Mass Spectrometry Publications

2009

Wang H, D Wingett, MH Engelhard, K Feris, KM Reddy, P Turner, J Layne, C Hanley, J Bell, D Tenne, CM Wang, and A Punnoose. 2009. "Fluorescent Dye Encapsulated ZnO Particles with Cell-specific Toxicity for Potential use in Biomedical Applications." Journal of Materials Science. Materials in Medicine 20(1):11-22. Abstract Fluorescein isothiocyanate (FITC)-encapsulated core-shell particles with a nanoscale ZnO finishing layer have been synthesized for the first time as multifunctional “smart” nanostructures for particle tracking and cell imaging using the visible fluorescence emission of the dye or UV fluorescence emission of ZnO, and anti-cancer/antibacterial treatments using the selective toxicity of the nanoscale ZnO outer surface. The chemical phase composition, morphology, size, and the layered core-shell architecture of the particles were characterized using detailed transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and UV-vis-NIR spectrophotometry. Systematic XPS studies after removing nanometer thick layers confirmed the expected layered structure in the order ZnO-SiO2-APTMS-FITC proceeding from the surface to the core of the ~200 nm sized particles. Detailed investigation of the fluorescence properties of these hydrophilic particles in bio-compatible media using fluorescence spectroscopy, flow cytometry and fluorescence confocal microscopy demonstrated that the silica/ZnO outer layer offers considerable protection to the encapsulated dye molecules from photobleaching and quenching due to reactive species such as oxygen in the solvent. These particles showed promise toward cell imaging, for example when the bacterium Escherichia coli was used as a test system, the green fluorescence of the particles allowed confocal microscopy to image the cells. The FITC encapsulated ZnO (FITC-ZnO) particles demonstrated excellent selectivity in preferentially killing Jurkat cancer cells (18% cell viability) without any significant toxicity to normal primary immune cells (75% cell viability) at 60 g/mL concentrations and inhibited the growth of both gram-positive and gram negative bacteria at concentrations ≥ 250-500 g/mL (for Staphylococcus aureus and Escherichia coli, respectively). These results indicate that the novel FITC encapsulated multifunctional particles with nanoscale ZnO surface layer are smart nanostructures for particle tracking, cell imaging, antibacterial treatments and cancer therapy.
Wu S, NM Lourette, N Tolic, R Zhao, R Robinson, AV Tolmachev, RD Smith, and L Pasa-Tolic. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8(3):1347-1357. Abstract We present an integrated top-down and bottom-up approach facilitated by concurrent liquid chromatography-mass spectrometry (LC-MS) analysis and fraction collection for comprehensive high-throughput intact protein profiling. The approach employs high resolution reversed phase (RP) LC separations coupled on-line with a 12T Fourier transform ion cyclotron resonance (FTICR) spectrometer to profile and tentatively identify modified proteins, using detected intact protein masses in conjunction with bare protein identifications from the bottom-up analysis of the same fraction. Selected identifications are incorporated into a target ion list for subsequent offline gas phase fragmentation that uses only an aliquot of the original fraction used for bottom-up analysis.
Chowdhury SM, L Shi, H Yoon, CK Ansong, LM Rommereim, AD Norbeck, KJ Auberry, RJ Moore, JN Adkins, F Heffron, and RD Smith. 2009. "A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis ." Journal of Proteome Research 8(3):1504-1514 . Abstract We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins― HimD, PduB and PhoP― with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .
Barry RC, Y Lin, J Wang, G Liu, and C Timchalk. 2009. "Nanotechnology-Based Electrochemical Sensors for Biomonitoring Chemical Exposures ." Journal of Exposure Science and Environmental Epidemiology 19:1-18. doi:10.1038/jes.2008.71 Abstract This manuscript highlights research focused on the development of field-deployable analytical instruments based on EC detection. Background information and a general overview of EC detection methods and integrated use of nanomaterials in the development of these sensors are provided. New developments in EC sensors using various types of screen-printed electrodes, integrated nanomaterials, and immunoassays are discussed. Recent applications of EC sensors for assessing exposure to pesticides or detecting biomarkers of disease are highlighted to demonstrate the ability to monitor chemical metabolites, enzyme activity, or protein biomarkers of disease. In addition, future considerations and opportunities for advancing the use of EC platforms for dosimetric studies are covered.
