Ion mobility-mass spectrometry (IM-MS), gas-phase hydrogen/deuterium (H/D) exchange ion molecule reactions and molecular modeling provide complimentary information and are used here for the characterization of peptide ion structure, including fine structure detail (i.e., cation-π interactions, β-turns, and charge solvation interactions). IM-MS experiments performed on tyrosine containing tripeptides show that the collision cross-sections of sodiated, potassiated and doubly sodiated species of gly-gly-tyr are smaller than that of the protonated species, while the cesiated and doubly cesiated species are larger. Conversely, all of the alkali-adducted species of try-gly-gly have collision cross-sections that are larger than that of the protonated species. The protonated and alkali metal ion adducted (Na+, K+ and Cs+) species of bradykinin and bradykinin fragments 1-5, 1-6, 1-7, 1-8, 2-7, 5-9 and 2-9 were also studied using IM-MS and the alkali metal ion adducts of these species were found to have cross-sections very close to those of the protonated species. Additionally, multiple peak features observed in the ATDs of protonated bradykinin fragments 1-5, 1-6 and 1-7 are conserved upon alkali metal ion adduction. It was observed from gas-phase H/D ion molecule reactions that alkali adducted species exchange slower and to a lesser extent than protonated species in the tyrosine- and arginine-containing peptides. Experimental and computational results are discussed in terms of peptide ion structure, specifically the intra-molecular interactions present how those interactions change upon alkali salt adduction, as well as with the sequence of the peptide. Additionally, IM-MS data suggests the presence of a compact conformation of bradykinin fragment 1-5 (RPPGF) when starting from organic solvent conditions. As water is added stepwise to methanolic solutions, a more extended conformation is populated. When the starting solution is composed of ≈90% water, two distinct mobility profiles are observed as well as a shoulder, indicating the presence of three gas-phase conformations for RPPGF. Gas-phase H/D exchange of [M+H]+ ions prepared from aqueous solvents show a bi-exponential decay, whereas samples prepared from organic solvents show a single exponential decay. The effect of solvent on gas-phase peptide ion structure, i.e., solution-phase memory effects, is discussed and gas-phase structures are compared to know solution-phase structures.

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.

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.

Thesis (Ph.D.)--Ohio University, November, 2004. / Includes bibliographical references (p. 168-177)

Thesis (Ph.D.)--Ohio University, November, 2004. / Title from PDF t.p. Includes bibliographical references (p. 168-177)

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

A utilização de ozônio como agente oxidante tem apresentado resultados positivos para a degradação de contaminantes orgânicos em subsuperfície. O ozônio apresenta alta reatividade, tanto com os compostos orgânicos de interesse quanto com os compostos inorgânicos presentes no meio, principalmente com os íons metálicos constituintes da matriz sólida, mobilizando os para a água subterrânea. Este estudo detectou e quantificou os íons metálicos de interesse presentes na matriz solida, sendo estes: Fe, Al, Mn, Cr, Pb, Ni e Zn. Também foram determinados os íons que foram mobilizados da matriz sólida, a partir da injeção do ozônio em solo proveniente de uma área contaminada por compostos orgânicos. / The use of ozone as an oxidizing agent has shown positive results for the degradation of organic contaminants in the subsurface. Ozone is highly reactive with both the organic compounds of interest as with inorganic compounds present in the environment, especially with the metal ions of the solid matrix constituents, mobilizing them into groundwater. This study detected and quantified the metal ions of interest present in the solid matrix, namely: Fe, Al, Mn, Cr, Pb, Ni and Zn. lons that have been mobilized from the solid matrix due to the ozone injection in soil from a contaminated area for organic compounds were also determined.

