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Dissertations / Theses on the topic 'Tandem mass spectrometry'

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Published: 4 June 2021

Last updated: 19 October 2024

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1

Offei, Felix. "Denoising Tandem Mass Spectrometry Data." Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etd/3218.

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Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of noisy data with the hope of aiding in better identification of proteins. We employ the method of binning to reduce the number of noise peaks in the data without sacrificing the alignment of the observed spectrum with the theoretical spectrum. In some cases, the alignment of the two spectra improved.

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2

Dabney, David E. "Analysis of Synthetic Polymers by Mass Spectrometry and Tandem Mass Spectrometry." University of Akron / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=akron1259021862.

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3

Jackson, Anthony Trevor. "Tandem mass spectrometry of polymeric materials." Thesis, University of Warwick, 1995. http://wrap.warwick.ac.uk/44296/.

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Mass spectrometry and tandem mass spectrometry (MS/MS) has been employed to analyse peptides (<600 daltons), synthetic polymers of low molecular weight (<10,000 daltons) and a mixture of polymer additives (300-1200 daltons). Mass spectrometry experiments were performed on a four sector mass spectrometer, a tandem quadrupole mass spectrometer and a time-of-flight instrument. High and low energy collision induced dissociation (CID) spectra were obtained by means of a four sector mass spectrometer and a tandem quadrupole instrument respectively. Surface induced dissociation (SID) spectra of peptides were obtained by means of a four sector mass spectrometer with a modified collision cell in the third field free region. Sequence data were generated by SID from protonated and cationated precursor ions of all four peptides analysed. Furthermore, broad metastable ion peaks were observed in the spectra, arising from fragmentation of precursor ions in the field free region between the electric sector and the magnetic sector of the second mass spectrometer. Field desorption was a good ionisation technique for the generation of molecular weight information from the polymer additives used. High energy eID was found to be more applicable than low energy eID to the structural determination of polymer additives as characteristic ions were observed in the spectra. Mechanisms have been proposed for the generation of some of the fragment ions observed. Ultraviolet-matrix assisted laser desorptionlionisation spectra of synthetic polymers of low molecular weight (<10,000 daltons) were used to calculate molecular weight averages. Furthermore, end group information was also obtained from CID spectra of the same polymer samples. End group and structural information was also obtained from polystyrene and a substituted polystyrene by means of FD-MS/MS.

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4

Goodwin, Lee. "Capillary electrophoresis-mass spectrometry and tandem mass spectrometry studies of ionic agrochemicals." Thesis, University of York, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.398906.

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5

Hsi, Kuang-Ying. "Peptide identification of tandem mass spectrometry from quadrupole time-of-flight mass spectrometers." Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p1462246.

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Thesis (M.S.)--University of California, San Diego, 2009.
Title from first page of PDF file (viewed May 4, 2009). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 45-46).

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6

Frank, Ari Michael. "Algorithms for tandem mass spectrometry-based proteomics." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3307704.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed August 13, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 187-205).

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7

Beisken, Stephan Andreas. "Informatics for tandem mass spectrometry-based metabolomics." Thesis, University of Cambridge, 2014. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708325.

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8

Liu, Xiumin. "Mass Spectrometry and Tandem Mass Spectrometry Analysis of Polymers and Polymer-Protein Interactions." University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1406838246.

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9

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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10

Roos, Felix Franz. "Algorithms for peptide identification by tandem mass spectrometry /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16844.

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11

Summerfield, Scott Graham. "The tandem mass spectrometry of oligopeptides and proteins." Thesis, University of Warwick, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308504.

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12

Mohan, Krishnan R. "Fast atom bombardment mass spectrometry and tandem mass spectrometry : conditions for measurement of reproducible spectra." Thesis, Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/27159.

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13

Catron, Brittany Lyn. "Analysis of Protein:RNA Cross-links by Inductively Coupled Plasma Mass Spectrometry and Tandem Mass Spectrometry." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1337885809.

