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.     

Parameterization and evaluation of a flexible water model

The thermodynamic, dielectric, and dynamic properties of a newly parameterized flexible water model are studied using molecular dynamics simulations. The potential function developed is based on the popular simple point charge (SPC) rigid model with the addition of appropriate harmonic and anharmonic energy terms for stretching and bending. Care was taken to account for the self-polarization and gas-phase monomer energy corrections during the parameterization, which have typically been ignored in past studies. The results indicate that an increased Lennard-Jones repulsive coefficient and slightly scaled partial charges are required when adding flexibility to the rigid model potential to reliably reproduce the experimental density, energy, and O ? O radial distribution function of water at 298 K and 1 atm. Analysis of the power spectrum derived from the H-velocity autocorrelation function allowed the water potential to be evaluated further and refined by adjusting the valence forces to fit the vibrational frequencies of the gas and liquid. Once a consistent set of parameters was determined, the static dielectric properties of the water model were calculated at two temperatures using the reaction field method to treat long-range forces and correlations. The dielectric constant of 75 ± 7 calculated at 300 K is in good agreement with the experimental value of 78.5. The Kirkwood g factor was also examined for temperature dependence and showed the correct increasing behavior with decreasing T. As a final check of the water potential, the free energies of solvation of a flexible water molecule and neon were predicted using thermodynamic perturbation methods. The calculated solvation energies of ?7.0 ± 0.8 for water and 2.7 ± 0.7 for neon are both consistent with the experimental values of ?6.3 and 2.7 kcal/mol. Comparisons are made throughout the study with the results of previous rigid and flexible model simulations. © 1995 by John Wiley & Sons, Inc.     

Resolution of photothermal tomographic imaging of subsurface defects in metals with ray optic reconstruction

A capacitive photopyroelectric tomographic technique to obtain photothermal images of cross-sections with subsurface defects of opaque solid samples is reported. Unlike the two-dimensional projection images obtained by conventional photothermal detection methods, a tomographic scanning sequence has been used for cross-sectional imaging of subsurface features. Ray-like propagation of thermal waves is assumed in reconstructing the images. Resolution of these tomographic images with multiple features is investigated. Sensitivity of this reconstruction method to the size and shape of a single subsurface defect is also discussed.     

Upper limit for thermal direct photon production in heavy-ion collisions at 60 and 200A·GeV

The production of direct photons has been investigated in reactions ofp and¹⁶O projectiles at 60 and 200A·GeV with C and Au nuclei. Photon and ⁰ spectra have been measured in the pseudorapidity range 1.52.1 for the transverse momentum region 0.4 GeV/cp _T 2.8 GeV/c employing the lead-glass spectrometer SAPHIR. An upper limit of 15% at the 90% confidence level for the direct photon signal relative to the neutral pion production is obtained from the comparison of measured photon spectra with Monte Carlo simulations of the hadronic background based on the reconstructed yield of ⁰ and mesons. Consequences for a possible phase transition to a quark-gluon plasma are discussed.     

N,N′‐Di­thio­bisphthal­imide–nitro­benzene (2/1): a Pn solvate with localized solvent mol­ecules ordered head‐to‐tail in channels

N,N′‐Di­thio­bisphthal­imide crystallizes from nitro­benzene solution as a solvate, 2C₁₆H₈N₂O₄S₂·C₆H₅NO₂, having space group Pn. The bisphthal­imide mol­ecules are linked by C—H?O hydrogen bonds and by aromatic π–π‐stacking interactions, forming a framework enclosing continuous channels running along the [100] direction and accounting for ca 20% of the unit‐cell volume. The nitro­benzene mol­ecules lie in these channels, ordered in a head‐to‐tail fashion and linked to the bis­phthal­imide framework by C—H?O and C—H?π(arene) hydrogen bonds.     

The origins of the colours of yellow,green and blue sapphires

The absorption spectra of natural yellow sapphires are shown to be due to single Fe³⁺ and Fe³⁺  O²⁻  Fe³⁺ pairs, with the latter dominant. Blue and green sapphires have spectra dominated by Fe³⁺  O²⁻  Ti⁴⁺ and Fe²⁺  O²⁻  Fe³⁺ pairs.     