Orientador: Fábio Cesar Gozzo / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-18T09:14:06Z (GMT). No. of bitstreams: 1 Santos_LuizFernandoArruda_D.pdf: 7340905 bytes, checksum: 51f81b49c01047e52881271fa910fada (MD5) Previous issue date: 2011 / Resumo: A função de uma proteína está diretamente relacionada com sua estrutura e conhecendo a estrutura de uma proteína é possível verificar onde estão localizados e como agem seus sítios ativos e de interação. Dentre os métodos empregados para análise estrutural de proteínas por espectrometria de massas (MS), experimentos de ligação cruzada vêm recebendo grande destaque. Nestes experimentos, após digestão enzimática três tipos de peptídeos contendo agentes de ligação cruzada (ALCs) podem ser formados: espécies intramoleculares, quando o ALC está ligado entre dois resíduos do mesmo peptídeo; espécies intermoleculares, quando o ALC une dois peptídeos distintos e dead-end, quando o ALC liga-se apenas a um resíduo, sendo que o outro lado de sua cadeia normalmente sofre hidrólise. A etapa crucial em experimento de ligação cruzada consiste na correta atribuição e identificação dos peptídeos modificados por ALC, etapa que pode ser facilitada conhecendo a fragmentação destes peptídeos. Desse modo, o foco principal deste trabalho foi realizar experimentos de fragmentação das diferentes espécies de peptídeos modificados por ALCs utilizando metodologias baseadas na técnica de espectrometria de massas, como dissociação induzida por colisão (CID), dissociação multifotônica por infravermelho (IRMPD) e dissociação por captura de elétrons (ECD). Os estudos realizados proporcionaram a visualização de um padrão de fragmentação de espécies inter e intramoleculares, bem como a presença de íons diagnósticos, capazes de auxiliar na identificação de peptídeos modificados por ACLs. Além disso, a técnica de mobilidade iônica, que consiste na separação de íons baseado em suas seções de choque, acoplada à espectrometria de massas (IMMS), foi emprega para realizar estudos para caracterização de peptídeos modificados por ALCs. Utilizando IMMS foi possível realizar a separação de espécies isoméricas do tipo dead-end, bem como verificar que peptídeos lineares e modificados por ALC, com m/z próximos possuem seções de choque semelhantes / Abstract: There are several advantages associated with the use of mass spectrometry (MS) applied to structural studies of proteins, such as unlimited mass of target protein or protein complex, very low time and sample consumption, ease of manipulation and interpretation of the data obtained. In chemical cross-linking coupled to MS, bifunctional reagents (cross-linkers, XL) are used to generate covalent bonds between the side chains of specific residues (usually lysine) and the distance constraints obtained are then used to model the structure of the protein and reveal interacting regions in the case of protein complexes. After enzymatic digestion, three types of peptides modified by the XL can be generated: intramolecular cross-linked, in which the cross-linker is linked to two residues of the same peptide; intermolecular cross-linked, when the reagent connects two peptides; and ¿dead-end¿, that occurs when the cross-linker is bound to only one residue and the other side is usually hydrolyzed. The critical step in a cross-linking experiment is the correct attribution and identification of the modified peptides, which is in turn based on the fragmentation of such species. So, the main focus of this work is to perform fragmentation studies of cross-linked peptides and rationalize fragmentation models to aid in the correct identification and attribution of modified peptides. In our studies we verified a fragmentation pattern of modified peptides, as well as diagnostic fragment ions, able to help in the identification of cross-linked peptides. Studies of ion mobility (IMS) coupled to mass spectrometry (IMMS) to analyze cross-linked peptides were also performed. It was possible to separate dead-end isomers and it was verified that linear and modified peptides, of similar m/z have similar collision cross-section / Doutorado / Quimica Organica / Doutor em Ciências

Orientador: Marcos Nogueira Eberlin / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-15T19:01:40Z (GMT). No. of bitstreams: 1 Lalli_PriscilaMicaroni_M.pdf: 4223184 bytes, checksum: 852704419d68edf5bd13623379abf7b4 (MD5) Previous issue date: 2010 / Resumo: Na espectrometria de mobilidade iônica, íons de diferentes tamanhos ou conformações espaciais em fase gasosa são separados de acordo com o tempo que levam para atravessar um gás sob a influência de um campo elétrico. O acoplamento dessa técnica à espectrometria de massas (IMMS) resulta numa ferramenta extremamente versátil, capaz de investigar a estrutura molecular e separar amostras complexas, incluindo isômeros. No capítulo I, diferentes gases foram utilizados na separação dos isômeros N-butil anilina e p-butil anilina a fim de investigar a interação íon/molécula durante o processo de mobilidade iônica. Mostramos que as moléculas do drift gas não atuam apenas como barreiras físicas que atrasam os íons, como geralmente são consideradas, mas podem interagir quimicamente com os íons. No caso desses isômeros, gases mais polarizáveis como eteno e CO2 mostraram melhorar consideravelmente a separação. Acredita-se que a grande diferença de polarizabilidade entre os isômeros esteja relacionada com este fato, pois o gás mais polarizável interagiria melhor com o isômero também mais polarizável atrasando-o numa intensidade maior. Gases mais massivos e pressões maiores também ajudam a melhorar consideravelmente a separação de isômeros. No capítulo II, a IMMS foi usada para determinar pela primeira vez a mobilidade intrínseca de uma série de agregados catiônicos e aniônicos de líquidos iônicos na fase gasosa. Os resultados são condizentes com as medidas feitas em solução por RMN, que mostram uma aparente anomalia em que os cátions, mais volumosos, viajam mais rápido do que os ânions. Esse comportamento ainda não é muito bem compreendido, entretanto, pode estar relacionado à orientação dos íons pelo campo ou a diferença de dureza entre cátions e ânions / Abstract: Ion mobility spectrometry separates ions with different sizes or spacial conformations in gas phase according to the time they take to travel through a gas under the influence of an electrical field. Coupling this technique to mass spectrometry provides an extremely versatile tool, able to investigate molecular structure and separate complex samples, including isomers. In Chapter I, different gases were used to separate the isomers N-butyl aniline and p-butil aniline in order to investigate the ion/molecule interaction during the ion mobility process. We have shown that drift gas molecules don¿t act only as physical barriers that slow down the ions, as they are usually considered, but they may interact chemically with them. In the case of these isomers, more polarizable gases such as ethene and CO2 have shown to improve considerably the isomer separation. We believe that the large difference of polarizability between both isomers is related to this fact, because more polarizable gases would interact better with the more polarizable isomer slowing it down more intensively. More massive gases and higher pressures also help improve isomer separation. In Chapter II, IMMS was used to perform the first measurements of the intrinsic mobility of a series of gaseous cationic and anionic aggregates of ionic liquids. Results confirm previous mobility measurements by NMR, which show an apparent anomaly in which the bulkier cations travel faster than respective anions. This behavior isn¿t well understood yet, however, it may be related to the ions orientation by the field or to the hardness difference between cations and anions / Mestrado / Quimica Analitica / Mestre em Química