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14

Chaicharoen, Kittisak. "Mass and Tandem Mass Spectrometric Studies on Synthetic Polymers." University of Akron / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=akron1217533390.

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15

Crnogorac, Goranka. "Analysis of dithiocarbamate fungicide residues by liquid chromatography, mass spectrometry and isotope ratio mass spectrometry." Aachen Shaker, 2008. http://d-nb.info/993691447/04.

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16

Cunningham, Connell Glish Gary L. "Improved methods of tandem mass spectrometry for proteomics applications in a quadrupole ion trap mass spectrometer." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2006. http://dc.lib.unc.edu/u?/etd,217.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2006.
Title from electronic title page (viewed Oct. 10, 2007). " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry. Chapel Hill 2006." Discipline: Chemistry; Department/School: Chemistry.

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17

Jiang, Jian Borchers Christoph H. "Immuno tandem mass spectrometry iMALDI assay for clinical diagnostics." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1456.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.
Title from electronic title page (viewed Apr. 25, 2008). " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Curriculum of Applied and Materials Sciences." Discipline: Applied and Materials Sciences; Department/School: Applied and Materials Sciences.

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18

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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19

Wetzel, Collin. "Global Identification and Mass Mapping of tRNA Isoacceptors Using Targeted Tandem Mass Spectrometry." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1448037316.

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20

Karu, Kersti. "Analysis of Oxysterols by capillary Liquid Chromatography Tandem Mass Spectrometry." Thesis, University College London (University of London), 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.509399.

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21

Thomas, Benjamin. "Tandem time-of-flight mass spectrometry incorporating quadratic-field technology." Thesis, University of Warwick, 2000. http://wrap.warwick.ac.uk/66998/.

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The study involved the desig~ constructio~ optimisation and utilisation of a novel tandem time-of-flight (TOF-TOF) instrument. The instrument was designed to use a laser ion source capable of laser desorption or matrix-assisted laser desorption/ionisation. The instrument used a twin ion mirror geometry in which the first ion mirror was a single-stage ion mirror, while the second ion mirror was a quadratic-field ion mirror. The instrument was designed for highenergy (>10keV) collision-induced dissociation (CID). The initial design criteria of a tandem time-of-flight spectrometer are discussed. The design and construction of the vacuum chamber and pumping system are discussed. The design and construction of the laser ion source are covered in detail. Computer simulations of typical ion trajectories were calculated using the SIMION program. The design and construction of the steering optics, single-stage ion mirror and pulsed mass gate are discussed. Computer simulations of ion trajectories were used to characterise the ion optical properties of the system. Experiments to characterise the energy focusing properties and transmission of the single-stage ion mirror were conducted. The mass resolving power of the single-stage ion mirror were characterised. The single-stage ion mirror achieved a resolution of2000 full-width half-maximum (FWHM). The design and construction of the differentially pumped collision-cell and the quadratic-field ion mirror are outlined. Experiments to demonstrate the transmission of the collision-cell and quadratic-field ion mirror are discussed. Experiments to characterise the energy focusing properties of the quadratic-field ion mirror were conducted. The full instrument achieved precursor mass resolving powers of approximately 7000 (FWHM) for laser desorbed species and 3500 (FWHM) for MALDI generated peptide species. Initial CID results are presented. The study thoroughly discusses the problems with the current instrument configuration and goes on to propose solutions to the problems encountered.

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22

Johnson, Richard S. (Richard Scott) 1961. "Determination of peptide and protein structure by tandem mass spectrometry." Thesis, Massachusetts Institute of Technology, 1988. http://hdl.handle.net/1721.1/14678.

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23

Lopez-Clavijo, Andrea F. "Tandem mass spectrometry of non-enzymatically glycated peptides and proteins." Thesis, University of Warwick, 2013. http://wrap.warwick.ac.uk/58994/.

