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Berezovskaya, Yana. "Investigation of protein-ion interactions by mass spectrometry and ion mobility mass spectrometry." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/7747.
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Protein‐ion interactions play an important role in biological systems. A considerable number of elements (estimated 25 – 30) are essential in higher life forms such as animals and humans, where they are integral part of enzymes involved in plethora of cellular processes. It is difficult to overestimate the importance of thorough understanding of how protein‐ion interplay affects living cell in order to be able to address therapeutic challenges facing humanity. Presented to the reader’s attention is a gas‐phase biophysical analysis of peptides’ and proteins’ interactions with biologically relevant ions (Zn2+ and I–). This investigation provides an insight into conformational changes of peptides and proteins triggered by ions. Mass spectrometry and ion mobility mass spectrometry are used in this work to probe peptide and protein affinities for a range of ions, along with conformational changes that take place as a result of binding. Observation of peptide and protein behaviour in the gas phase can inform the investigator about their behaviour in solution prior to ionisation and transfer from the former into the latter phase. Wherever relevant, the gas‐phase studies are complemented by molecular dynamics simulations and the results are compared to solution phase findings (spectroscopy). Two case studies of protein‐ion interactions are presented in this thesis. Firstly, sequence‐to‐structure relationships in proteins are considered via protein design approach using two synthetic peptide‐based systems. The first system is a synthetic consensus zinc finger sequence (vCP1) that is responsive to zinc: it adopts a zinc finger fold in the presence of Zn2+ by coordinating the metal ion by two cysteines and two histidines. This peptide has been selected as a reference for the zinc‐bound state and a simple model to refine the characterisation method in preparation for analysis of a more sophisticated second system – dual conformational switch. This second system (ZiCop) is designed to adopt either of the two conformations in response to a stimulus: zinc finger or coiled coil. The reversible switch between the two conformational states is controlled by the binding of zinc ion to the peptide. Interactions of both peptide systems with a number of other divalent metal cations (Co2+, Ca2+ and Cu2+) are considered also, and the differences in binding and switching behaviour are discussed. Secondly, protein‐salt interactions are investigated using three proteins (lysozyme, cytochrome c and BPTI) using variable temperature ion mobility mass spectrometry. Ion mobility measurements were carried out on these proteins with helium as the buffer gas at three different drift cell temperatures – ‘ambient’ (300 K), ‘cold’ (260 K) and ‘hot’ (360 K), and their conformational preferences in response to HI binding and temperature are discussed.
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Woods, Lucy Ann. "Characterising amyloid assembly using ion mobility spectrometry-mass spectrometry." Thesis, University of Leeds, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590277.
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From small molecules to macromolecules, mass spectrometry has evolved significantly over the past decade, progressing from a tool to identify chemical elements to a powerful technique able to elucidate structural information for large protein complexes. With the interfacing of ion mobility spectrometry to mass spectrometry (IMS-MS), mass spectrometric analyses now occupy an extra dimension, providing unrivalled separation and structural characterisation of lowly-populated species in heterogeneous mixtures. One biological system that has benefitted enormously from such advances is the study of in vitro amyloid formation. The ability of amyloidogenic proteins to assemble into insoluble fibrils is associated with over twenty-five different disease states. Beta-2 microglobulin (β2m) is one such protein able to assemble into amyloid fibrils in vitro, although assembly can only be initiated upon destabilisation of the native structure. Identifying which states initiate fibril formation is challenging. as few techniques are able to separate and characterise such transient species. In addition, recent research has identified a number of small molecule inhibitors of fibrillation and understanding their mechanism of action is a topic of current interest. Here, the power of IMS-MS has been harnessed to achieve the separation and characterisation of monomeric and oligomeric precursors of amyloid fibril formation of the protein β2m. Analysis of oligomeric species populated during fibril formation, in addition to the effects of small molecule inhibitors on oligomer population, has led to the identification of oligomeric species on-pathway to fibril formation. Further investigation into fibrils of different morphologies has also been conducted using IMS and limited proteolysis, Differences in oligomeric populations have been revealed, together with differences in fibril structure. Each of these results highlights how MS can be used to give insights into the mechanism of amyloid formation and highlight the potentials of this approach for screening for potential inhibitors of any assembly reaction.
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Zhou, Li. "Enhanced Electrospray Ionization for Mass Spectrometry and Ion Mobility Spectrometry." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1384.pdf.
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Ismail, Vian Sdiq Ismail. "Probing lipidation of membrane active peptides and integral membrane proteins by liquid chromatography-mass spectrometry and ion mobility separation-mass spectrometry." Thesis, Durham University, 2017. http://etheses.dur.ac.uk/12424/.
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Liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS2) are shown to have the sensitivity and functionality to detect protein/peptide modifications by fatty acyl chains in vitro and in vivo studies. Further analysis was also performed by direct infusion ion mobility separation coupled with mass spectrometry (IMS-MS) or tandem mass spectrometry (IMS-MS2). Peptide lipidation in vitro was investigated using the membrane active peptide, melittin. Non-enzymatic melittin lipidation by lysophospholipids has been observed for the first time. When the effect of lysophospholipids was studied in direct competition with diacylphospholipids, the acyl transfer from the lysophospholipids is seen to be preferential with acylation visible after just 3 hour. The longer the interaction time, the greater the amount and number of modifications with double and triple acylation observed after 96 hour. The locations of the modifications identified through LC-MS2 were assigned on different sites of the peptide, including N-terminus, K7, S18, K21, K23, R22 and R24 and with the highest reactivity towards N-terminus and K23. Comparing the lipidation of synthetic melittin (SynM) with the lipidation of naturally occurring melittin from venom of honey bee (BVM) highlights the effect of the PLA2 enzyme that is naturally present in BVM. Here, the action of the enzyme to hydrolyse the diacylphospholipid at the sn-2 position to give the corresponding lysophospholipid is reflected in the acyl transfer to the BVM such that the resulting lysophospholipid clearly dominates the acyl transfer to BVM. In contrast, the acyl transfer to SynM clearly demonstrates that acyl transfer is possible in the absence of an enzyme. In vivo protein lipidation of one of the most abundant integral membrane proteins in mammalian eye lens, AQP0, was also studied. A wide range of acyl groups are shown to modify this protein at the known modification sites, N-terminus and at the amino acid residue K238, many of which are reported here for the first time. These acyl group modifications reflect the biological lipid composition of the membrane leaflet that the acylation sites are proximal to. In an attempt to further distinguish between different forms of lipidated melittin, whether with the same acyl chain modification to different amino acids or to discriminate between palmitoylation and oleoylation modifications, travelling wave ion mobility spectrometry (TWIMS) coupled with MS or MS2 was applied. Results suggested that resolving positional isomers of diacylphospholipids and lysophospholipids (sn-1 vs sn-2 positions) is not possible under the conditions described herein. However, the presence of fatty acyl chains covalently bound to melittin change the conformation of acylated melittin in the gas-phase such that for lower charge states it is possible to suggest a small degree of separation between palmitoylated and oleoylated melittin or their isomers including acylation on N-terminus vs K23. This small degree of separation is enough so that when combined with tandem mass spectrometry, the time-aligned product ion spectra are clearer and improve characterisation. To conclude, the research in this thesis has shown that two of the most abundant biomolecules, lipid and peptides/proteins that are known to exist in close proximity to each other, or interact with each other, are not as chemically inert as previously thought. This reactivity has been reflected herein via aminolysis reaction between membrane lipid composition and each of membrane active peptide, melittin and integral membrane protein, AQP0.
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Ding, Luyi. "Studies of electrospray/ion mobility spectrometry/time-of-flight mass spectrometry." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0015/NQ48344.pdf.
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Chawner, Ross. "Combined tandem mass spectrometry and ion mobility spectrometry in proteome analyses." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/combined-tandem-mass-spectrometry-and-ion-mobility-spectrometry-in-proteome-analyses(3ba76f18-4703-4f6e-a97f-ee2b1dfb1deb).html.
