Sample preparation for high throughput accurate mass analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

An automated sample preparation for high throughput accurate mass determinations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been developed. Sample preparation was performed with an automated workstation and automated mass analyses were performed with a commercial MALDI-TOF mass spectrometer. The method was tested with a 41-sample library. MALDI-TOFMS was found to give the needed sensitivity, accurate mass measurement, and soft ionization necessary for structure confirmation, even of mixtures. A mass accuracy of 5 ppm or less was obtained in over 80% of known compound measurements. A mass accuracy better than 10 ppm was obtained for all measurements of known compounds. Analyses of parallel synthesis products resulted in 77% of the measurements with a mass accuracy of 5 ppm or better.     

UV absorption spectra of HO2, CH3O2, C2H5O2, and CH3C(O)CH2O2 radicals and mechanism of the reactions of F and Cl atoms with CH3C(O)CH3

Pulse radiolysis techniques were used to measure the gas phase UV absorption spectra of the title peroxy radicals over the range 215–340 nm. By scaling to σ(CH₃O₂)_{240 nm} = (4.24 ± 0.27) × 10^?18, the following absorption cross sections were determined: σ(HO₂)_{240 nm} = 1.29 ± 0.16, σ(C₂H₅O₂)_{240 nm} = 4.71 ± 0.45, σ(CH₃C(O)CH₂O₂)_{240 nm} = 2.03 ± 0.22, σ(CH₃C(O)CH₂O₂)_{230 nm} = 2.94 ± 0.29, and σ(CH₃C(O)CH₂O₂)_{310 nm} = 1.31 ± 0.15 (base e, units of 10^?18 cm² molecule^?1). To support the UV measurements, FTIR‐smog chamber techniques were employed to investigate the reaction of F and Cl atoms with acetone. The F atom reaction proceeds via two channels: the major channel (92% ± 3%) gives CH₃C(O)CH₂ radicals and HF, while the minor channel (8% ± 1%) gives CH₃ radicals and CH₃C(O)F. The majority (>97%) of the Cl atom reaction proceeds via H atom abstraction to give CH₃C(O)CH₂ radicals. The results are discussed with respect to the literature data concerning the UV absorption spectra of CH₃C(O)CH₂O₂ and other peroxy radicals. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 283–291, 2002     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Structures and cytotoxic properties of sponge-derived bisannulated acridines

A reinvestigation of sponge natural products from additional Indo-Pacific collections of Xestospongiacf. carbonaria and X. cf. exigua has provided further insights on the structures, biological activities, and biosynthetic origin of bisannulated acridines. These alkaloids include one known pyridoacridine, neoamphimedine (2), and three new analogues, 5-methoxyneoamphimedine (4), neoamphimedine Y (5), and neoamphimedine Z (6). A completely new acridine, alpkinidine (7), was also isolated. A disk diffusion soft agar assay, using a panel of five cancer cell lines (solid tumors and leukemias) and two normal cells, was used to evaluate the differential cytotoxicity (solid tumor selectivity) of the sponge semipure extracts and selected compounds including amphimedine (1), 2, 4, and 7. While all four compounds were solid tumor selective, 1 and 2 were the most potent and 4 was the most selective. The rationale used to characterize the new structures is outlined along with the related biosynthetic pathways envisioned to generate 2 and 7.     

Secondary bonding interactions observed in two arsenic thiolate complexes

Treatment of N-(2-mercaptoethyl)-1,8-naphthalimide (HL) with stoichiometric amounts of AsCl(3) and base affords AsL(2)Cl and AsL(3) complexes stabilized in part by secondary As...O bonding interactions.     

H2/CO2 separations in multicomponent metal-adeninate MOFs with multiple chemically distinct pore environments