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The thesis presents the study of the reaction of glyoxal (ethanedial) with polypeptides. This reaction is important in the food industry as well as during ageing and diabetes mellitus. To study this reaction a Fourier transform ion cyclotron resonance mass spectrometer coupled with electron capture dissociation and collisionally activated dissociation was used. Initially this reaction was carried out in the neuropeptide Substance P to set up the reaction conditions, sample preparation, as well as the instrumental parameters in the mass spectrometer. The results in Substance P revealed two compounds, with mass additions assigned as C2O and C2H2O2 from glyoxal, were formed. MS/MS results showed that the modification site for both species could be located at either the arginine residue or at the N-terminus. Thus, in order to distinguish N-terminus from arginine modification the position of the arginine was varied in four model peptides. The results indicated that both mass additions C2O, C2H2O2 were located at the arginine residue. Interestingly, two of those model peptides showed an unusual mass addition of 21.9843 Da, which was assigned as a new type of glyoxal modification at the arginine residue showing the addition of two carbon atoms from glyoxal and the loss of two hydrogen atoms from the peptide (C2-H2), herein referred to as 2-imino-imidazole. In order to assess the involvement of other residues in the reaction with glyoxal a new set of experiments in acetylated and non-acetylated undecapeptides were carried out. Unexpectedly, these experiments revealed that two species with the same mass (16.01092 Da) were being formed in the non-acetylated peptide. One of the species corresponded to diglycation, where the results suggest that the glyoxal binding at the lysine residue is crosslinked with the N-terminus. The second species showing the addition of 116.01092 Da was formed at the arginine residue forming a species, here called a glyoxal dimer, at the arginine residue. The formation of the glyoxal dimer species was also observed in the acetylated peptide. Although is clear that crosslinking between the lysine residue and the N-terminus is not possible in the acetylated peptide, the results seem to indicate that crosslinking between the amino group of the lysine and the amide group of glutamine could occur. However, a systematic study varying the position of the lysine relative to the glutamine residue and also relative to the N-terminus needs to be addressed in the future in order to determine the extent of the involvement of the N-terminus and amide group in the glyoxal glycation reaction.

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24

Quiniou, Michel L. M. "Development and application of tandem time-of-flight mass spectrometry." Thesis, University of Edinburgh, 2001. http://hdl.handle.net/1842/12820.

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A novel tandem time-of-flight (TOF) mass spectrometer has been developed for studying the photo-induced dissociation of large molecules and elemental clusters. It consists of a linear first stage TOF analyser for primary mass separation and precursor ion selection, and a second orthogonal reflecting field TOF analyser for product ion analysis. The instrument is equipped with a large volume throughput molecular beam source chamber allowing the production of jet-cooled molecules and molecular clusters, as well as elemental clusters, using either a pulsed laser vaporisation source (LVS) or a pulsed arc cluster ion source (PACIS). A second differentially pumped chamber can be used with effusive sources, or for infrared laser desorption of large molecules, followed by laser ionisation. These primary ions can then be irradiated with a second, high energy laser to induce photodissociation. Detailed information about the fragmentation mechanisms can be deduced from the product ion mass spectra. A theoretical overview of the technique of tandem time-of-flight mass spectrometry is presented, together with a detailed description of the experimental procedures and equipment used. In order to assist with the design and optimisation of the instrument a "virtual" mass spectrometer was drawn to scale using the SIMION software program, in order to simulate ion trajectories for differing voltage, geometry's and dimensions of the ion optics. An ion gate was designed and manufactured to provide primary mass selection following the first time-of-flight mass analyser. The device consisted of four layers of interleaved wires; primary ions could be selectively transmitted by application of a fast rising high voltage pulse to the middle set of wires. The mass gate was measured to have a mass resolving power, m/Dm = 30.

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25

Tabb, David L. "Bioinformatics of proteomic tandem mass spectra : selection, characterization, and identification /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/10847.