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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.
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Koeniger, Stormy Lee Ann. "Multidimensional ion mobility spectrometry coupled to time-of-flight mass spectrometry." [Bloomington, Ind.] : Indiana University, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3230539.
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Thesis (Ph. D.)--Indiana University, Dept. of Chemistry, 2006.Title from PDF t.p. (viewed Nov. 5, 2008). Source: Dissertation Abstracts International, Volume: 67-08, Section: B, page: 4395. Adviser: David E. Clemmer.
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Shliaha, Pavel Vyacheslavovich. "Investigation of protein abundance and localization by mass spectrometry and ion-mobility spectrometry-mass spectrometry methods." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708661.
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Smiljanic, Danijela. "Mass Spectrometry Interfaced with Ion Mobility or Liquid Chromatography Separation for the Analysis of Complex Mixtures." University of Akron / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=akron1323149449.
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Hofmann, Johanna [Verfasser]. "Ion Mobility-Mass Spectrometry of Complex Carbohydrates / Johanna Hofmann." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1141678438/34.
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Knight, Andrew Keith. "Advanced Detection Technology for Ion Mobility and Mass Spectrometry." Diss., The University of Arizona, 2006. http://hdl.handle.net/10150/193700.
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The development of new technologies and the advancement of existing technical expertise can allow for dramatic improvements to be realized in analytical instrumentation. The development of an integrating solid-state ion detector, designed to have a high sensitivity as well as maintaining a high-level of stability, is described and evaluated. Several versions of the charge-transimpedance amplifier (CTIA) technology were constructed with different operating features. The CTIA-1 is a 32-pixel array detector designed for mass spectrometry. It has the capability to simultaneously detect multiple ion channels with a detection limit less than 100 ions. The CTIA-2 detector features an independent selectable gain for each detection channel. The CTIA-2 is a 4-channel device designed for ion mobility. Further design features were built into the CTIA-5 such as differential noise reduction capabilities.The CTIA-1 technology was evaluated for use in isotope ratio mass spectrometry on a custom-built Mattauch-Herzog mass spectrometer. An evaluation was conducted in terms of the detector sensitivity, stability, accuracy, precision, resolution, and mass bias. The CTIA-2 was tested on a sector mass spectrometer for its response to low ion currents of both positive and negative ions. The detector stability, its accuracy, and its precision were studied.The technique of ion mobility spectrometry is rapidly growing, as it is the main technology used for the detection of explosives at security checkpoints. The need to improve the sensitivity of existing ion mobility instruments has led to the exploration of using the CTIA detector in ion mobility instruments. Improvements in sensitivity of two to three orders of magnitude have been demonstrated using the described CTIA detectors. Additional applications that use ion mobility instruments for the detection of analytes have been presented, the chemical mapping of a halogen-contaminated sand bed, the detection of pesticides, as well as the detection of TNT in drinking water.Results indicate that the CTIA detector technology is well suited for use in both mass spectrometry and ion mobility. The sensitive and stable multi-array CTIA detectors perform well in isotope ratio mass spectrometry. Ion mobility instruments of all types can benefit from the added sensitivity supplied by this technology.
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Ma, Xin. "Ion Mobility Mass Spectrometry of DNA/SgrAI Nuclease Oligomers." Thesis, The University of Arizona, 2012. http://hdl.handle.net/10150/247282.
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SgrAI is a restriction endonuclease (ENase) that cuts a long recognition sequence and exhibits self-modulation of cleavage activity and sequence specificity. Previous research has shown that SgrAI forms large oligomers when bound to particular DNA sequences and under the same conditions where SgrAI exhibits accelerated DNA cleavage kinetics. However, the detailed structure and stoichiometry of SgrAI:DNA as well as the basic building block of the oligomers, has not been fully characterized. Ion mobility mass spectrometry (IM-MS) was employed to analyze SgrAI/DNA complexes and show that the basic building block of the oligomers is the DNA-bound SgrAI dimer (DBD). The oligomers are heterogeneous containing a mixture of species with variable numbers of DBD. The collision cross sections (CCS) of the oligomers were found to have a linear relationship with the number of DBD. Models of the SgrAI/DNA oligomers were constructed and a head-to-tail arrangement was most consistent with the experimental CCS.
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Katzenmeyer, Bryan C. "Interfacing Liquid Chromatography or Ion Mobility Separation with Mult-Dimensional Mass Spectrometry for the Structural Characterization of Polymeric Materials." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1367252830.
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Faull, Peter Allen. "Exploring gas-phase protein conformations by ion mobility-mass spectrometry." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3851.
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Analysis and characterisation of biomolecules using mass spectrometry has advanced over the past decade due to improvements in instrument design and capability; relevant use of complementary techniques; and available experimental and in silico data for comparison with cutting-edge research. This thesis presents ion mobility data, collected on an in-house modified QToF mass spectrometer (the MoQTOF), for a number of protein systems. Two haemoproteins, cytochrome c and haemoglobin, have been characterised and rotationally-averaged collision cross-sections for a number of multimeric species are presented. Intact multiply-charged multimers of the form [xCyt c + nH]z+ where x = 1 (monomer), x = 2 (dimer) and x = 3 (trimer) for cytochrome c have been elucidated and for species with x ≥ 2, reported for the first time. Fragment ions possibly attributed to a novel fragmentation mechanism, native electron capture dissociation, are reported with a brief discussion into their possible production from the dissociation of the gas-phase dimer species. Haemoglobin monomer globin subunits, dimers and intact tetramer have been successfully transferred to the gas phase, and their cross-sections elucidated. Comparisons with in silico computational data have been made and a discussion of the biologically-active tetramer association/dissociation technique is presented. Three further proteins have been studied and their gas-phase collision cross-sections calculated. Two regions of the large Factor H (fH) complement glycoprotein, fH 10-15 and fH 19-20, have been characterised for the first time by ion mobility-mass spectrometry. Much work using nuclear magnetic resonance spectroscopy has previously been achieved to produce structural information of these protein regions, however further biophysical characterisation using mass spectrometry may aid in greater understanding of the interactions these two specific regions have with other biomolecules. The DNA-binding core domain of the tumour suppressor p53 has been characterised and cross-sections produced in the presence and absence of the zinc metal ion that may control the domain’s biological activity. Within this core domain, p53 inactivation mutations have been shown to occur in up to 50% of human cancers, therefore the potential exists to further cancer-fighting activity through research on this region. Anterior Gradient-2 (AGR2) protein facilitates downregulation of p53 in an as yet unclear mechanism. Recent work using peptide aptamers has demonstrated that this downregulation can be disrupted and levels of p53 restored. Collision cross-sections for six peptide aptamers have been calculated, as well as cross-sections for multimers of AGR2 protein. A complex between one aptamer with the protein has also been elucidated. Use of the commercially available Synapt HDMS ion mobility-mass spectrometer at Waters MS Technologies Centre (Manchester, UK) allowed data to be collected for both Factor H protein regions and for the DNA-binding core domain of p53. Data are compared in the appropriate chapters with data collected using the MoQTOF.
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Soyk, Matthew W. "Instrumentation development for coupling ion/ion reactions and ion mobility in biological mass spectrometry." [Ames, Iowa : Iowa State University], 2008.
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Cool, Lydia R. "Identifying and Distinguishing Isomers Using Mass Spectrometry and Ion Mobility." University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1460470683.
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Göth, Melanie [Verfasser]. "Investigation of Protein-Ligand Complexes by Native Mass Spectrometry and Ion Mobility-Mass Spectrometry / Melanie Göth." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1149050594/34.
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Brown, Lauren J. "Field asymmetric waveform ion mobility spectrometry-mass spectrometry studies of peptides and proteins." Thesis, Loughborough University, 2013. https://dspace.lboro.ac.uk/2134/12001.
