Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.     

Structures of Addition Products of Acetylenedicarboxylic Acid Esters with Various Dinucleophiles. An application of C,H-spin-coupling constants

Heterocyclic compounds obtained by addition of acetylenedicarboxylic acid esters to thioureas, cyclic amidines and o-difunctionalized aromatic systems have been studied by ¹³C-NMR. In particular, C, H-spin-coupling constants over two and three bonds were used to differentiate between the various constitutional isomers and to establish the configuration of trisubstituted exocyclic C, C-double bonds. The configurational significance and diagnostic value of vicinal cis and trans C,H-spin coupling is again demonstrated in the present series.     

The electronic structure of small sodium clusters

Ab initio molecular orbital calculations using the STO3-21G basis set has been carried out for the cluster series Na _n ⁺ , Na _n , and Na _n ^– (wheren=2–7). The basis set is shown to be reliable compared with more extensive basis sets at the Hartree-Fock level. Thirty-one optimized structures are reported and discussed, many of which (especially for the anions) have not been considered. The STO3-21G//STO3-21G calculations suggest that for most of the species the optimum geometries are planar. In particular, the optimized structures for the anionic species should provide a starting point for more sophisticated configuration interaction calculations.     

In-situ HEED structure analysis of AlNx films grown by the simultaneous use of a radical beam source and ICB technique

A reactive ionized cluster beam technique (RICB) which was composed of a conventional ICB source and a radical beam source has been used to deposit stable and metastable polycrystalline AlN_x (0x1) films. Using in-situ high energy electron diffraction (HEED) at grazing incidence geometry, crystallographic properties such as structure, preferred orientation and interplanar dspacing values were determined and the relation to deposition parameters investigated. It could be shown that the simultaneous use of the ICB technique and a radical beam source to separately control the kinetic energy of the Al ions and the dissociation rate of molecular nitrogen, allows AlN films to be deposited with variable composition and crystal structures. In-situ HEED used in the transmission mode is an effective tool to investigate the crystallography of growing compound films such as AlN_x.     

SynCar: an approach to automated synthesis

The automation of all aspects of manual solution-phase synthesis into one integrated, efficient, and reliable system could be regarded as something of an unmet challenge in organic chemistry. The requirements for modern solution-phase libraries in mainstream drug discovery is typically 50-250 high-purity compounds on a 10-100-mg scale, whether for target class libraries or lead optimization, and short cycle time in combination with high capacity is critical. To achieve these goals, in a codevelopment between Aventis and Accelab GmbH, Kusterdingen, Germany, we designed a completely novel system of independent workstations connected by a shuttle transfer system produced by Montech, Derendingen, Switzerland. Seven modular workstations process four reactions on each shuttle in parallel, with the ability to perform synthesis (temperature control and liquid reagent handling), filtration, liquid-liquid extraction, evaporation, weighing, solid-phase extraction, and HPLC/MS analysis. The modular design enables the continuous loading of shuttles at any time, and each shuttle can have its own workflow. The design also allows easy expansion for future needs. The result is a combination of high flexibility and high throughput.     

Die Struktur des Pentaphenyldisilans

Structure of Pentaphenyldisilane For the first time Pentaphenyldisilane was prepared by Gilman and Goodman. It is produced by the reaction of Ph₃SiLi with Ph₂ClSiH. The crystal structure presents an ideally staggered conformation. The distance d(Si? Si) = 235.7 pm corresponds to a normal single bond length. This emphasizes the complete relief of the central Si? Si bond by the insertion of only one hydrogen atom.     

HO2 ELIMINATION FROM α-HYDROXYALKYLPEROXYL RADICALS IN AQUEOUS SOLUTION

Abstract— In aqueous solutions α-hydroxyalkylperoxyl radicals undergo a spontaneous and a base catalysed HO₂ elimination. From kinetic deuterium isotope effects, temperature dependence, and the influence of solvent polarity it was concluded that the spontaneous reaction occurs via an HO₂ elimination followed by the dissociation of the latter into H⁺ and O₂^-. The rate constant of the spontaneous HO₂ elimination increases with increasing methyl substitution in α-position ( k (CH₂(OH)O₂) < 10s^-1 k (CH₃CH(OH)O₂) = 52s^-1 k ((CH₃)₂C(OH)O₂) = 665 s^-1). The OH^- catalysed reaction is somewhat below diffusion controlled. The mixture of peroxyl radicals derived from polyhydric alcohols eliminate HO₂ at two different rates. Possible reasons for this behaviour are discussed. The mixture of the six peroxyl radicals derived from d -glucose are observed to eliminate HO₂ with at least three different rates. The fastest rate is attributed to the HO₂ elimination from the peroxyl radical at C-l ( k > 7000s^-1). Because of the HO₂ eliminations the peroxyl radicals derived from d -glucose do not undergo a chain reaction in contrast to peroxyl radicals not containing an α-OH group. In competition with the first order elimination reactions the α-hydroxylalkylperoxyl radicals undergo a bimolecular decay. These reactions are briefly discussed.     

A theoretical comparison of the lowest-lying singlet and triplet states of H2CBe and of HCBeH

The low-lying singlet and triplet states of H₂CBe and HCBeH are examined using ab inito molecular orbital theory. In agreement with earlier results, the lowest-lying structure of H₂CBe has C_2v symmetry and is a triplet with one π electron (³ B₁). The results presented here suggest that the lowest-energy singlet structure is the (¹B₁) open-shell singlet, also with C_2v symmetry, at least 2.5 kcal/mol higher in energy. The singlet C_2v structure with two π electrons (¹A₁) is 15.9 kcal/mol higher than ³B₁. All of these structures are bound with respect to the ground state of methylene and the beryllium atom. In HCBeH, linear equilibrium geometries are found for the triplet (³Σ) and singlet (¹Δ) states. The triplet is more stable than the singlet (¹Δ) by 35.4 kcal/mol, and is only 2.9 kcal/mol higher in energy than triplet H₂ CBe. Since the transition structure connecting these two triplet molecules is found to be 50.2 kcal/mol higher in energy than H₂ CBe, both triplet equilibrium species might exist independently. The harmonic vibrational frequencies of all structures are also reported.     

The collisional quenching of O2*(1Δg) by NO and CO2

Rate coefficients for the collisional quenching of O₂^*(¹Δ_g) by NO and CO₂ at 2–8 torr and 300 K have been determined. k_NO = (2.48 ± 0.23) × 10^?17 cm³ molecule^?1 s^?1 and

= (2.56 ± 0.12) × 10^?18 cm³ molecule^?1 s^?1.     

The electronic structure of molecules by a many-body approach : II. Ionization potentials one-electron properties of pyridine and phosphoridine

The valence ionization potential (IPs) of pyridine and phosphoridine are studied by an ab initio many-body approach which includes the effects of electron correlation and reorganization beyond the Hartree-Fock approximation. For pyridine the order of the first three IPs is a₂(π), a₁(n), b₁(π), but the IPs of the a₂ and a₁ orbitals are so close together that they have to be regarded as identical in binding energy, which is also concluded from experiment. Whereas for pyridine the ordering of the IPs calculated in the HF approximation is incorrect, it is correct for phosphoridine. For this latter molecule the first three ionization potentials are due to ionization from the b₁(π), a₂(π), and a₁(n) orbitals. Several one-electron properties are calculated and compared with experimental and other theoretical data. The localized molecular orbitals are discussed as well.