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26

Fälth, Savitski Maria. "Improved Neuropeptide Identification : Bioinformatics and Mass Spectrometry." Doctoral thesis, Uppsala universitet, Institutionen för farmaceutisk biovetenskap, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9400.

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Bioinformatic methods were developed for improved identification of endogenous peptides using mass spectrometry. As a framework for these methods, a database for endogenous peptides, SwePep, was created. It was designed for storing information about endogenous peptides including tandem mass spectra. SwePep can be used for identification and validation of endogenous peptides by comparing experimentally derived masses of peptides and their fragments with information in the database. To improve automatic peptide identification of neuropeptides, targeted sequence collections that better mimic the peptidomic sample was derived from the SwePep database. Three sequence collections were created: SwePep precursors, SwePep peptides, and SwePep predicted. The searches for neuropeptides performed against these three sequence collections were compared with searches performed against the entire mouse proteome, and it was observed that three times as many peptides were identified with the targeted SwePep sequence collections. Applying the targeted SwePep sequence collections to identification of previously uncharacterized peptides yielded 27 novel potentially bioactive neuropeptides. Two fragmentations studies were performed using high mass accuracy tandem mass spectra of tryptic peptides. For this purpose, two databases were created: SwedCAD and SwedECD for CID and ECD tandem mass spectra, respectively. In the first study, fragmentation pattern of peptides with missed cleaved sites was studied using SwedCAD. It was observed that peptides with two arginines positioned next to each other have the same ability to immobilize two protons as peptides with two distant arginines. In the second study, SwedECD was used for studying small neutral losses from the reduced species in ECD fragmentation. The neutral losses were characterized with regard to their specificity and sensitivity to function as reporter ions for revealing the presence of specific amino acids in the peptide sequence. The results from these two studies can be used to improve identification of both tryptic and endogenous peptides. In summary, a collection of methods was developed that greatly improved the sensitivity of mass spectrometry peptide identification.

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27

Granholm, Viktor. "The accuracy of statistical confidence estimates in shotgun proteomics." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-100769.

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High-throughput techniques are currently some of the most promising methods to study molecular biology, with the potential to improve medicine and enable new biological applications. In proteomics, the large scale study of proteins, the leading method is mass spectrometry. At present researchers can routinely identify and quantify thousands of proteins in a single experiment with the technique called shotgun proteomics. A challenge of these experiments is the computational analysis and the interpretation of the mass spectra. A shotgun proteomics experiment easily generates tens of thousands of spectra, each thought to represent a peptide from a protein. Due to the immense biological and technical complexity, however, our computational tools often misinterpret these spectra and derive incorrect peptides. As a consequence, the biological interpretation of the experiment relies heavily on the statistical confidence that we estimate for the identifications. In this thesis, I have included four articles from my research on the accuracy of the statistical confidence estimates in shotgun proteomics, how to accomplish and evaluate it. In the first two papers a new method to use pre-characterized protein samples to evaluate this accuracy is presented. The third paper deals with how to avoid statistical inaccuracies when using machine learning techniques to analyze the data. In the fourth paper, we present a new tool for analyzing shotgun proteomics results, and evaluate the accuracy of its statistical estimates using the method from the first papers. The work I have included here can facilitate the development of new and accurate computational tools in mass spectrometry-based proteomics. Such tools will help making the interpretation of the spectra and the downstream biological conclusions more reliable.

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28

Nielsen, Michael Lund. "Characterization of Polypeptides by Tandem Mass Spectrometry Using Complementary Fragmentation Techniques." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7409.

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29

Brian, Carrillo. "Optimization of data directed acquisition in tandem mass spectrometry for proteomics." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80003.