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Field asymmetric waveform ion mobility spectrometry (FAIMS) is a gas phase atmospheric pressure separation technique that exploits the difference in the mobility of ions in alternating low and high electric fields as they are carried between two electrodes. In this thesis, a miniaturised FAIMS separation step has been applied to increase selectivity, enhance sensitivity and improve the quality of mass spectral data for rapid, high-throughput protein and peptide analysis. In Chapter 2, charge state separations were used to generate pseudo-peptide mass fingerprint data by FAIMS-MS, permitting confident protein identification using ESI sample introduction as an alternative to MALDI-TOF-MS methods. In addition, pre-cursor ions were targeted prior to MS/MS analysis. Chapter 3 describes the analysis of intact proteins by miniaturised FAIMS-MS. Multiple charge states of intact proteins were separated on the basis of differences in differential mobility. Higher charge states were found to be transmitted at similar CVs suggesting that the miniaturised FAIMS device was separating ions on the basis of 3D structure. In addition, multiple species could be observed at the same m/z suggesting the presence of different protein conformers. In Chapter 4, miniaturised FAIMS was used to select ions on the basis of differential mobility prior to in-source collision-induced dissociation CID, LC and ToF-MS analysis for qualitative and quantitative analysis of peptides mixtures. This was applied to the analysis of co-eluting model peptides and tryptic peptides derived from human plasma proteins, allowing precursor ion selection and CID to yield product ion data suitable for peptide identification via database searching.
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Garabedian, Alyssa Lynn. "Study of Proteoforms, DNA and Complexes using Trapped Ion Mobility Spectrometry-Mass Spectrometry." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3567.
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The characterization of biomolecules and biomolecular complexes represents an area of significant research activity because of the link between structure and function. Drug development relies on structural information in order to target certain domains. Many traditional biochemical techniques, however, are limited by their ability to characterize only certain stable forms of a molecule. As a result, multidimensional approaches, such as ion mobility mass spectrometry coupled to mass spectrometry (IMS-MS), are becoming very attractive tools as they provide fast separation, detection and identification of molecules, in addition to providing three-dimensional shape for structural elucidation. The present work expands the use and application of trapped ion mobility spectrometry-coupled to mass spectrometry (TIMS-MS) by analyzing a range of biomolecules (including proteoforms, intrinsically disordered peptides, DNA and molecular complexes). The aim is to i) evaluate the TIMS platform measuring sensitivity, selectivity, and separation of targeted compounds, ii) pioneer new applications of TIMS for a more efficient and higher throughput methodologies for identification and characterization of biomolecular ions, and iii) characterize the dynamics of selected biomolecules for insight into the folding pathways and the intra-or intermolecular interactions that define their conformational space.
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Lu, Yao. "Forensic Applications of Gas Chromatography-Differential Mobility Spectrometry, Gas Chromatography/Mass Spectrometry, and Ion Mobility Spectrometry with Chemometric Analysis." Ohio University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1267816777.
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Gwak, Seongshin. "Comprehensive Analysis of Emerging New Psychoactive Substances by Ion Mobility Spectrometry and Mass Spectrometry." FIU Digital Commons, 2015. http://digitalcommons.fiu.edu/etd/2291.
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In the new era of drug abuse, the proliferation of new psychoactive substances (NPS), commonly referred to as designer drugs or legal highs, has been a global concern. These substances are produced to circumvent current legislation for controlled substances with minor modifications in their chemical structure. Although many efforts have been made previously, the characterization of such substances are still challenging because of (1) the continual emergence of newly identified substances, (2) the lack of a universal screening test for NPS that are structurally similar to each other, and (3) the complex and time-consuming chromatographic techniques currently used. Therefore, it is necessary to develop novel analytical methods that can be readily adapted by forensic laboratories to overcome these challenges.
In this dissertation, various analytical techniques have been evaluated for qualitative analysis of these emerging NPS. For rapid screening purposes, a commercial ion mobility spectrometry with a 63Ni ion source (63Ni-IMS) and also direct analysis in real time coupled to a quadrupole time-of-flight mass spectrometer (DART-QTOF-MS) were investigated first. The results showed that rapid detection by 63Ni-IMS and identification by DART-QTOF-MS can be achieved with sub-nanogram detection capability and high speed total analysis time less than two minutes. In recent developments of gas chromatography mass spectrometry (GC-MS), gas chromatography (GC) has been coupled to state-of-the-art mass spectrometers, including triple quadrupole (MS/MS) and quadrupole time-of-flight (QTOF). It was revealed that the application of GC-MS/MS and GC-QTOF facilitates the unambiguous identification of emerging NPS with a chemical ionization (CI) source. In addition, constitutional isomers of NPS were differentiated with the capabilities of product ion scan and multiple reaction monitoring (MRM) modes. Finally, the coupling of IMS with a mass spectrometer (IMS-MS) was investigated as an alternative confirmatory technique. With the development of an optimal solvent system in the electrospray ionization (ESI) process, the rapid analysis and identification of synthetic cathinone was successfully achieved less than five minutes. As a proof-of-concept, seized drugs samples provided by a local forensic laboratory were analyzed using these developed methods by various analytical techniques. The results from these seized samples are also presented in this evaluation.
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Knapman, Thomas William. "Structural analysis of biomolecules by nanoESI and travelling wave ion mobility spectrometry-mass spectrometry." Thesis, University of Leeds, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.535122.
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Harry, Emma. "The development of ion mobility-mass spectrometry for complex mixture analysis." Thesis, Loughborough University, 2011. https://dspace.lboro.ac.uk/2134/9119.
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Multidimensional ion mobility (IM) and mass spectrometry separations have been applied successfully to the analysis of a wide range of analytes and demonstrate potential as a selective and high throughput analytical technique. The direct analysis of pharmaceutical formulations from non-bonded reversed-phase thin layer chromatography (RP-TLC) plates by desorption electrospray ionisation (DESI) combined with drift tube ion mobility-mass spectrometry (IM-MS) has been investigated. The detection of active pharmaceutical ingredients is demonstrated with, and without, chromatographic separation of the active ingredients and formulation excipients. Varying the solvent composition of the DESI spray using a gradient allows selective desorption of pharmaceutical ingredients from the surface of the RP-TLC plate. The potential of IM-MS in combination with high performance liquid chromatography (LC) for the metabonomic analysis of rat urine is reported. The approach allowed the acquisition of nested data sets, with mass spectra acquired at regular intervals during each IM separation and several IM spectra acquired during the elution of an LC peak. The application of LC combined with field asymmetric waveform ion mobility spectrometry (FAIMS) and ion trap mass spectrometry to a metabonomic study of rat urine, with subsequent data mining by artificial neural networks, allowed discrimination between young and old rats on the basis of LC-FAIMS-MS profiles. The application of IM-MS to real-time reaction monitoring has also been investigated. Real-time reaction monitoring was carried out over a period of several hours, with the reaction mixture sampled and analysed at intervals of several minutes. Results indicate that spectral quality is improved when employing IM-MS, compared to mass spectrometry alone, as the complexity of the reaction mixture increases with time. The combined IM-MS approach has potential as a rapid and selective technique to aid pharmaceutical process control and for the elucidation of reaction mechanism.
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Malkar, Aditya. "Analytical methods based on ion mobility and mass spectrometry for metabolomics." Thesis, Loughborough University, 2014. https://dspace.lboro.ac.uk/2134/14524.
