Thesis (M.S.)--Youngstown State University, 2009. / Includes bibliographical references (leaves 116-118). Also available via the World Wide Web in PDF format.

Photodissociation methods have been implemented and compared to collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer for the structural analysis of peptides, proteins, oligosaccharides, DNA and DNA/drug complexes. Infrared multiphoton dissociation (IRMPD) was applied to N-terminally sulfonated peptides which offers efficient photo-fragmentation and detection of important low m/z fragments in comparison to CID. Upon IRMPD of these modified peptides a simplified MS/MS spectrum comprised of only characteristic y ions allows for better identification through de novo software analysis. Oligonucleotides can undergo highly efficient IRMPD due to the phosphate moiety located on along their backbone structure which yields excellent photon absorption at [lambda] = 10.6 [mu]m. IRMPD fragmentation pathways of DNA and DNA/drug complexes were shown to be comparable to CID, yielding cleavage at the [w / (a - B )] bond, except IRMPD allows for significantly improved MS/MS sensitivity through the secondary dissociation of uninformative duplex base losses which can further dissociate into useful fragment ions for sequencing. Ultraviolet photodissociation (UVPD) has been applied to chromophorederivatized peptides and oligosaccharides which retains the advantages associated with IRMPD, but also has additional benefits due to the greater energy per photon at 355 nm (3.5 eV / photon) in comparison to 10.6 [mu]m (0.12 eV / photon). Primarily, UVPD provides highly efficient secondary dissociation of chromophore-containing fragments allowing for simplified MS/MS spectra of chromophore-derivatized peptides. This concept was also implemented for the characterization of branched fluorescently-labeled oligosaccharides which produces different fragment ions complementary to CID experiments. Secondly, UVPD provides an ion activation method which is independent of the bath gas helium pressure in the ion trap in contrast to CID or IRMPD permits for optimal trap performance without compromise. Coordination of a chromogenic 18-crown-6 molecule to the lysine side chain of a peptide facilitates UVPD at both 266 nm and 355 nm. Energy absorbed by the crown ether is transferred intermolecularly to the peptide via the strong hydrogen bonds which hold the complex together, resulting in activation and fragmentation of the peptide. CID or IRMPD of these crown ether/peptide complexes results only in their disassembly without peptide fragmentation. / text

Surface-Assisted Laser Desorption/Ionization Mass Spectrometry (SALDI-MS) is an analytical technique enabling direct chemical analysis of solid samples. Analytes could be desorbed/ionized upon nitrogen laser irradiation from a SALDI substrate-coated sample, then analyzed by MS. The substrate is involved in the transfer of laser energy to the analytes, and eventually assists the desorption/ionization of analytes. The analytical performance of SALDI-MS, such as detection sensitivity, is dependent on different parameters of the substrate, such as size, morphology and form. In this thesis, the effects of several substrate parameters on the SALDI process were investigated. SALDI-MS based Imaging Mass Spectrometry (IMS) method was also developed using efficient SALDI substrate identified in the fundamental studies. IMS is a chemical-specific mapping technique which allows parallel mapping of multiple analytes in solid samples. The desorption mechanism of SALDI is investigated using two groups of substrate, the carbon allotropes and the noble metal nanoparticles. Ion desorption efficiency and internal energy transfer were probed and correlated in carbon-based SALDI. It was found that the ion desorption efficiency and internal energy transfer was in opposite order. Substrate that transferred more internal energy to ions did not show higher ion desorption efficiency. This result could not be explained by the Thermal Desorption model which was a generally believed mechanism of the SALDI desorption process. A non-thermal model, the Phase Transition model is proposed to account for the SALDI desorption process. The Phase Transition model suggests that the substrate is melted/ restructured upon laser irradiation, and this will assist ion desorption. The Phase Transition model is supported by the morphological change of carbon substrates after SALDI and high initial velocity of ions desorbed by carbon-based SALDI (> 1,000 ms-1). SALDI-MS is useful for small molecule analysis due to the relatively clean background in the low mass region. SALDI-IMS is developed and applied to the imaging of spatial distribution of small molecules in forensic and biological samples. Gold nanoparticles (AuNPs) was selected as the substrate from several other noble metal NPs. A solvent-free method, argon ion sputtering, was employed for coating AuNPs on sample surface prior to SALDI-IMS analysis. Fine details of the samples, such as the fine pattern of latent fingerprints and handwriting on questioned documents can be preserved and imaged reliably by avoiding the use of solvent. Fatty acids, drugs and ink components can be imaged in forensic samples including latent fingerprints, banknotes and checks. The solvent-free SALDI-IMS method was also applied to image the distribution of metabolites in intact animal tissues. Spatial distributions of neurotransmitters, nucleobases and fatty acids can be imaged from mouse brain and tumor tissue sections. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Photon-based tandem mass spectrometry provides a versatile ion activation strategy for the analysis of polypeptides, proteins, and lipids. 351-nm ultraviolet photodissociation mass spectrometry (UVPD-MS) is a facile and selective tandem dissociation technique used to elucidate chromophore-modified peptides within large mixtures. A bis-aryl chromogenic chemical probe was utilized to target solvent exposed primary amine residues within native protein states. Collision-induced dissociation (CID) was employed to indiscriminatly characterize the complete proteolytic digest while chromophore containing peptides were selectively dissociated with 351-nm UVPD; thus streamlining the identification of targeted peptides with structurally informative residues. Protein amine residue reactivities were then compared with predicted solvent exposures to elucidate protein tertiary structures, their mechanistic properties, and ligand-binding interactions. High-energy 193-nm UVPD is a fast, high-energy tandem mass spectrometry method and frequently generates fragment ions typically inaccessible to CID-based methods. Native mass spectrometry was coupled to top-down 193-nm UVPD for the gas phase characterization of non-covalent protein-ligand and protein-protein complexes. This method yielded a unique array of fragment ions for a comprehensive analysis of protein structures. UVPD of non-covalent complexes generated many polypeptide backbone fragments to characterize the primary sequence of proteins. Furthermore, top-down UVPD engendered cleavages with intact electrostatic interactions; this provided insight into the binding interfaces within protein-ligand complexes and the higher order structural architectures of oligomeric complexes. High-resolution 193-nm UVPD was paired with high performance liquid chromatography (LC) for the streamlined structural analysis of amphiphilic glycolipids within complex mixtures. For all glycolipids, UVPD provided the most comprehensive structural analysis tool by affording a diverse array of fragment ions to characterize both hydrophobic and hydrophilic moieties. UVPD based LC-MS separations of gangliosides shed light on the ceramide lipid bases, glycan moieties, and their isobaric structural variants. UVPD activation of lipid A and lipooligosaccharides (LOS) compounds generated a mixture of C-C, C-O, and C-N fragment ions to illustrate the hydrophobic acyl structures, while cleavages within the glycosidic, and cross-ring cleavages allowed the determination of acylation patterns. Novel LC-MS separation strategies were developed to elucidate and structurally characterize complex mixtures of lipopolysaccharide containing compounds. / text

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