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LC-QTOF tandem mass spectrometers behave according to user controlled switching parameters, duty-cycle and repetition rate, which guide the selection of peptides and the timing of their fragmentation. Using a novel algorithm which analyses all spectra simultaneously, it has been found that the majority of available peptides are not fragmented with the current switching scheme. Unfortunately, it is not practical to experiment with the mass spectrometer to determine optimal switching parameters. In this study, simulation coupled with intensity surface analysis was used as a method of evaluating mass spectrometer performance. Algorithms that mimic the mass spectrometer were created in order to simulate its response to various data sets. The simulations resulted in operating curves displaying the trade-off between quality and quantity of fragment spectra. The optimal operating curve demonstrated that the current switching scheme is sub-optimal, and that new switching parameters with fewer duty cycles and fewer repetitions should be selected.

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30

Wei, Benqian. "Characterization of supramolecular peptide-polymer bioconjugates using multistage tandem mass spectrometry." University of Akron / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron1554221356363952.

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31

Barton, Sheila Janet. "Statistical analysis of proteomic profile data generated by tandem mass spectrometry." Thesis, London School of Hygiene and Tropical Medicine (University of London), 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.536923.

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32

Nicolaou, Anna, Mojgan Masoodi, and Adnan A. Mir. "Lipidomic analysis of prostanoids by liquid chromatography-electrospray tandem mass spectrometry." Springer, 2009. http://hdl.handle.net/10454/4575.

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

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33

Ruan, Dongliang. "Study of maillard reaction and early reaction products by mass spectrometry." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B42664688.

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34

An, Yan. "Study of organic cations in the gas phase by tandem mass spectrometry." Thesis, University of Ottawa (Canada), 1996. http://hdl.handle.net/10393/10232.

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The structure elucidation of gas-phase isomeric species $\rm C\sb2H\sb4X\sp+$ (X = F, Cl, Br and I), $\rm C\sb3H\sb6X\sp+$ (X = Cl, and Br), $\rm(C\sb2H\sb5)\sb2O\sp+C\sb2H\sb4X$ (X = Cl and Br), and $\rm C\sb3H\sb6O\sb2\sp{+\cdot}$ has been accomplished by employing tandem mass spectrometric techniques, i.e. metastable ion (MI) mass spectrometry, collision induced dissociation (CID) mass spectrometry, collision induced dissociative ionization (CIDI) mass spectrometry and neutralization reionization (NR) mass spectrometry. For $\rm C\sb2H\sb4X\sp+$ cations, apart from the $\alpha$-isomer, $\rm CH\sb3CHX\sp+,$ the cyclic ethylenehalonium ions, $\rm{\buildrel{{X\sp+}\atop\enspace}\over{CH\sb2\ CH\sb2}}$ are also stable for X = Cl, Br and I (Chapter 3). The two isomers have readily been characterized by CID mass spectrometry and their neutral counterparts have been produced and studied by NR mass spectrometry. It was found that based on an analysis of the heat of formation values of these ions and the electronegativity and polarizibility data of the X atoms, the relative stability of the two isomers is essentially controlled by the C-X bond strength. The relative stability of the cyclic species, however, is also controlled by the polarizibility of the X atom, which indicated that its polarization by the charge-centered carbon involved the outer-electrons in the X atom to form a back-donating bond with the charge-centered carbon. The isomeric halogen substituted triethyloxonium ions $\rm (C\sb2H\sb5)\sb2O\sp+C\sb2H\sb4X,$ (X = Cl and Br) were generated by appropriate gas phase ion molecular reactions between diethylether and appropriate $\rm C\sb2H\sb4XBr\sp{+\cdot}$ via Br$\sp\cdot$ loss (Chapter 4). The $\alpha$-substituted isomer, $\rm (C\sb2H\sb5)\sb2O\sp+CHXCH\sb3,$ and the $\beta$-substituted isomer, $\rm (C\sb2H\sb5)\sb2O\sp+CH\sb2CH\sb2X,$ are both stable in the gas-phase and do not interconvert on a time scale of $10\sp{-5}$s. Three $\rm C\sb3H\sb6X\sp+$ isomers (at least) were found to be stable in the gas-phase (Chapter 5). They are $\rm CH\sb3{-}\sp+CX{-}CH\sb3,\ CH\sb3{-}{\buildrel{{X\sp+}\atop\enspace}\over{CH{-}CH\sb2}},$ and $\rm{\buildrel{CH\sb2-X\sp+\atop\enspace}\over{CH\sb2{-}CH\sb2}}.$ These ions were characterized by their CID mass spectra and their different behavior in forming oxonium ions--$\rm(C\sb2H\sb5)\sb2O\sp+C\sb3H\sb6X$--with diethyl ether. The distonic radical cations $\rm \sp\cdot CH\sb2CH\sb2O\sp+CHOH$ and $\rm \sp\cdot CH\sb2CH\sb2\sp+C(OH)\sb2$, have been directly generated and characterized by their MI and CID mass spectra (Chapter 7). Comparing the dissociative process of $\rm\sp\cdot CH\sb2CH\sb2O\sp+CHOH$ to that of $\rm HCOOCH\sb2CH\sb3\sp{+\cdot}$ led to the conclusion that this distonic ion is the key intermediate in the dissociation of the latter. Thus the previous proposal, based only on the dissociation of HCOOCH$\sb2$CH$\sb3\sp{+\cdot},$ was confirmed. The heat of formation of $\rm\sp\cdot CH\sb2CH\sb2O\sp+CHOH$ was estimated from an appearance energy measurement to be 137 $\pm$ 4 kcalmol$\sp{-1};$ this is 16 kcalmol$\sp{-1}$ lower in energy than HCOOCH$\sb2$CH$\sb3\sp{+\cdot}.$ A detailed study of distonic ions is presented in Chapter 6, including a survey of the common methods to generate and characterize these ions. Properties of such ions which were considered were: stability, isomerization, bond cleavage and ring-strain. The results showed that the characteristics of distonic ions which distinguish them from their conventional counterparts result from the specific interaction of charge and radical sites.