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Travelling wave ion mobility spectrometry (TWIMS) in combination with ultra-high performance liquid chromatography (UHPLC) and mass spectrometry (MS) has been applied successfully for the untargeted, global metabolic profiling of biofluids such as mouse plasma and saliva. Methods based on UHPLC-MS alone and in combination with ion mobility spectrometry (UHPLC-IM-MS) have been developed and validated for the untargeted metabolite profiling of saliva, obtained non-invasively by passive drool. Three separate metabolic profiling studies have been carried out in conjunction with bioinformatics strategies to identify potential metabolomic biomarker ions that are associated with efficacy of rice bran in colorectal cancer, physiological stress and that have the potential for the diagnosis of asthma. The advantages offered by the utility of ion mobility in UHPLC-MS based metabolic profiling studies, including the increased analytical space, mass spectral clean-up of contaminants such as PEG post-UHPLC-IM-MS analysis, enhancement of the selectivity of targeted metabolites as well as the potential for the identification of metabolites by comparison of ion mobility drift times have been highlighted. Ten potential metabolic biomarker ions of asthma have been identified from the moderate asthmatics from untargeted metabolite profiling of saliva by UHPLC-MS. A predictive model based on partial least squares discriminant analysis (PLS-DA) has been constructed using these ten discriminant ions, which demonstrates good predictive capability for moderate asthmatics and controls. Potential metabolic biomarker ions of physiological stress have been identified through untargeted metabolite profiling analysis of saliva samples collected before and after exercise by UHPLC-IM-MS. Valerolactam has been identified as a potential biomarker of physiological stress from saliva by comparison of retention time, ion mobility drift time and MS/MS spectra with a standard of δ-valerolactam.
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Du, Chen. "Architectural Characterization of Polyhedral Oligomeric Silsesquioxanes by Ion Mobility Mass Spectrometry." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1525355186538632.
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Solak, Nilüfer. "Structural Characterization and Quantitative Analysis by Interfacing Liquid Chromatography and/or Ion Mobility Separation with Multi-Dimensional Mass Spectrometry." University of Akron / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=akron1270744150.
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Harris, Glenn A. "Fundamentals of ambient metastable-induced chemical ionization mass spectrometry and atmospheric pressure ion mobility spectrometry." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41147.
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Molecular ionization is owed much of its development from the early implementation of electron ionization (EI). Although dramatically increasing the library of compounds discovered, an inherent problem with EI was the low abundance of molecular ions detected due to high fragmentation leading to the difficult task of the correct chemical identification after mass spectrometry (MS). These problems stimulated the research into new ionization methods which sought to "soften" the ionization process. In the late 1980s the advancements of ionization techniques was thought to have reached its pinnacle with both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Both ionization techniques allowed for "soft" ionization of large molecular weight and/or labile compounds for intact characterization by MS. Albeit pervasive, neither ESI nor MALDI can be viewed as "magic bullet" ionization techniques. Both techniques require sample preparation which often included native sample destruction, and operation of these techniques took place in sealed enclosures and often, reduced pressure conditions.
New open-air ionization techniques termed "ambient MS" enable direct analysis of samples of various physical states, sizes and shapes. One particular technique named Direct Analysis In Real Time (DART) has been steadily growing as one of the ambient tools of choice to ionize small molecular weight (< 1000 Da) molecules with a wide range of polarities. Although there is a large list of reported applications using DART as an ionization source, there have not been many studies investigating the fundamental properties of DART desorption and ionization mechanisms.
The work presented in this thesis is aimed to provide in depth findings on the physicochemical phenomena during open-air DART desorption and ionization MS and current application developments. A review of recent ambient plasma-based desorption/ionization techniques for analytical MS is presented in Chapter 1. Chapter 2 presents the first investigations into the atmospheric pressure ion transport phenomena during DART analysis. Chapter 3 provides a comparison on the internal energy deposition processes during DART and pneumatically assisted-ESI. Chapter 4 investigates the complex spatially-dependent sampling sensitivity, dynamic range and ion suppression effects present in most DART experiments. New implementations and applications with DART are shown in Chapters 5 and 6. In Chapter 5, DART is coupled to multiplexed drift tube ion mobility spectrometry as a potential fieldable platform for the detection of toxic industrial chemicals and chemical warfare agents simulants. In Chapter 6, transmission-mode DART is shown to be an effective method for reproducible sampling from materials which allow for gas to flow through it. Also, Chapter 6 provides a description of a MS imaging platform coupling infrared laser ablation and DART-like phenomena. Finally, in Chapter 7 I will provide perspective on the work completed with DART and the tasks and goals that future studies should focus on.
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Adams, Kendra J. "Discovery and Targeted Monitoring of Biomarkers Using Liquid Chromatography, Ion Mobility Spectrometry , and Mass Spectrometry." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3568.
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The complexity of biological matrices makes the detection and quantification of compounds of interest challenging. For successful targeted or untargeted identification of compounds within a biological environment, the use of complementary separation techniques is routinely required; in many situations, a single analytical technique is not sufficient. In the present dissertation, a multidimensional analytical technique was developed and evaluated, a combination of new sample preparation/extraction protocols, liquid chromatography, trapped ion mobility and mass spectrometry (e.g., LC-TIMS-MS and LC-TIMS-MS/MS). The performance of these techniques was evaluated for the detection of polybrominated diphenyl ethers metabolites, polychlorinated biphenyls metabolites in human plasma, opioid metabolites in human urine, and lipids in Dictyostelium discoideum cells. The new workflows and methods described in the body of this dissertation allows for rapid, selective, sensitive and high-resolution detection of biomarkers in biological matrices with increased confidence, sensitivity and shorter sample preparation and analysis time.
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Spencer, John Edward. "ION MOTION AND AN OPTIMIZATION OF TANDEM MASS SPECTROMETRY." UKnowledge, 2005. http://uknowledge.uky.edu/gradschool_theses/211.
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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.
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Benigni, Paolo. "Trapped Ion Mobility Spectrometry coupled to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for the analysis of Complex Mixtures." FIU Digital Commons, 2017. https://digitalcommons.fiu.edu/etd/3547.
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Analytical Characterization of complex mixtures, such as crude oil, environmental samples, and biological mixtures, is challenging because of the large diversity of molecular components. Mass spectrometry based techniques are among the most powerful tools for the separation of molecules based on their molecular composition, and the coupling of ion mobility spectrometry has enabled the separation and structural elucidation using the tridimensional structure of the molecule. The present work expands the ability of analytical chemists by furthering the development of IMS-MS instrumentation by coupling Trapped Ion Mobility Spectrometry to Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (TIMS-FT-ICR MS). The TIMS-FT-ICR MS platform combines the high-resolution separation of TIMS, which has mobility resolving powers up to 400, and ultra-high mass resolution of FT-ICR MS, with mass resolving power over 1,000,000. This instrumentation allows the assignment of exact chemical composition for compounds in a complex mixture, as well as measurement of the collision cross-section of the molecule. Herein, the principles of the TIMS separation and its coupling to FT-ICR MS are described, as well as how the platform can be applied to targeted analysis of molecules, and untargeted characterization of complex mixtures.
Molecular standards were analyzed by TIMS-MS in order to develop a computational workflow that can be utilized to elucidate molecular structure, using the measured collision cross-section of the ion. This workflow enabled identification of structural, cis/trans isomers, and chelated molecules and provides the basis for unsupervised structural elucidation of a complex mixture, and in particular for the elucidation of hydrocarbons from fossil fuels. In summary, this work presents the coupling of TIMS-FT-ICR MS and provides examples of applications as a proof of concept of the potential of this platform for solving complex analytical challenges.
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Jin, Lan. "Investigating glycosaminoglycan conformations by ion mobility mass spectrometry and nuclear magnetic resonance." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/12304.
