to be an effective fragmentation technique for sequencing of glycopeptides, even for ions in lower charge states. In addition, the online LC-hot ECD approach was applied to characterize extensively modified glycoproteins from biological sources in which all glycosylation sites could be unambiguously determined. This study expands the applications of IMS, CID and ExD to structural analysis of various biomolecules, and explores the analytical potential of combining them for investigation of complex biological systems, in particular, enzyme mechanisms.

Mamalian protein ubiquitination and SUMOylation are reversible post translational modifications, which are involved in a multitude of important complex regulatory processes within the cell. Current mass spectrometry approaches that involve bottom-up proteomics to comprehensively analyse these modifications, have proved to be problematic. In this work, analytical approaches are carried out to improve and enhance the comprehensive analysis of these modifications. Tryptic proteolysis of ubiquitinated proteins results in the generation of isopeptides bearing adi-glycine (GG) remnant. Current mass spectrometry approaches used to identify these isopeptides are predominantly reliant on detecting the signature mass shift of the GG remnant (114.043 Da). The lack of sequence information from the GG remnant post MS/MS acquisition results in database search algorithms falsely identifiying these isopeptides. Reductive methylation chemistry was employed to derivatize these isopeptides. Upon collision induced dissociation of the isopeptides two robust ions were released from the iso-N-terminus of the GG remnant ; i) an a1’ ion at m/z 62.09, corresponding to the G of the remnant and ii) a b2’ ion at m/z 147.11, corresponding to the full GG remnant. Post-acquisition data extraction of these unique diagnostic ions demonstrated enhanced selectivity towards identifying these isopeptides. Tryptic proteolysis of SUMOylated proteins results in the generation of isopeptides bearing a substantial iso-C-terminal SUMO remnant. The CRA(K) (Consecutive Residue Addition tolysines (K)) approach combined independant use of proteolytic enzymes and unbiased consecutive residue addition of amino acids pertaining to these iso-C-terminal SUMOremnants, on all lysine residues. This approach enabled the identification of analytically useful novel wildtype isopeptides derived from the proteolysis of SUMO(1/2/3)ylated proteins, bearing GG, TGG and QTGG remnants. The analytically useful isopeptides derived from proteolysis of SUMO(2/3)ylated proteins lacked robust diagnostic information from their iso-C-terminal bearing TGG and QTGG remnants. Reductive methylation chemistry was utilised to derivatize these isopeptides and enabled diagnostic a’ and b’ ions to be released from their iso-N-termini; i) a1’ (m/z 133.13),b2’ (m/z 262.17) and b4’ (m/z 376.22) ions, corresponding to the QTGG remnant and ii) (m/z106.10), b2’ (m/z 191.14) and b3’ (m/z 248.14) ions, corresponding to the TGG remnant. Post-acquisition data extraction of these unique diagnostic ions, enabled comprehensive structural elucidation of these isopeptides and enhanced selectivity towards identification.

By using two electrospray emitters containing different solutions (“dual-spray”) we have recently conducted in-source hydrogen/deuterium exchange (HDX) reactions and synthesized organometallic species. For dual-spray HDX reactions, peptide and protein solutions were electrosprayed through one emitter and the deuterating agent D2O through the secondary electrospray emitter. Clear shifts in isotope distributions indicated hydrogen-deuterium exchange occurring within the ion source. By ion mobility, simultaneous deuterium exchange for two isobaric species, the oxytocin monomer and dimer, was observed. Lysozyme has a linear relation between the charge state and the average number of exchanges, indicating that lysozyme becomes increasingly unfolded as the charge state increases. Based on deuterium uptake data and the lack of a temperature dependence, the dual-spray HDX reaction is thought to occur mostly in the gas phase. Tris(2,2’-bipyridine)ruthenium(II) and similar complexes containing the 1,10-phenanthroline ligand were formed by spraying a ligand solution and the ruthenium trichloride solution through two independent ESI emitters. This was confirmed by comparing ion mobility drift time, mass spectra, and CID fragmentation with the reference standard compounds. Tris(2,2’-bipyridine)iron(II), tris(1,10-phenantroline)iron(II) and mixed ligand complexes of iron(II) formed by dual-spray showed two additional hydrogens bonded to the complex. By CID, these unique gas phase complexes showed similar initial ligand loss to the reference standards however the secondary ligand loss showed dissimilar dissociation channels and energetics. Using DFT calculations, geometry optimizations for the [Fe(phen)3 + 2H]2+ complex and its fragment ions were done. After the initial ligand loss, the additional hydrogens are believed to transfer to the central iron atom. The relative energy of the dissociation channels showed good agreement with experimental breakdown curves.

No description available.