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35

Guo, Xu. "Application of electrospray tandem mass spectrometry to the determination of biomolecular structure." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0027/MQ59174.pdf.

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36

Li, Huilin. "Studies of protein post-translational modifications using high resolution tandem mass spectrometry." Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/54993/.

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Electron capture dissociation (ECD) is a powerful and superior tandem mass spectrometry (MS) fragmentation technique in the study of protein post-translational modifications (PTMs) due to its unique features of preserving labile modifications and providing more detailed sequence information, which has been used to study protein platination and disulfide linked proteins. Cisplatin was found cross-linking multiple methionine (Met) pairs on calmodulin (CaM). The cross–linking of cisplatin to apo–CaM or Ca–CaM can inhibit the ability of CaM to recognize its target proteins as proved by a melittin binding assay. To further establish MS strategies to quickly assign the platinum-modification sites, a series of peptides with potential cisplatin binding sites were reacted with cisplatin and then analyzed by ECD. Radical-mediated side chain losses from the charge-reduced M+Pt species (such as CH3S• or CH3SH from Met, SH• from Cys, CO2 from Glu or Asp, and NH2• from amine groups) were found to be characteristic indicators for rapid and unambiguous localization of the Pt-modification sites on certain amino acid residues. Furthermore, the potential of cisplatin as a protein crosslinking reagent was further explored and demonstrated on other peptides and proteins. Many of the inherent features of cisplatin make it an interesting cross-linking reagent, such as targeting new protein functional groups (thioether and imidazole groups), its unique isotopic pattern, its inherent positive charges, its potential of binding to different functional groups, etc. However, it was found that the distance constraints obtained from NMR structures of CaM are inconsistent with the measured distance constraints by cross–linking. Therefore, a newly developed flexibility simulation method was applied to explore whether the flexibility motions of CaM might contribute to the observed Pt-crosslinking on CaM. The flexibility analysis showed that the structural flexibility of CaM is key to cisplatin crosslinking CaM. ECD mechanism of disulfide bonds is still under debate. To further explore the ECD mechanism of sulfur– containing species, a series of disulfide (S–S), sulfur–selenium (S–Se), and diselenide (Se–Se) bond–containing peptides was studied by ECD. The results demonstrate that the radical has higher tendency to stay at selenium rather than sulfur after cleavage of Se–S bonds by ECD and suggest that direct electron capture at Se–Se and C–Se bonds is the main process during ECD of inter–chain diselenide peptides. Last but not least, a new active ion ECD (AI-ECD) method, named Shots-ECD, was developed and applied to improve Top-down ECD backbone fragmentation efficiency of disulfide-rich proteins. The results show that the Shots–ECD approach can not only cleave multiple disulfide bonds but also significantly improve the backbone cleavage efficiency. This strategy is fast, efficient, and with no need of chemical reduction of samples and instrument modification, and therefore can be a powerful approach to improve top-down ECD efficiency of not only disulfide bonded proteins but all proteins by Fourier transform ion cyclotron mass spectrometry (FTICR MS).