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The aim of this project is to develop and test methodologies for conformational studies of free and bound GAGs. Gas phase conformations of heparin-derived oligosaccharides were studied by using Ion Mobility Mass Spectrometry (IMMS) and molecular modelling. Gas phase conformations were modelled using the AMBER force field. Their theoretical collision cross-sections were compared with the IMMS data and a good agreement was obtained. The gas phase conformations of heparin oligosaccharides were more compact than those observed in solution or crystal structures of heparin-protein complexes. This was attributed to the effects of sodium cations interacting with the negatively charged sulphate and carboxyl groups of oligosaccharides. Adiabatic maps of dihedral angles vs. potential energy of disaccharide fragments of the tetrasaccharides were calculated in the absence of the sodium cations. New NMR methods for the measurement of scalar and dipolar 1H-1H coupling constants and 13C-13C coupling constants in natural abundance 13C samples were developed. Performance of these methods was tested extensively. Solution conformation of the fully sulphated heparin-derived tetrasaccharide was studied by NMR spectroscopy. 1H-1H scalar coupling constants were used to characterize the dynamic equilibria of flexible monosaccharide rings. 1H-1H and 1H-13C RDCs were used in the study of the conformation of the glycosidic linkages. RDC-refined structures were obtained from molecular dynamics with explicit water and sodium cations. Interactions of the heparin-derived fully sulphated tetrasaccharide with factor H modules, fH~19, 20 and fH~7, were studied using AUTODOCK. Conformation of a spin-labelled heparin-derived fully sulphated disaccharide was studied by NMR and molecular modelling.
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Sivalingam, G. N. "Advances in computational ion mobility mass spectrometry : with application to α1-antitrypsin." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1467251/.
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A new method for deconvolution of electrospray ionisation mass spectrometry (ESI-MS) spectra was produced, allowing for the masses of overlapping charge state series to be correctly indentified. The algorithm also determines the abundance of individual molecular species with a much higher accuracy for congested spectra. Several new methods for representing TWIM-MS data were developed. The combination of the deconvolution algorithm with travelling wave ion mobility data creates plots with collision cross section (CCS) axes which can be directly compared with X-ray crystallography structures and computational models. Difference plots have allowed multidimensional analysis of changes in condition, and spectral averaging can produce a single representative spectrum from multiple replicates. Gas-phase unfolding experiments using TWIM-MS are a popular method for probing protein stability in response to conditions such as ligand binding. The algorithms for processing these data are however in their infancy. This thesis describes the first deconvolution algorithm for gas-phase unfolding data, allowing for the accurate interpretation of conformation cross sections and abundances during the unfolding procedure. The methodologies developed were then applied to 1-antitrypsin, a metastable, aggregation prone protein. The protein was bound to a ligand, Ac- TTAI-NH2, which has been shown to block aggregation as a titration and the MS deconvolution method was used to quantify the abundances of each bound state in each mass spectrum. The first use of IM-MS to analyse ex vivo aggregates are shown, and the ion mobility methods created were used to determine the CCS values of the monomeric and dimeric species. The interaction between 1-antitrypsin and Ac-TTAI-NH2 was probed using gas-phase unfolding experiments, determining that the ligand stabilises the protein, with a specific pattern of gas-phase unfolding observed for each state.
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Lapthorn, Cristian Lewis. "The application of ion mobility mass spectrometry to molecules of pharmaceutical significance." Thesis, University of Greenwich, 2016. http://gala.gre.ac.uk/18125/.
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Ion mobility-mass spectrometry experiments have been conducted to measure the drift-time and calculate collision cross-sections (CCSs) using travelling wave ion mobility spectrometry, and determine the CCS using drift-tube ion mobility spectrometry systems of analytes. The aim of the study was to identify if predictive approaches could facilitate rapid and definitive assignment of charge location sites and chemical structure. Molecular modelling was conducted to determine the energy minimised/geometry optimised structures and charge distribution of the protonated molecules studied. The geometry and charge distribution data were utilised in subsequent ion mobility calculations using two main methods 1) projection approximation and 2) trajectory method. Fluoroquinolone antibiotics were investigated as previous literature had postulated the ion mobility separation of charge location isomers differing only by their protonation site with little expected difference in their geometry (see Chapter 2). Projection approximation prediction of theoretical CCSs (tCCSs) for the singly protonated molecules of norfloxacin (with the proton assigned to all possible oxygen or nitrogen-containing protonation sites to generate candidates) revealed < 2 Å2 difference in tCCSs based on molecular modelling. In stark contrast the experimental CCS (eCCS) demonstrated > 10 Å2 difference between different components. The product ion spectra are consistent with the hypothesis of charge location isomer mobility separated components. Investigations with other fluoroquinolones, with both drift-tube ion mobility and travelling wave ion mobility, and using the trajectory method, remain consistent with the hypothesis of charge location isomers (see Chapter 3). A larger scale study sought to probe the accuracy of tCCSs over a large number of small molecule drug structures. If tCCSs accurately predict eCCSs, then tCCSs could be used to identify compounds and isomers based on their CCSs (see Chapter 4). Finally, software was developed to considerably accelerate the calculation of trajectory method tCCSs from 8-100 times faster than existing published approaches depending on available computing infrastructure (see Chapter 5). In summary this research project has explored whether eCCSs and tCCSs may be useful as a key structural tool alongside other traditional measurements including chromatographic retention time and m/z.
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Fuller, Daniel Raymond. "Probing Structure and Stability of Biomolecules with Ion Mobility-mass Spectrometry Techniques." Thesis, Indiana University, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10844168.
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Ion mobility spectrometry – mass spectrometry (IMS-MS) based techniques have significantly advanced the study of both the structure and stability of biomolecules. Solution phase, biologically relevant peptide/protein conformations have been analyzed utilizing electrospray ionization (ESI) coupled to IMS-MS. The work presented here focuses on the development and application of IMS-MS for the study of the structure and stability of peptides and proteins. Structures originating in solution can be related to the biological activity of the system. Specifically, we examine the influence of both proline isomerization and metal binding on the conformational preferences and stabilities of a series of peptides and proteins.
The first study uses IMS-MS to examine the conformation specific binding of Zn2+ to oxytocin (OT). When bound to Zn, OT has an increased affinity for its receptor. We observe two conformations which are the result of the cis-trans orientation of the Cys6-Pro 7 bond. We find that Zn2+ binds preferentially to the trans configuration demonstrating that cis-trans isomerization regulates the binding of Zn2+ to OT, therefore linking the orientation of the Cys6-Pro7 bond to the biological activity of the molecule. In another series of experiments, we look at the role of penultimate proline on the stability of bradykinin along with a library of penultimate proline containing peptides. For BK, we find that the Pro2-Pro3 bond, which is enzymatically resistant, is cleaved with 100% specificity when incubated at high temperatures. With IMS-MS, we are able to monitor the mass spectral and conformational changes as a function of time, and find that cis-trans isomerization of a single bond regulates the rate of dissociation, and hence the stability of the system. Finally, we look at the thermal stability of the insulin-zinc hexamer complex. Utilizing temperature-controlled nano-ESI IMS-MS, we capture the dissociation of the insulin hexamer and the unfolding of insulin dimer and monomer, occurring simultaneously with increasing solution temperature. We show the ability of IMS-MS to observe the conformation specific melting temperatures of a protein complex, demonstrating a fast and sensitive assay for stability characterization.
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Da, Costa Caitlyn. "Applications of desorption electrospray ionisation mass spectrometry and ion mobility spectrometry to petroleomic and lubricant analysis." Thesis, Loughborough University, 2016. https://dspace.lboro.ac.uk/2134/21617.
