Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

We describe the application of capillary liquid chromatography (LC) time-of-flight (TOF) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. Previously (Lipton et al., Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049) the peptides from a series of growth conditions of Deinococcus radiodurans have been characterized using capillary LC MS/MS and accurate mass measurements which are captured as an accurate mass and time (AMT) tag database. Using this AMT tag database, detected peptides can be assigned using measurements obtained on a TOF due to the additional use of elution time data as a constraint. When peptide matches are obtained using AMT tags (i.e., using both constraints) unique matches of a mass spectral peak occurs 88% of the time. Not only are AMT tag matches unique in most cases, the coverage of the proteome is high; approximately 3500 unique peptide AMT tags are found on average per capillary LC run. From the results of the AMT tag database search, approximately 900 ORFs detected using LC-TOFMS, with approximately 500 ORFs covered by at least two AMT tags. These results indicate that AMT database searches with modest mass and elution time criteria can provide proteomic information for approximately one thousand proteins in a single run of <3 h. The advantage of this method over using MS/MS based techniques is the large number of identifications that occur in a single experiment as well as the basis for improved quantitation. For MS/MS experiments, the number of peptide identifications is severely restricted because of the time required to dissociate the peptides individually. These results demonstrate the utility of the AMT tag approach using capillary LC-TOF MS instruments, and also show that AMT tags developed using other instrumentation can be effectively utilized.     

Estimation of zeta potential by electrokinetic analysis of ionic fluid flows through a divergent microchannel

The streaming potential is generated by the electrokinetic flow effect within the electrical double layer of a charged solid surface. Surface charge properties are commonly quantified in terms of the zeta potential obtained by computation with the Helmholtz-Smoluchowski (H-S) equation following experimental measurement of streaming potential. In order to estimate a rigorous zeta potential for cone-shaped microchannel, the correct H-S equation is derived by applying the Debye-Hückel approximation and the fluid velocity of diverging flow on the specified position. The present computation provides a correction ratio relative to the H-S equation for straight cylindrical channel and enables us to interpret the effects of the channel geometry and the electrostatic interaction. The correction ratio decreases with increasing of diverging angle, which implies that smaller zeta potential is generated for larger diverging angle. The increase of Debye length also reduces the correction ratio due to the overlapping of the Debye length inside of the channel. It is evident that as the diverging angle of the channel goes to nearly zero, the correction ratio converges to the previous results for straight cylindrical channel.     

The Characteristics of Direct Hydroxylation of Benzene to Phenol with Molecular Oxygen Enhanced by Pulse DC Corona at Atmospheric Pressure

The direct hydroxylation of benzene using molecular oxygen by atmospheric pulse DC corona discharge was investigated. The conversion of benzene increased with the increase of oxygen content and input voltage but the selectivity of phenol decreased due to the formation of polymerized products. The reactivity was also influenced by the kind and content of background inert gas. By using argon as background gas, we could get 2.2% of phenol yield at 60°C and 1 atm with energy consumption of 50 W. The strategy of reductive oxidation, which added hydrogen to the reactant, was not favorable to the phenol formation in this reaction system. The polymerized product showed the oligomeric character and the analysis of its chemical structure with FT–IR was presented.     

Oxygen binding to sulfur in nitrosylated iron--thiolate complexes: relevance to the Fe-containing nitrile hydratases

Iron-nitrosyl complex containing S-bonded monosulfinate [PPN][(NO)Fe(S,SO2-C6H4)(S,S-C6H4)] (3) has been isolated from sulfur oxygenation of complex [PPN][(NO)Fe(S,S-C6H4)2] (2) which is obtained from addition of NO molecule to [PPN][(C4H8O)Fe(S,S-C6H4)2] (1) in organic solvents. This result reveals that binding of NO to the iron center promotes sulfur oxygenation of iron dithiolates by dioxygen and stabilizes the S-bonded sulfinate iron species. Analysis of the bond angles for complexes 2 and 3 reveals that iron is best described as existing in a distorted trigonal bipyramidal coordination environment surrounded by one NO, three thiolates, and one sulfinate in complex 3, whereas the distorted square pyramidal geometry is adopted in complex 2. Complex 3 further reacts in organic solvents with molecular oxygen in the presence of [PPN][NO2] to produce the dinuclear bis(sulfinate) complex [PPN]2[(NO)Fe(SO2,SO2-C6H4)(S,S-C6H4)]2 (4). Complex 3 showed reaction with PPh3 in THF/CH2Cl2 to yield complex 2 and Ph3PO. Upon photolysis of CH2Cl2 solution of complex 3 under N2 purge at ambient temperature, the UV-vis and IR spectra consistent with the formation of complex 2 demonstrate that complex 2 and 3 are photochemically interconvertible. Obviously, complex 3 is thermally quite stable but is photochemically active toward [O] release. Also described are the X-ray crystal structures of 3 and 4.     