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37

Fong, Bonnie Mei Wah. "Development and applications of liquid chromatography-tandem mass spectrometry in clinical areas." HKBU Institutional Repository, 2013. http://repository.hkbu.edu.hk/etd_ra/1530.

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38

Bushey, Jared M. Glish Gary L. "Improvements in electrospray ionization source design and advances in tandem mass spectrometry." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,2008.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.
Title from electronic title page (viewed Feb. 17, 2009). " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.

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39

Gupta, Nitin. "Computational and comparative proteogenomics annotating genomes and proteomes using tandem mass spectrometry /." Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3372792.

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Thesis (Ph. D.)--University of California, San Diego, 2009.
Title from first page of PDF file (viewed October 13, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 119-132).

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40

Mendoza, Jhoana Avendaño. "Studies of intact and modified ziconotide by liquid chromatography - tandem mass spectrometry." [Gainesville, Fla.] : University of Florida, 2009. http://purl.fcla.edu/fcla/etd/UFE0024845.

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41

Yu, Xiang. "Glycan sequencing and isoaspartate characterization by electron activated dissociation tandem mass spectrometry." Thesis, Boston University, 2013. https://hdl.handle.net/2144/11092.

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Thesis (Ph.D.)--Boston University
In this study, we carefully examined several types of electron activated dissociation (ExD) processes and developed new ExD techniques that should facilitate biological research, placing particular emphasis on glycan and protein characterization. The first part of this study focused on determination of ExD fragmentation mechanisms and application of ExD to glycan de novo sequencing. Through variation of the electron energy and metal charge carriers, the behaviors of model glycans were systematically studied and a new ExD fragmentation process, designated as electronic excitation dissociation (EED), was found to be the most informative. By identifying and controlling the key parameters, we improved the EED efficiency, to a level that now allows EED to be performed on a time scale that is compatible with the peak widths in high performance liquid chromatography. Theoretical modeling was employed to gain insights into the charge remote fragmentation behavior inherent in the EED process. The experimental results demonstrated that EED has the potential to provide the experimental basis for highthroughput, de novo glycan sequencing. The second part of this study focused on the determination of deamidation of asparagine residues and isomerization of aspartate residues within proteins. In order to avoid the generation of artifacts during trypsin digestion, a comprehensive top-down ExD method was developed to identify both asparagine deamidation and isoaspartate formation at the level of the intact protein With the consideration that the top-down strategy will eventually fail for high molecular weight proteins, a middle-down ExD method was next developed, for the analysis of peptides generated by proteolysis with Staphylococcal serine protease Protease V8 (GluC), carried out at slightly acidic conditions. In addition, the potential for use of in-source decay in isoaspartate analyses was evaluated and its fragmentation mechanisms were investigated. This research established new tools for structural determinations of glycans and significant improvements in methods for the isomer- and site-specific analysis of proteins that contain Asp or Asn residues that can undergo conversion to isoAsp, and provides insight toward understanding and controlling the fundamental processes that lead to the types of fragment ions observed in electron activated dissociation mass spectra.