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The use of mass spectrometry for the analysis of petrochemical products and crude oils enables the generation of detailed molecular data essential for chemical characterisation and product development. However, the need for multistage sample preparation techniques can be time consuming and may result in the loss of information. Ambient ionisation in combination with mass spectrometry enables the direct analysis of compounds present on a surface with minimal or no sample preparation. The work presented in this thesis evaluates the application of mass spectrometry (MS) hyphenated with ambient ionisation and ion mobility for the analysis of chemical additives used in lubricant and petrochemical products and also crude oil. A technique called desorption electrospray ionisation (DESI) pioneered the ambient ionisation field. An in-house designed and constructed DESI source has been developed to enable hyphenation of DESI with MS and ion-mobility mass spectrometry (IM-MS) for the interrogation of chemical additives used in lubricant and petrochemical oils directly from multiple surface substrates. The approach has been successfully applied to the analysis of a range of chemical additives as standards and when present in a lubricating oil matrix. Data has also shown that DESI-MS can be used to map additive deposition on a surface. The quantitative capabilities of DESI-MS have been assessed using a lubricant antioxidant additive present in a lubricant oil matrix and deposited on a surface. The DESI-MS method showed good linearity with a limit of detection (LOD) for the antioxidant additive below that used in typical commercial formulations. The use of a suitable internal standard in the DESI-MS analysis has been shown to significantly improve the repeatability of the approach. Hyphenation of DESI with post ionisation separation methods, such as high field asymmetric waveform ion mobility spectrometry (FAIMS), can improve mass spectral response for targeted analytes through selective transmission. The analysis of a series of corrosion inhibitor additives in a base oil matrix has been carried out using electrospray (ESI) and DESI hyphenated with FAIMS-MS. FAIMS selection of target ions improved the sensitivity of ESI and DESI through enhanced analyte transmission and a reduction in the chemical noise resulting from the oil matrix. DESI-FAIMS-MS was shown to improve target analyte response compared to DESI-MS alone using the corrosion inhibitors as model compounds, showing how the combined technique can be used for the rapid analysis of analytes directly from surfaces with no sample preparation or pre concentration. Direct analysis in real time (DART) is an alternative ambient ionisation approach to DESI. The use of DART-MS for the direct analysis of lubricant and oil additives has been evaluated. All selected additives were successfully detected by DART-MS as standards and in an oil matrix. The surface material, DART helium gas temperature and the presence of an oil matrix were all shown to effect the desorption and ionisation of target analytes. The quantitative capabilities of DART-MS were assessed using the antioxidant additive in a lubricant oil matrix and in the presence of an internal standard. The technique showed good linearity and repeatability. The untargeted analysis of chemical additives present in a fully formulated lubricant oil has been carried out by DESI and DART ionisation techniques. The effect of DESI electrospray solvent and DART helium temperature were both shown to impact the observed mass spectral response for the sample. The analysis of crude oil is particularly problematic due to the high complexity of the sample. A crude oil sample has been analysed using ESI combined with high resolution MS, ESI-FAIMS-MS and DESI-MS. High resolution mass spectrometry enabled the identification of molecular ions that could be characterised using specialist software. The use of FAIMS resulted in shift in the observed chemical profile for the crude oil sample showing selective transmission of molecular species based upon the differential mobility of ions rather than factors such as polarity or solubility that are typically used for sample fractionation. Molecular species from within the crude oil sample were successfully desorbed and ionised by DESI-MS using a DESI solvent composition of 6:4 toluene:methanol.
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Zhao, Qin. "Development of ion mobility mass spectrometry coupled with ion/ion reactions instrumentation and applications for protein analysis /." [Ames, Iowa : Iowa State University], 2009.
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Harvey, Sophie Rebecca. "Biophysical studies into the structure and interactions of proteins and peptides." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9654.
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Investigating the structure of proteins and their interactions with other biomolecules or drug molecules, coupled with the consideration of conformational change upon binding, is essential to better understand their functions. Mass spectrometry (MS) is emerging as a powerful tool to study protein and peptide structure and interactions due to the high dynamic range, low sample consumption and high sensitivity of this technique, providing insight into the stoichiometry, intensity and stability of interactions. The hybrid technique of ion mobility-mass spectrometry (IM-MS) can provide insight into the conformations adopted by protein and peptide monomers and multimers, in addition to complexes resulting from interactions, which when coupled with molecular modelling can suggest candidate conformations for these in vacuo species and by inference their conformations in solution prior to ionisation and desolvation. The work presented in this thesis considers a number of different peptide and protein systems, highlighting how the combination of MS and IM-MS based techniques, in conjunction with other biophysical techniques such as circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM) and isothermal titration calorimetry (ITC) can provide insight into these dynamic systems. First a case study into the ability of MS and IM-MS to study disorder-to-order transitions is presented. The transcription factor c-MYC can only perform its function upon binding with its binding partner MAX; deregulation of c-MYC is, however, implicated in a number of human cancers. c-MYC and MAX comprise intrinsically disordered regions which form a leucine zipper upon binding. The work presented here focuses on the leucine zipper regions of both c-MYC and MAX, their individual conformations and changes upon binding. Inhibiting the c-MYC:MAX interaction is a current target for drug therapy and hence the inhibition of this interaction with a previously identified small drug-like molecule was also examined using these techniques, to determine if such an approach may be appropriate for investigation of future therapeutics. Next the ability of MS-based techniques to preserve, transmit and distinguish between multiple conformations of a metamorphic protein was examined. The chemokine lymphotactin has been shown to exist in two distinct conformations in equilibrium in a ligand-free state. The existence of such metamorphic proteins has called into question whether traditional structural elucidation tools have been inadvertently biased towards consideration of single conformations. Here, the potential of gas-phase techniques in the study of conformationally dynamic systems is examined through the study of wild type lymphotactin and a number of constructs designed either as a minimum model of fold or to mimic one of the distinct folds. Interactions between chemokines and glycosaminoglycans (GAGs) are thought to be essential for the in vivo activity of these proteins. The interactions between the distinctive chemokine lymphotactin and a model GAG were hence probed. As with the structural studies, additional protein constructs were considered either to represent the minimum model of fold, one distinct fold of the metamorphic protein or designed to diminish its GAG binding propensity. The ability of each construct to bind GAGs, the stoichiometry of the interactions and conformations adopted by the resulting complexes in addition to aggregation occurring upon the introduction of the GAG is considered. Finally, the similarities, with respect to structure and function, between the chemokine superfamily of proteins and the human β-defensin subfamily of antimicrobial peptides are considered. The tendency of human β-defensins 2 and 3 to bind a model GAG is examined; the stoichiometry of binding and conformations adopted and aggregation occurring here are considered and compared with that of chemokines.
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Alexander, Nicolas Edward. "Multidimensional Mass Spectrometry of Amphiphilic Systems." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1532773038466757.
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Molano-Arévalo, Juan Camilo. "Conformational Dynamics of Biomolecules by Trapped Ion Mobility Spectrometry Dynamics." FIU Digital Commons, 2018. https://digitalcommons.fiu.edu/etd/3647.
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One of the main goals in structural biology is to understand the folding mechanisms and three-dimensional structure of biomolecules. Many biomolecular systems adopt multiple structures as a function of their microenvironment, which makes them difficult to be characterized by traditional structural biology tools (e.g., NMR, X-ray crystallography). As an alternative, complementary tools that can capture and sample multiple conformations needed to be developed. In the present work, we pioneered the application of a new variant of ion mobility spectrometry, trapped ion mobility spectrometry (TIMS), which provides high mobility resolving power and the possibility to study kinetically trapped intermediates as a function of the starting solution (e.g., pH and organic content) and gas-phase conditions (e.g., collisional activation, molecular dopants, hydrogen/deuterium back-exchange). When coupled to mass spectrometry (TIMS-MS), action spectroscopy (IRMPD), molecular dynamics and biochemical approaches (e.g., fluorescence lifetime spectroscopy), a comprehensive description of the biomolecules dynamics and tridimensional structural can be obtained. These new set of tools were applied for the first time to the study of Flavin Adenine Dinucleotide (FAD), Nicotineamide Adenine Dinucleotide (NAD), globular protein cytochrome c (cyt c), the 31 knot YibK protein, 52 knot ubiquitin C terminal hydrolase (UCH) protein, and the 61 knot halo acid dehydrogenase (DehI) protein.
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Birdwell, David. "Soft Landing Ion Mobility Mass Spectrometry: History, Instrumentation and an Ambient Pressure Application." Thesis, University of North Texas, 2010. https://digital.library.unt.edu/ark:/67531/metadc33136/.