Jiang W, and WJ Weber. 2009. "Anisotropy of disorder accumulation and recovery in 6H-SiC irradiated with Au2+ ions at 140 K." Journal of Nuclear Materials 389(2):332-335. doi:10.1016/j.jnucmat.2009.02.023 Abstract Single crystal <0001>-oriented 6H-SiC was irradiated with Au2+ ions to fluences of 0.032, 0.058 and 0.105 ions/nm2 at 140 K and was subsequently annealed at various temperatures up to 500 K. The relative disorder on both the Si and C sublattices has been determined simultaneously using in-situ D+ ion channeling along the <0001> and <2-201> axes. A higher level of disorder on both the Si and C sublattices is observed along the <2-201>. There is a preferential C disordering and more C interstitials are aligned with <0001>. Room-temperature recovery along <2-201> occurs, which is associated with the <0001>-aligned interstitials that annihilate due to close-pair recombination. Disorder recovery between 400 and 500 K is primarily attributed to annihilation of interstitials that are misaligned with <0001>. Effects of stacking order in SiC on disorder accumulation are insignificant; however, noticeable differences of low-temperature recovery in Au2+-irradiated 6H-SiC and 4H-SiC are observed.
Sowell SM, L Wilhelm, AD Norbeck, MS Lipton, CD Nicora, DF Barofsky, C carlson, RD Smith, and SJ Giovannoni. 2009. " Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3(1):93-105. Abstract The northwestern Sargasso Sea is part of the North Atlantic subtropical oceanic gyre that is characterized as seasonally oligotrophic with pronounced stratification in the summer and autumn. Essentially a marine desert, the biological productivity of this region is reduced during stratified periods as a result of low concentrations of phosphorous and nitrogen in the euphotic zone. To better understand the mechanisms of microbial survival in this oligotrophic environment, we used capillary LC-tandem mass spectrometry to study the composition of microbial proteomes in surface samples collected in September 2005. A total of 2279 peptides that mapped to 236 SAR11 proteins, and 3208 peptides that mapped to 404 Synechococcus proteins, were detected. Mass spectra from SAR11 periplasmic binding proteins accounted for a disproportionately large fraction of the peptides detected, consistent with observations that these extremely small cells devote a large proportion of their volume to periplasm. Abundances were highest for periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars, and spermidine. Although the data showed that a large fraction of microbial protein synthesis in the Sargasso Sea is devoted to inorganic and organic nutrient acquisition, the proteomes of both SAR11 and Synechococcus also indicated that these populations were actively growing. Our findings support the view that competition for multiple nutrients in oligotrophic systems is extreme but sufficient to sustain microbial community activity.
Zelenyuk A, J Yang, EY Choi, and DG Imre. 2009. "SPLAT II: An Aircraft Compatible, Ultra-Sensitive, High Precision Instrument for In-Situ Characterization of the Size and Composition of Fine and Ultrafine Particles." Aerosol Science and Technology 43(5):411-424. Abstract The properties of aerosols depend on the size and internal compositions of the individual particles. The vast majority of atmospheric aerosols are smaller than 200 nm, yet the single particle mass spectrometers, the only instruments that can characterize the size and internal compositions of individual particles, typically detect these small particles with extremely low efficiencies. In this paper we describe a new instrument called SPLAT II that provides unparalleled sensitivity to small particles, detecting 100% of particles that are larger than 125 nm and 40% of 100 nm particles. This instrument also brings an increase by a factor of 10 in temporal resolution, sizing up to 500 particles per second and characterizing the composition of up to 100 of them. SPLAT II uses a two-laser, two-step process to evaporate the particles and generate ions, producing high quality, reproducible mass spectra of the refractive and non-refractive aerosol fractions to yield the complete compositions of individual particles. The instrument control board provides for size dependent delays for lasers’ triggers to eliminate a size dependent hit rate. The mass spectra are recorded with 14-bit vertical resolution and analyzed using custom software packages. The instrument’s high sizing resolution and sensitivity makes it possible to combine it with the differential mobility analyzer(s) and measure particle size, composition, density, dynamic shape factor, hygroscopicity, and fractal dimension.