Hydro­gen‐bonded adducts of ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol): monomeric and polymeric adducts with 1,2‐bis(4‐pyridyl)­ethene and 1,6‐di­amino­hexane

In the adduct ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–1,2‐bis(4‐pyridyl)­ethene (1/1), [Fe(C₁₈H₁₅O)₂]·C₁₂H₁₀N₂, there is an intramolecular O—H?O hydrogen bond in the ferro­cene­diol component and a single O—H?N hydrogen bond linking the diol to the di­amine, which is disordered over two sets of sites, so forming a finite monomeric adduct. In the adduct ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–1,6‐di­amino­hexane (2/1), 2[Fe(C₁₈H₁₅O)₂]·C₆H₁₆N₂, the amine lies across a centre of inversion in space group P. There is an intramolecular O—H?O hydrogen bond in the ferrocenediol, and the molecular components are linked by O—H?N and N—H?O hydrogen bonds, one of each type, into a C(13)[R(12)] chain of rings.     

Synthesis of S(+) and R(-)-3-(2-aminopropyl)indole from ethyl-D- and L-tryptophanate

A stereospecific requirement for hallucinogenesis applies to certain molecules containing an asymmetric center. Thus, only the R-isomers of substituted phenylisopropylamines and lysergic acid diethylamide are psychotomimetic. The enantiomers of a minor hallucinogen, S(+)- and R(-)-3-(2-aminopropyl)indole (α-methyltryptamine) ( 6a and 6b ) were synthesized via a 5-step manipulation from D - and L -tryptophan ethyl ester hydrochloride, respectively. Optical purity of these two isomers was determined by pmr spectroscopy of their complexes with a europium chiral shift reagent using the indole C₂ H signal.     

A generic approach to the impurity profiling of drugs using standardised and independent capillary zone electrophoresis methods coupled to electrospray ionisation mass spectrometry

Three standardised, capillary zone electrophoresis-electrospray ionisation mass spectrometry (CZE-ESI-MS) methods were developed for the analysis of six drug candidates and their respective process-related impurities comprising a total of 22 analytes with a range of functional groups and lipophilicities. The selected background electrolyte conditions were found to be: 60/40 v/v 10 mM ammonium formate pH 3.5/organic, 60/40 v/v 10 mM ammonium acetate pH 7.0/organic and 10 mM piperidine, pH 10.5, where the organic solvent is 50/50 v/v methanol/acetonitrile. The coaxial sheath flow consisted of either 0.1% v/v formic acid in 50/50 v/v methanol/water, or 10 mM ammonium acetate in 50/50 v/v methanol/water, depending on the mixture being analysed. Factor analysis and informational theory were used to quantify the orthogonality of the methods and predict their complementarities. The three selected CZE-ESI-MS methods allowed the identification of 21 out of 22 of all the drug candidates and their process-related impurities and provided orthogonality with four established high-performance liquid chromatography-mass spectrometry (HPLC-MS) methods. These methodologies therefore form the basis of a generic approach to impurity profiling of pharmaceutical drug candidates and can be applied with little or no analytical method development, thereby offering significant resource and time savings.     

Adducts of 1,1,1‐tris(4‐hydroxyphenyl)ethane with diamines: three‐dimensional hydrogen‐bonded frameworks formed with 1,6‐diaminohexane and 2,2′‐bipyridyl

The adduct 1,6‐di­amino­hexane–1,1,1‐tris(4‐hydroxy­phenyl)­ethane (1/2) is a salt {hexane‐1,6‐diyldiammonium–4‐[1,1‐bis(4‐hydroxyphenyl)ethyl]phenolate (1/2)}, C₆H₁₈N₂²⁺·2C₂₀H₁₇O₃^?, in which the cation lies across a centre of inversion in space group P. The anions are linked by two short O—H?O hydrogen bonds [H?O 1.74 and 1.76 Å, O?O 2.5702 (12) and 2.5855 (12) Å, and O—H?O 168 and 169°] into a chain containing two types of R(24) ring. Each cation is linked to four different anion chains by three N—H?O hydrogen bonds [H?O 1.76–2.06 Å, N?O 2.6749 (14)–2.9159 (14) Å and N—H?O 156–172°]. In the adduct 2,2′‐bipyridyl–1,1,1‐tris(4‐hydroxy­phenyl)­ethane (1/2), C₁₀H₈N₂·2C₂₀H₁₈O₃, the neutral di­amine lies across a centre of inversion in space group P2₁/n. The tris­(phenol) mol­ecules are linked by two O—H?O hydrogen bonds [H?O both 1.90 Å, O?O 2.7303 (14) and 2.7415 (15) Å, and O—H?O 173 and 176°] into sheets built from R(38) rings. Pairs of tris­(phenol) sheets are linked via the di­amine by means of a single O—H?N hydrogen bond [H?N 1.97 Å, O?N 2.7833 (16) Å and O—H?N 163°].