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Preparative mass spectrometry is an important method for the synthesis of new materials. Recently, soft landing mass spectrometry has been used to land ions on surfaces to coat or otherwise alter them. Commercial soft landing instruments do not yet exist, and the physical phenomenon of soft landing has not yet been fully described. For future ion mobility soft landing research, the theory of ion mobility, ion optics and soft landing is discussed, and 2 soft landing instruments have been built and described, along with proof of concept experiments for both instruments. Simulations of the process of ion mobility and ion optics for use in these instruments, as well as some preliminary results for the optics are included. Surfaces described include copper on mica and iron on silicon. Self assembly of soft landed ions is observed on the surfaces.
The instruments constructed will be useful for future soft landing research, and soft landing can be used for future materials research with special attention focused on the self-assembly of the landed ions.
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Aguilar, Ayala Roberto. "Applications of Metallic Clusters and Nanoparticles via Soft Landing Ion Mobility, from Reduced to Ambient Pressures." Thesis, University of North Texas, 2018. https://digital.library.unt.edu/ark:/67531/metadc1248434/.
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Nanoparticles, simple yet groundbreaking objects have led to the discovery of invaluable information due to their physiological, chemical, and physical properties, have become a hot topic in various fields of study including but not limited to chemistry, biology, and physics. In the work presented here, demonstrations of various applications of chemical free nanoparticles are explored, from the determination of a non-invasive method for the study of the exposome via using soft-landing ion mobility (SLIM) deposited nanoparticles as a matrix-assisted laser desorption/ionization (MALDI-MS) matrix replacement, to the direct SLIM-exposure of nanoparticles onto living organisms. While there is plenty of published work in soft-landing at operating pressures of 1 Torr, the work presented here shows how this technology can be operated at the less common ambient pressure. The ease of construction of this instrument allows for various modifications to be performed for a wide array of applications, furthermore the flexibility in metallic sample, operating pressure, and deposition time only open doors to many other future applications. The work presented will also show that our ambient SLIM system is also able to be operated for toxicological studies, as the operation at ambient pressure opens the door to new applications where vacuum conditions are not desired.
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Hopper, Jonathan T. S. "Studying protein-ligand complexes in the gas-phase using ion mobility-mass spectrometry." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.576159.
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This thesis presents studies which investigate the application of electrospray ionisation-mass spectrometry (ESI-MS) to non-covalent protein-ligand complexes. The structural effect of desolvation on protein-ligand (P-L) complexes has been a hotly debated issue in this field and has been examined in this work. Single point mutagenesis has allowed specific non-covalent interactions to be probed as well as their contribution to gas-phase protein- ligand stability. Results suggest that these specific interactions are preserved in the gas-phase using ESI. Other solution based effects that result from ligand binding, such as increased protein structural stability, was also confirmed in the gas-phase. A combination of collisional activation and ion mobility spectrometry is presented as an approach capable of probing such subtle stability differences. Some discrepancies between the behaviour of protein- ligand complexes in solution and the gas-phase are also presented and highlight potential areas of caution in certain biological systems. Common alkali metal adducts have been shown to severely decrease the stability of protein-ligand complexes in the gas-phase, possibly by a Coulomb assisted dissociation mechanism. Novel approaches to allow greater control of charge state distributions, without the requirement of instrumental modifications, are also presented. Reducing the charge state of protein complexes in the gas-phase allows weak interactions to be more readily preserved and more accurate affinity measurements to be made. The approach is also confirmed to reduce the amount of alkali metal adduction observed in protein ions generated by ESI.
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Wright, Victoria E. "Ion mobility-mass spectrometry studies of organic and organometallic complexes and reaction monitoring." Thesis, Loughborough University, 2013. https://dspace.lboro.ac.uk/2134/14275.
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Ion mobility (IM) spectrometry is a gas-phase electrophoretic technique in which ions are separated on the basis of their relative mobility in the presence of a weak electric field gradient and a buffer gas. Ion mobility-mass spectrometry (IM-MS) has the capability of separating ions based on m/z, size and shape, providing additional structural information compared to using mass spectrometry on its own. In this thesis, IM-MS has been used to investigate organic and organometallic complexes and identify reactants, intermediates and products in reaction mixtures. Collision cross sections (CCS) have been measured for three salen ligands, and their complexes with copper and zinc using travelling-wave ion mobility-mass spectrometry (TWIMS) and drift tube ion mobility-mass spectrometry (DTIMS), allowing a comparative size evaluation of the ligands and complexes. CCS measurements using TWIMS were determined using peptide and TAAH calibration standards with good intra-day and inter-day reproducibility. TWIMS measurements gave significantly larger CCS than DTIMS derived data in helium, indicating that the choice of calibration standards is important in ensuring the accuracy of TWIMS derived CCS measurements. The CCS data obtained from IM-MS measurements have been compared to CCS values obtained from X-ray coordinates and modelled structures. The analysis of small organic and organometallic molecules has been extended to investigations of the potential of IM-MS for reaction monitoring and structural studies of the components of catalytic cycles. Reaction mixtures of an organocatalysed Diels-Alder cycloaddition reaction have been monitored using IM-MS and high-field asymmetric waveform ion mobility-mass spectrometry (FAIMS-MS). Reactant, product, catalyst and reaction intermediates, including an intermediate not previously detected, were identified and the catalyst and intermediates monitored over time. An organometallic catalytic cycle using a palladium catalyst has been analysed using IM-MS and the CCS of reactants, intermediates and products have been measured and compared to theoretical CCS calculations. Good agreement was observed between measured and calculated data. Species not amenable to electrospray ionisation were covalently bound to an ionisable tag containing a quaternary ammonium ion allowing the tagged molecules to be detected by IM-MS.
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Jurneczko, Ewa. "Resolving intrinsically disordered proteins of the cancer genome with ion mobility mass spectrometry." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8844.
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For proteins the link between their structure and their function is a central tenet of biology. A common approach to understanding protein function is to ‘solve’ its structure and subsequently probe interactions between the protein and its binding partners. The first part of this approach is non-trivial for proteins where localised regions or even their entire structure fail to fold into a three-dimensional structure and yet they possess function. These so called intrinsically or inherently disordered proteins (IDP’s) or intrinsically disordered regions (IDR’s) constitute up to 40% of all expressed proteins. IDPs which have crucial roles in molecular recognition, assembly, protein modification and entropic chain activities, are often dynamic with respect to both conformation and interaction, so in the course of a protein’s ‘lifespan’ it will sample many configurations and bind to several targets. For these proteins, there is a need to develop new methods for structure characterization which exploit their biophysical properties. The solvent free environment of a mass spectrometer is ideally suited to the study of intrinsic interactions and how they contribute to structure. Ion mobility mass spectrometry is uniquely able to observe the range of structures an IDP can occupy, and also the effect of selected binding partners on altering this conformational space. This thesis details the technique of ion mobility mass spectrometry and illustrates its use in assessing the relative disorder of p53 protein. The tumour suppressor p53 is at the hub of a plethora of signalling pathways that maintain the integrity of the human genome and regulate the cell cycle. Deregulation of this protein has a great effect on carcinogenesis as mutated p53 can induce an amplified epigenetic instability of tumour cells, facilitating and accelerating the evolution of the tumour. Herein mass spectrometry provides a compelling, detailed insight into the conformational flexibility of the p53 DNA-binding domain. The plasticity of the p53 DNA-binding domain is reflected in the existence of more than one conformation, independent of any conformational changes prompted by binding. The in vacuo conformational phenotypes exhibited by common cancer-associated mutations are determined and the second-site suppressor mutation from loop L1, H115N, is probed whether it could trigger conformational changes in p53 hotspot cancer mutations. The structural basis of the binding promiscuity of p53 protein is investigated; of particular interest is the molecular interaction of the p53 N-terminus with the oncoprotein murine double minute 2, as well as with the antiapoptotic factor B-cell lymphoma-extralarge.