Orientadores: Marco Aurélio Zezzi Arruda, Fábio Cesar Gozzo / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-25T19:33:28Z (GMT). No. of bitstreams: 1 Pessoa_GustavodeSouza_D.pdf: 3326542 bytes, checksum: b4f5f4d1d6ae42d8ab1de1b683232723 (MD5) Previous issue date: 2014 / Resumo: ANÁLISE DE ESPECIAÇÃO DE METAIS E METALÓIDES LIGADOS A ANIDRASE CARBÔNICA EMPREGANDO MOBILIDADE IÔNICA E ICP-MS. No Capítulo 1, é proposta a técnica de mobilidade iônica na modalidade TWIMS, acoplada a um espectrômetro de massas do tipo ESI-Q-ToF MS/MS para análise de especiação da anidrase carbônica ligada a metais divalentes e em diferentes estados de oxidação, bem como ligada a espécies de selênio em diferentes estados de oxidação. O método é aplicado com sucesso na separação de espécies com diferentes estados de oxidação, mesmo quando as espécies de Se4+ e Se6+são adicionadas em uma mistura com a anidrase carbônica. O método também é aplicado para avaliação do estado de enovelamento da anidrase carbônica, em condições nativas e desnaturadas, sendo considerado satisfatório na elucidação das diferentes conformações da proteína. No Capítulo 2, a técnica de ICP-MS é usada na análise de especiação isotópica de Zn ligado à anidrase. A exatidão das medidas aproximou-se das condições naturais observadas para a razão isotópica de Zn ao final das otimizações. A precisão obtida situa-se dentro da margem observada para analisadores de m/z do tipo quadrupolo. Os principais desafios enfrentados neste capítulo foram minimizar os efeitos de discriminação de massas e a remoção de interferências poliatômicas. A enzima foi enriquecida com os isótopos 67Zn e 68Zn, sendo observada maior razão isotópica para anidrase ligada 67Zn. A atividade da anidrase enriquecida com isótopos de Zn apresentou resultados estatisticamente semelhantes / Abstract: SPECIATION ANALYSIS OF METALS AND METALLOIDS BOUND TO CARBONIC ANHYDRASE USING ION MOBILITY AND ICP - MS . In Chapter 1, ion mobility in TWIMS mode was proposed, coupled to a ESI-Q-ToF MS/MS mass spectrometer for speciation analysis of carbonic anhydrase bound to Ba2+, Zn2+, Cu+, Cu2+, Pb2+, Pb4+, Se4+ and Se6+. The method was successfully applied to separation of selenium species with different oxidation states, even when the species Se4+ and Se6+ were incubated in a mixture with carbonic anhydrase. The method was also applied to evaluation of carbonic anhydrase folding state in native and denatured conditions, and it was considered as satisfactory in the elucidation of different conformations of the protein. In Chapter 2, an ICP-MS was used for the isotopic speciation analysis of Zn bound to anhydrase. The accuracy measurements were closer to natural conditions for Zn isotope ratio, in the end of the optimization. The precision was within the range observed for m/z analyzer such as quadrupole. The main challenges in this chapter were to minimize the effects of mass discrimination and the removal of polyatomic interferences. The enzyme was enriched with 67Zn and 68Zn isotopes, and the highest isotope ratio was observed for 67Zn bound to anhydrase. Anhydrase activity of Zn enriched isotopes yielded similar statistical results / Doutorado / Quimica Analitica / Doutor em Ciências