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42

Song, Zhao Xu Dong. "Bioinformatics methods for protein identification using peptide mass fingerprinting data." Diss., Columbia, Mo. : University of Missouri--Columbia, 2009. http://hdl.handle.net/10355/6125.

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Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 16, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dissertation advisor: Dr. Dong Xu. Vita. Includes bibliographical references.

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43

Ruan, Dongliang, and 阮棟梁. "Study of maillard reaction and early reaction products by mass spectrometry." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B42664688.

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44

Lu, Yu. "Absolute quantification of target proteins in complex mixtures using visible isotope-coded affinity tags and tandem mass spectrometry /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/8661.

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45

Cao, Jie. "Proton affinities of organic molecules by the kinetic method and a mass spectrometric study of immonium ions by tandem mass spectrometry." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/NQ66132.pdf.

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46

Ramirez, Alejandro Javier Chambliss C. Kevin Brooks Bryan William. "Determination of pharmaceuticals and personal care products in fish using high performance liquid chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry." Waco, Tex. : Baylor University, 2007. http://hdl.handle.net/2104/5119.

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47

Perchalski, Robert John. "Characteristics and application of a laser ionization/evaporation source for tandem mass spectrometry." Gainesville, FL, 1985. http://www.archive.org/details/characteristicsa00perc.

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48

Ackloo, Suzanne. "Structural analysis of ginsenosides and sugars : an electrospray and tandem mass spectrometry study /." *McMaster only, 2001.

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49

Collin, Olivier L. "Development of a Novel Tandem Mass Spectrometry Technique for Forensic and Biological Applications." View abstract, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3292877.

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50

Marques, Pereira M. L. "Analysis of pharmaceutical products and nucleotides by LC-MS and tandem mass spectrometry." Thesis, Swansea University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.638005.

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Tandem mass spectrometry and chromatographic techniques coupled with mass spectrometry are demonstrated to be extremely useful in independent investigations of biochemical and pharmacological compounds. The first chapter gives some insight into the theory behind the chromatographic and mass spectrometric techniques used. Cyclic nucleotides are vital components in biochemical signal transduction and regulation, and thus the enzymes which regulate their intracellular levels are of great interest as pharmacological targets. In chapter 2, fast atom bombardment - collision induced dissociation and mass analysed ion kinetic energy spectrometry is compared with electrospray - tandem mass spectrometry, in a quadrupole ion trap, for the structural characterisation of cyclic nucleotides and cyclic nucleotide analogues. These are used as site selective activators of cyclic nucleotide - dependent protein kinases. The activity of a multifunctional phosphodiesterase is analysed in chapter 3, using electrospray - tandem mass spectrometric techniques. This includes the differentiation and relative quantification of the isomeric products of the active enzyme preparation and the effect of several cyclic nucleotide binding agents on the enzyme activity. In chapter 4 mass spectrometric data is obtained for two lots of a diagnostic drug, manufactured by two distinct synthetic routes, and for a number of related substances, the aim being to help the manufacturer to optimise the synthetic process. Micro liquid chromatography - atmospheric pressure chemical ionisation - mass spectrometry proved to be the technique of choice for the screening of residues of sulphonamides in milk. In chapter 5, this technique is compared with conventional high performance liquid chromatography with atmospheric pressure chemical ionisation - mass spectrometric detection and capillary zone electrophoresis with electrospray - mass spectrometric detection. The former technique is sensitive and selective allowing the quantification and confirmation of the presence of 10 sulphonamides at levels below the regulatory levels in milk.

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