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Frerichs, Niklas. "Ion mobility mass spectrometry as a powerful tool to analyze complex macromolecular systems." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://hdl.handle.net/21.11130/00-1735-0000-0005-1560-7.
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Smith, Robert W. "An evaluation of miniaturised field asymmetric waveform ion mobility spectrometry hyphenated with time-of-flight mass spectrometry." Thesis, Loughborough University, 2014. https://dspace.lboro.ac.uk/2134/17837.
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In this thesis, the performance of a miniaturised field asymmetric waveform ion mobility spectrometry (FAIMS) device hyphenated with time-of-flight mass spectrometry is studied and evaluated for analysis of a variety of compounds in different sample matrices. FAIMS is a selective spectrometer which is highly orthogonal to mass spectrometry and has the potential for enhancing sensitivity and improve selectivity of rapid analyses. In Chapter 2, the performance of the miniaturised FAIMS device is tested for stability and transmission under a wide range of ion source conditions. An investigation of three different systems, including pairs of isobaric, isomeric and near-mass ions shows that miniaturised FAIMS has the ability to distinguish between analytes that are challenging to separate by mass spectrometry. Chapter 3 explores the effect of changing the composition of the carrier gas by observing the effect of adding gas modifiers on the FAIMS spectra of small molecules, peptides and proteins. Chapter 4 investigates the advantages of combining a fast FAIMS separation with mass spectrometry in the analysis of nitrogen-containing pharmaceutical impurities, where FAIMS is found to offer additional selectivity. In Chapter 5, the development of a UHPLC-FAIMS-MS method for the quantitative determination of a drug metabolite in urine is reported. UHPLC-FAIMS-MS shows improvements in signal-to noise and linear dynamic range as well as a reduction in chemical noise, demonstrating the potential of combining FAIMS with mass spectrometry.
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Young, Lydia Mary. "Defining the mechanism of small molecule inhibition of amyloid fibril formation using ion mobility spectrometry-mass spectrometry." Thesis, University of Leeds, 2015. http://etheses.whiterose.ac.uk/11887/.
Full textAbstract:
The study of protein/peptide folding, misfolding, structure, and interactions are vital to understanding complex biological problems. The work presented in this thesis describes the development and application of mass spectrometry -based techniques to investigate protein structure, aggregation and interference with aggregation, providing insights into the self-assembly and inhibition of several disease-related peptides. Mass spectrometry has evolved significantly over the past decade, its applications varying from small molecules to macromolecules. Travelling wave ion mobility spectrometry (TWIMS), when combined with mass spectrometry (MS), has the unique and unrivalled capability of separating molecular ions based on their collision cross-sectional area in addition to their mass-to-charge ratio, thus facilitating structural studies of co-populated protein conformations and structural isomers of protein complexes that cannot be separated by molecular weight alone. One biological system that has benefitted enormously from such advances is the study of in vitro amyloid formation. The ability of amyloidogenic protein/peptides to assemble into insoluble fibrils is the basis of a vast array of human disorders. Human islet amyloid polypeptide (hIAPP) is one such peptide able to readily assemble into amyloid fibrils in vitro at neutral pH, despite being intrinsically disordered. Identifying oligomeric states occupied between monomer and final fibrils creates an enormous challenge, given that few techniques are able to separate and characterise such lowly-populated and transient species. In addition to characterisation of fibril precursors, recent research has focussed on the identification of small molecule inhibitors of the amyloid cascade and understanding their mechanism of action is of great interest to this field. In the work presented here, the power of TWIMS-MS has been harnessed to achieve the separation and characterisation of oligomeric precursors of the type-2 diabetes-related peptide hIAPP along with IAPP mutants and peptides corresponding to its core sequence. In addition, the effects of small molecule inhibitors on oligomer population and fibril formation have been studied and described in detail. Further, an experimentally simple, in vitro MS-based screen has been developed and implemented that provides rapid and accurate analysis of protein aggregation and its inhibition. All of the results highlight the powers of MS to provide important insights into the mechanism of amyloid formation and demonstrate the potential of this approach for screening for novel inhibitors of disease-related amyloid assembly.
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Alawani, Nadrah. "Structural Characterization of Synthetic Polymers and Copolymers Using Multidimensional Mass Spectrometry Interfaced with Thermal Degradation, Liquid Chromatography and/or Ion Mobility Separation." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1386591497.
Full text
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Verbeck, Guido Fridolin. "Development of a variable-temperature ion mobility/ time-of-flight mass spectrometer for separation of electronic isomers." Texas A&M University, 2005. http://hdl.handle.net/1969.1/2310.
Full textAbstract:
The construction of a liquid nitrogen-cooled ion mobility spectrometer coupled
with time-of-flight mass spectrometry was implemented to demonstrate the ability to
discriminate between electronic isomers. Ion mobility allows for the separation of ions
based on differing cross-sections-to-charge ratio. This allows for the possible
discrimination of species with same mass if the ions differ by cross-section. Time-offlight
mass spectrometry was added to mass identify the separated peak for proper
identification.
A liquid nitrogen-cooled mobility cell was employed for a two-fold purpose.
First, the low temperatures increase the peak resolution to aid in resolving the separated
ions. This is necessary when isomers may have similar cross-sections. Second, low
temperature shortens the mean free path and decreases the neutral buffer gas speeds
allowing for more interactions between the ions and the drift gas. Kr2+ study was
performed to verify instrument performance.
The variable-temperature ion mobility spectrometer was utilized to separate the
distonic and conventional ion forms of CH3OH, CH3F, and CH3NH2 and to discriminate
between the keto and enol forms of the acetone radical cation. Density functional theory
and ab initio calculations were employed to aid in proper identification of separating
isomers. Monte Carlo integration tools were also developed to predict ion cross-section
and resolution within a buffer gas.
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Gray, Christopher. "Comprehensive stereochemical sequencing of carbohydrates and characterisation of their binding partners using hyphenated mass spectrometry methods." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/comprehensive-stereochemical-sequencing-of-carbohydrates-and-characterisation-oftheir-binding-partners-using-hyphenated-mass-spectrometry-methods(0f606678-b7d1-4a5c-817a-fff2b9fab90a).html.
Full textAbstract:
Glycans and their conjugates form the largest and most diverse class of biological molecules found within nature. These glycosides are vital for numerous cellular functions including recognition events, protein stabilisation and energy storage, to name a few. Additionally, abnormalities within these structures are associated with a wide range of disease states. As a result, robust analytical techniques capable of in depth characterisation of carbohydrates and their binding partners are required. Currently, liquid chromatography coupled with tandem mass spectrometry (MS2) is the 'gold standard' for characterising these species. However there are inherent challenges for 'sequencing' carbohydrates given that most structures are diastereomeric. As a result MS alone is insufficient to fully elucidate all stereochemical and often regiochemical information and alternative analytical techniques have inherent issues meaning that they are not suitable for medium/high throughput analysis. To facilitate elucidation of these structures, ion mobility spectrometry (IMS) has been used in-line with MS2. IMS of mono- and di-saccharide product ions generate by collision-induced dissociation (CID) of various glycans and their conjugates enables unambiguous identification of the monomer and the regio-/stereo-chemistry of the glycosidic bond, independent of the precursor structure. Also, given the prominence of glycans in biological recognition events, high-throughput techniques capable of elucidating and characterising carbohydrate to glycan-binding protein (GBP) interactions are highly sought after. Historically, (micro)array strategies are employed to screen large numbers of biological interactions, with detection conventionally achieved with fluorescent tagging. The major disadvantage of this approach is the requirement of a labelling step to facilitate detection of glycan-GBP binding. MS offers the ability to unambiguously identify GBPs when combined with routine bottom-up proteomics strategies, namely on-chip proteolysis followed by mass fingerprinting and MS2 analysis and subsequent comparison to protein databases. It is anticipated that these methodologies developed throughout these studies, both for carbohydrate sequencing and the characterisation of glycan-binding proteins, will greatly add to the Glycomics toolbox.