Sub part-per-million mass accuracy by using stepwise-external calibration in fourier transform ion cyclotron resonance mass spectrometry

A new external calibration procedure for FT-ICR mass spectrometry is presented, stepwise-external calibration. This method is demonstrated for MALDI analysis of peptide mixtures, but is applicable to any ionization method. For this procedure, the masses of analyte peaks are first accurately measured at a low trapping potential (0.63 V) using external calibration. These accurately determined (< 1 ppm accuracy) analyte peaks are used as internal calibrant points for a second mass spectrum that is acquired for the same sample at a higher trapping potential (1.0 V). The second mass spectrum has a approximately 10-fold improvement in detection dynamic range compared with the first spectrum acquired at a low trapping potential. A calibration equation that accounts for local and global space charge is shown to provide mass accuracy with external calibration that is nearly identical to that of internal calibration, without the drawbacks of experimental complexity or reduction of abundance dynamic range. For the 609 mass peaks measured using stepwise-external calibration method, the root-mean-square error is 0.9 ppm. The errors appear to have a Gaussian distribution; 99.3% of the mass errors are shown to lie within three times the sample standard deviation (2.6 ppm) of their true value.     

Combining low and high mass ion accumulation for enhancing shotgun proteome analysis by accurate mass measurement

A simple procedure is described that increases sensitivity and dynamic range for the analysis of a proteome batch digest by FT-ICR mass spectrometry. Ions at the low and high mass ranges are preferentially collected using two different sets of tuning conditions. By combing data collected using tuning conditions that favor low mass (m/z < 2000) and high mass (m/z > 2000) ions, 277 proteins are identified for a whole cell lysate of Methanococcus maripaludis in a single HPLC-MALDI FT-ICR mass spectrometry experiment, a 70% improvement compared with previous analyses using a wide mass range acquisition. This procedure improves the detection of low abundance ions and thereby increases the range of proteins that are observed. Because the observed mass range is effectively narrower for each spectrum, mass calibration is more accurate than for the standard method that provides a wide range of masses. The trap plate potential on the analyzer cell may be set to a higher value than used for wide mass range measurements, increasing the ion capacity of the analyzer cell and extending the dynamic range, while still maintaining mass accuracy.     

Integration of genomic data for pharmacology and toxicology using Internet resources

Genome based technologies such as sequencing and gene expression profiling using microarrays are creating massive amounts of data. Results from these studies have provided unique insights into targets, biochemical pathways, and biological systems affected by drug or xenobiotic chemical treatments. Moreover, these genomic technologies offer the potential to identify biomarkers for pharmacological development or toxicological prediction. Nonetheless, microarray studies involving a single compound produce useful although limited data. To gain further power from these individual studies, the ability to combine datasets through integration schemes has become imperative. In the current study, we describe and analyze currently available Internet resources designed to address this problem. Many functionalities, such as ability to cross reference orthologous genes across species or to combine same technology platform data, are present in these resources. Nonetheless, these resources are limited in the number of technology platforms they can support. While the ability to integrate all currently existing gene expression datasets remains enigmatic, the current tools provide a partial solution that may still yield unique insights into the affects of exogenous molecules at the level of gene expression.     

What makes the cylinder-shaped N72 cage stable?

Recent theoretical studies have suggested that the stabilizing factors for large nitrogen cages tend to favor more five-membered rings, more three-membered rings, and cylindrical structures with large numbers of layers. One of the major issues in this study of the all-nitrogen molecule is the determination of what brings about the stabilizing factors. Herein, the cylinder-shaped molecule of N72 (D3d) has been studied in detail. The geometry and energies are examined at B3LYP/cc-pVDZ, and single-point energy calculations at MP2/cc-pVDZ are carried out for the purposes of determining relative thermodynamic stability. Natural bond order (NBO) analysis and atoms in molecules (AIM) analysis are applied to investigate the bonding properties of the cage molecule. The major result of this study is the identification of intramolecular interactions, whether it is at B3LYP/cc-pVDZ or at MP2/cc-pVDZ, as the dominant stabilizing factor for the large all-nitrogen cage. The length of the cylinder-shaped molecule is about 2.2 nm. N72 (D3d) might be one novel nanomaterial which is environment friendly, and as a beeline nanotube or a beeline "nano-bar", it is expected to impact a wide range of applications.     

Grignard reagents in ionic liquids

Grignard reagents were generated from magnesium and organic iodides in the ionic liquid n-butylpyridinium tetrafluoroborate, [bpy][BF4], and they showed different reactivity from classical Grignard reagents in organic solvents.     

Structure and properties of a new double-stranded tetranuclear [Cu(II)2]2 helicate

A novel double-stranded tetranuclear helicate composed of a pair of [Cu(II)(2)] dimers has been prepared and characterized by exploiting the flexibility, chelating ability and bridging potential of a hexadentate bis-oximate ligand.     

Studies of substituent effect on asymmetric epoxidation of chromenes by chiral dioxirane

A series of 6- and 8-substituted chromenes has been investigated for asymmetric epoxidation using chiral ketone catalysts. Up to 93% ee was achieved. Higher ee's are obtained when substrates are substituted at the 6-position. The enhanced enantioselectivity is likely due to the beneficial interaction between the 6-substituent of the substrate and the N-aryl or alkyl group of the ketone catalyst.     

Design and synthesis of a near infra-red luminescent hexanuclear Zn-Nd prism

The use of the Schiff-base ligand N,N'-bis(5-bromo-3-methoxysalicylidene)propylene-1,3-diamine (H2L) and 1,4-benzenedicarboxylate (BDC) enables the construction of the hexanuclear luminescent Zn-Nd complex [Zn4Nd2L4(1,4-BDC)2].[Nd(NO3)5(H2O)].Et2O.2EtOH.3H2O.     

Unprecedented formation of an acetamidate-bridged dinuclear platinum(II) terpyridyl complex-correlation of luminescence properties with the crystal forms and dimerization studies in solution

An [corrected] acetamidate-bridged dinuclear platinum(ii) terpyridyl complex has been isolated in two crystal forms, a red form and a dark form, with different luminescence properties; electronic absorption, emission and (1)H NMR studies revealed the presence of a dimerization process in the solution state.     

The diversity challenge in directed protein evolution

Over the past decade, we have witnessed a bloom in the field of evolutive protein engineering which is fueled by advances in molecular biology techniques and high-throughput screening technology. Directed protein evolution is a powerful algorithm using iterative cycles of random mutagenesis and screening for tailoring protein properties to our needs in industrial applications and for elucidating proteins' structure function relationships. This review summarizes, categorizes and discusses advantages and disadvantages of random mutagenesis methods used for generating genetic diversity. These random mutagenesis methods have been classified into four main categories depending on the method employed for nucleotide substitutions: enzyme based methods (Category I), synthetic chemistry based methods (Category II), whole cell methods (Category III) and combined methods (Category I-II, I-III and II-III). The basic principle of each method is discussed and varied mutagenic conditions are summarized in Tables and compared (benchmarked) to each other in terms of: mutational bias, controllable mutation frequency, ability to generate consecutive nucleotide substitutions and subset diversity, dependency on gene length, technical simplicity/robustness and cost-effectiveness. The latter comparison shows how highly-biased and limited current diversity creating methods are. Based on these limitations, strategies for generating diverse mutant libraries are proposed and discussed (RaMuS-Flowchart; KISS principle). We hope that this review provides, especially for researchers just entering the field of directed evolution, a guide for developing successful directed evolution strategies by selecting complementary methods for generating diverse mutant libraries.