The use of static pressures of heavy gases within a quadrupole ion trap

The performance of quadrupole ion traps using argon or air as the buffer gas was evaluated and compared to the standard helium only operation. In all cases a pure buffer gas, not mixtures of gases, was investigated. Experiments were performed on a Bruker Esquire ion trap, a Finnigan LCQ, and a Finnigan ITMS for comparison. The heavier gases were found to have some advantages, particularly in the areas of sensitivity and collision-induced dissociation efficiency; however, there is a significant resolution loss due to dissociation and/or scattering of ions. Additionally, the heavier gases were found to affect ion activation and deactivation during MS/MS, influencing the product ion intensities observed. Finally, the specific quadrupole ion trap design and the ion ejection parameters were found to be crucial in the quality of the spectra obtained in the presence of heavy gases. Operation with static pressures of heavy gases can be beneficial under certain design and operating conditions of the quadrupole ion trap.     

Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry

There is an increasing need to be able to conduct quantitative lipidomics analyses as a complement to proteomics studies. The highest specificity for proteomics analysis can be obtained using methodology based on electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) coupled with liquid chromatography/tandem mass spectrometry (LC/MS/MS). For lipidomics analysis it is often necessary to be able to separate enantiomers and regioisomers. This can be very challenging when using methodology based on conventional reversed-phase chromatography. Normal-phase chromatography using chiral columns can provide dramatic improvements in the resolution of enantiomers and regioisomers. However, conventional ESI- and APCI-MS/MS has limited sensitivity, which makes it difficult to conduct studies in cell culture systems where only trace amounts of non-esterified bioactive lipids are present. The use of electron capture APCI-MS/MS overcomes this problem. Enantiomers and regioisomers of diverse bioactive lipids can be quantified using stable isotope dilution methodology coupled with normal-phase chiral chromatography and electron capture APCI-MS/MS. This methodology has allowed a lipidomics profile from rat epithelial cells maintained in culture to be delineated and allowed the effect of a non-selective lipoxygenase inhibitor to be assessed.     

Indium-mediated one-pot reductive conversion of nitroarenes to N-arylacetamides

N-Arylacetamides were prepared in excellent yields from nitroarenes in the presence of acetic anhydride, acetic acid and indium by a one-pot procedure.     

‘Me2CuLi·TMSCl in CH2Cl2’. The most powerful methylating agent for sterically congested α,β-enoates

The reaction of Me₂CuLi with sterically congested α,β-unsaturated esters in the presence of TMSCl in CH₂Cl₂ proceeded very smoothly to produce the conjugate addition products in high yields.     

Novel silicon-based alternating copolymers: synthesis,photophysical properties,and tunable EL colors

We synthesized novel silicon-based alternating copolymers for tunable electroluminescent (EL) colors by Heck synthetic method. Their thermal, photophysical and electroluminescent properties were studied. Most of them exhibited a blue-green EL color at the operating voltage of lower than 12 V. Unusually, we observed the white EL color from a EL device based on SiPhPVK. From photophysical studies and the time-resolved PL spectroscopies, it might be attributed to the formation of stabilized excited state in SiPhPVK. Furthermore, in order to reduce the operating voltage of their LED with increasing the electron affinity of the main chain in silicon-based alternating copolymers, we synthesized the silicon-based copolymers containing electron transporting oxadiazole units in main chain. We also studied their photophysical and electroluminescent properties.     

Novel transition metal oxalatophosphates with a two-dimensional honeycomb structure: (H3TREN)[M2(HPO4)(C2O4)2.5] x 3H2O (M = Mn(II) and Fe(II), TREN = tris(2-aminoethyl)amine)

Two new layered transition metal oxalatophosphates, (H(3)TREN)[M(2)(HPO(4))(C(2)O(4))(2.5)].3H(2)O (M = Mn(II) and Fe(II)), have been synthesized by hydrothermal methods in the presence of a structure-directing organic amine, tris(2-aminoethyl)amine, and characterized by single-crystal X-ray diffraction and magnetic susceptibility. They are the first metal oxalatophosphates which adopt a two-dimensional honeycomb structure with the organic cations and water molecules intercalated in between. Within a layer, there are 12-membered pores made from 6 Mn, 1 phosphate, and 5 oxalate units. Measurements of field dependence of magnetization and variable-temperature susceptibilities under different fields were performed on a polycrystalline sample of the manganese compound. The results indicate a phase transition from a paramagnetic to an antiferromagnetic coupled state at about 12 K. Crystal data for the manganese compound follow: triclinic, space group Ponemacr; (No. 2), a = 8.8385(6) A, b = 9.0586(6) A, c = 16.020(1) A, alpha = 77.616(1) degrees, beta = 83.359(1) degrees, gamma = 68.251(1) degrees, and Z = 2. Crystal data for the iron compound are the same as those for the manganese compound except a = 8.7776(9) A, b = 8.9257(9) A, c = 15.884(2) A, alpha = 78.630(2) degrees, beta = 84.018(2) degrees, and gamma = 67.372(2) degrees.