Yang J, M Stewart, GD Maupin, DR Herling, and A Zelenyuk. 2009. "Single Wall Diesel Particulate Filter (DPF) Filtration Efficiency Studies Using Laboratory Generated Particles." Chemical Engineering Science 64(8):1625-1634. Abstract Diesel offers higher fuel efficiency, but produces higher exhaust particulate matter. Diesel particulate filters are presently the most efficient means to reduce these emissions. These filters typically trap particles in two basic modes: at the beginning of the exposure cycle the particles are captured in the filter holes, and at longer times the particles form a "cake" on which particles are trapped. Eventually the "cake" removed by oxidation and the cycle is repeated. We have investigated the properties and behavior of two commonly used filters: silicon carbide (SiC) and cordierite (DuraTrap® RC) by exposing them to nearly-spherical ammonium sulfate particles. We show that the transition from deep bed filtration to "cake" filtration can easily be identified by recording the change in pressure across the filters as a function of exposure. We investigated performance of these filters as a function of flow rate and particle size. The filters trap small and large particles more efficiently than particles that are ~80 to 200 nm in aerodynamic diameter. A comparison between the experimental data and a simulation using incompressible lattice-Boltzmann model shows very good qualitative agreement, but the model overpredicts the filter’s trapping efficiency.
Bae IT, W Jiang, CM Wang, WJ Weber, and Y Zhang. 2009. "Thermal evolution of microstructure in ion-irradiated GaN." Journal of Applied Physics 105(8):083514, 1-7. doi:10.1063/1.3106606 Abstract The thermal evolution of the microstructure created by irradiation of a GaN single crystal with 2 MeV Au2+ ions at 150 K is characterized following annealing at 973 K using transmission electron microscopy. In the as-irradiated sample characterized at 300 K, Ga nanocrystals with the diamond structure, which is an unstable configuration for Ga, are directly observed together with nitrogen bubbles in the irradiation-induced amorphous layer. Upon thermal annealing, the thickness of the amorphous layer decreases by ~13.1 %, and nano-beam electron diffraction analysis indicates no evidence for residual Ga nanocrystals, but instead reveals a mixture of hexagonal and cubic GaN phases in the annealed sample. Nitrogen molecules, captured in the as-irradiated bubbles, appear to debond and react with the Ga nanocrystals during the thermal annealing to form crystalline GaN. In addition, electron energy loss spectroscopy measurements reveal an atomic volume change of 18.9 % for the as-irradiated amorphous layer relative to the virgin single crystal GaN. This relative swelling of the damaged layer reduces to 7.7 % after thermal annealing. Partial recrystallization and structural relaxation of the GaN amorphous state are believed responsible for the volume change.
Lower BH, R Yongsunthon, L Shi, L Wildling, HJ Gruber, NS Wigginton, CL Reardon, GE Pinchuk, T Droubay, JF Boily, and SK Lower. 2009. "Antibody recognition force microscopy shows that outer membrane cytochromes OmcA and MtrC are expressed on the exterior surface of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 75(9):2931-2935. Abstract Antibody-recognition force microscopy showed that OmcA and MtrC are expressed on the exterior surface of living Shewanella oneidensis MR-1 cells during anaerobic growth, when Fe(III) served as the terminal electron acceptor. OmcA was localized to the interface with hematite, while MtrC was more uniformly displayed on the bacterium’s exterior cell surface. Both cytochromes were also found associated with extracellular material.

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