Metal–organic frameworks constructed from multiple (≥3) components often exhibit dramatically increased structural complexity compared to their 2 component (1 metal, 1 linker) counterparts, such as multiple chemically unique pore environments and a plurality of diverse molecular diffusion pathways. This inherent complexity can be advantageous for gas separation applications. Here, we report two isoreticular multicomponent MOFs, bMOF-200 (4 components; Cu, Zn, adeninate, pyrazolate) and bMOF-201 (3 components; Zn, adeninate, pyrazolate). We describe their structures, which contain 3 unique interconnected pore environments, and we use Kohn–Sham density functional theory (DFT) along with the climbing image nudged elastic band (CI-NEB) method to predict potential H₂/CO₂ separation ability of bMOF-200. We examine the H₂/CO₂ separation performance using both column breakthrough and membrane permeation studies. bMOF-200 membranes exhibit a H₂/CO₂ separation factor of 7.9. The pore space of bMOF-201 is significantly different than bMOF-200, and one molecular diffusion pathway is occluded by coordinating charge-balancing formate and acetate anions. A consequence of this structural difference is reduced permeability to both H₂ and CO₂ and a significantly improved H₂/CO₂ separation factor of 22.2 compared to bMOF-200, which makes bMOF-201 membranes competitive with some of the best performing MOF membranes in terms of H₂/CO₂ separations.

Tailorable multicomponent MOFs and MOF membranes for efficient H₂/CO₂ separation.     

Measuring the metabolome: current analytical technologies

The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.     

A method for calculating <Superscript>16</Superscript>o/<Superscript>18</Superscript>o peptide ion ratios for the relative quantification of proteomes

A method is described for the identification and relative quantification of proteomes using accurate mass tags (AMT) generated by nLC-dual ESI-FT-ICR-MS on a 7T instrument in conjunction with stable isotope labeling using 16O/18O ratios. AMTs were used for putative peptide identification, followed by confirmation of peptide identity by tandem mass spectrometry. For a combined set of 58 tryptic peptides from bovine serum albumin (BSA) and human transferrin, a mean mass measurement accuracy of 1.9 ppm +/-0.94 ppm (CIM99%) was obtained. This subset of tryptic peptides was used to measure 16O/18O ratios of 0.36 +/- 0.09 (CIM99%) for BSA (micro = 0.33) and 1.48 +/- 0.47 (CIM99%) for transferrin (micro = 1.0) using a method for calculating 16O/18O ratios from overlapping isotopic multiplets arising from mixtures of 16O, 18O1, and 18O2 labeled C-termini. The model amino acid averagine was used to calculate a representative molecular formula for estimating and subtracting the contributions of naturally occurring isotopes solely as a function of peptide molecular weight. The method was tested against simulated composite 16O/18O spectra where peptide molecular weight, 16O/18O ratio, 18O1/18O2 ratios, and number of sulfur atoms were varied. Relative errors of 20% or less were incurred when the 16O/18O ratios were less than three, even for peptides where the number of sulfur atoms was over- or under-estimated. These data demonstrate that for biomarker discovery, it is advantageous to label the proteome representing the disease state with 18O; and the method is not sensitive to variations in 18O1/18O2 ratio. This approach allows a comprehensive differentiation of expression levels and tentative identification via AMTs, followed by targeted analysis of over- and under-expressed peptides using tandem mass spectrometry, for applications such as the discovery of disease biomarkers.     

Electrophoretic purification of the alpha and beta subunits of phosphorylase kinase and evidence in support of the deduced amino acid sequences

A simple, rapid sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) method is presented for isolating the alpha, alpha' and beta subunits of rabbit muscle phosphorylase kinase. The SDS-PAGE procedure can yield milligram amounts of alpha and beta from a single preparative gel and also allows isolation of the alpha' isozyme free of alpha. Notably the method provides the purified subunits in a form amenable to structural analysis. Edman degradation of alpha and alpha' reveal identical NH2-terminal structures. Amino acid analysis of the electrophoretically purified alpha and beta subunits are in good agreement with their deduced primary structures. The amino acid sequence of 488 residues in alpha and 713 residues in beta were determined by gas phase Edman degradation. The data support the recently deduced primary structures of alpha (Zander et al., Proc. Natl. Acad. Sci. USA, 1988, 85, 9381-9385).     

Copolymeric (lR-trans)-N,N'-1,2-cyclohexylene-bisbenzamide oligodimethylsiloxane chiral stationary phase for gas chromatography

A copolymeric stationary phase, consisting of a chiral selective part, i.e. (1R-trans)-N,N'-1,2-cyclohexylenebisbenzamide, and an efficient siloxane oligomeric part, was successfully applied to open tubular column GC analysis. The efficiency and the chiral selectivity of this stationary phase were studied in detail, and high capacity and efficiency at elevated GC temperatures were especially noted. Several drugs and other enantiomeric pairs were separated. The shown examples demonstrate a broad application range for this type of chiral stationary phase in GC analysis.