bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of anatomical shoulder prostheses and the proximal humeri of Chinese people
Authors: Zhang L , Yuan B , Wang C , Liu Z
Published: December 2007

Reconstruction of normal anatomy is important to a successful proximal humeral arthroplasty, in which the surgeon needs to know multiple measured anatomical parameters during the surgery. Based on three-dimensional computed tomography scanning data, computer models of the proximal humeri of 180 Chinese people were built. They came from 77 males and 103 females; their ages ranged from 19 to 86 years. Anatomical parameters including the curvature diameter of the head, the head height, the inclination, and the retro-version were measured using the software in these three-dimensional proximal humerus models. The methodology was valid and the measured results showed marked variations in all those parameters. On average, the curvature diameter of the head was 44.6 mm, ranging from 36.4 to 55.5 mm. The head height was located at 16.7 ± 1.9 mm (minimum, 12.4 mm; maximum, 22.0 mm). The inclination angle ranged from 122.35° to 147.09° (mean, 132.4 ± 4.7°). The proximal humeral retroversion was found to be extremely variable, ranging from -4.71° to 52.46°, and has a mean of 21.11°. Then these measured results were compared with four commonly used anatomical prostheses. The wide range of variation in the normal values makes it difficult to restore anatomical characteristics individually. Thus, the use of an accurate three-dimensional model to guide surgery preoperatively can improve the outcome of some serious cases, such as gross degenerative change and large-bone-loss surgery.
In-vitro method for assessing femoral implant—bone micromotions in resurfacing hip implants under different loading conditions
Authors: Cristofolini L , Varini E , Viceconti M
Published: December 2007

Although prosthesis-bone micromotion is known to influence the stability of total hip replacement, no protocol exists to investigate resurfacing hip implants. An in-vitro protocol was developed to measure prosthesis-bone micromotions of resurfaced femurs. In order to assess the effect of all loading directions, the protocol included a variety of in-vitro loading scenarios covering the range of directions spanned by the hip resultant force in the most typical motor tasks. Gap-opening and shear-slippage micromotions were measured in the locations where they reach the maximum value. The applicability of the protocol was assessed on two commercial designs and different head sizes. Intra-specimen repeatability and inter-specimen reproducibility were excellent (comparable with the best protocols for cemented hip stems). Results showed that the protocol is accurate enough to detect prosthesis-bone micromotions of the order of a few microns. Statistically significant differences were observed in relation to the direction of the applied force. Using the whole range of hip loads enabled detection of maximum micromotions for any design (the peak value could be different for different loading directions). Application of the protocol during a test to failure indicated that the system could track micromotion up to the last instant prior to failure. The protocol proposed is thus completely validated and can be applied for preliminary screening of new epiphyseal designs.
Fabrication and evaluation of calcium phosphate cement scaffold with controlled internal channel architecture and complex shape
Authors: Li X , Li D , Lu B , Wang L , Wang Z
Published: December 2007

The ability to have precise control over internal channel architecture, porosity, and external shape is essential for tissue engineering. The feasibility of using indirect stereo-lithography (SL) to produce scaffolds from calcium phosphate cement materials for bone tissue engineering has been investigated. The internal channel architecture of the scaffolds was created by removal of the negative resin moulds made with SL. Scanning electron microscopy (SEM) showed highly open, well-interconnected channel architecture. The X-ray diffraction examination revealed that the hydroxyapatite phase formed at room temperature in the cement was basically stable up to 850 °C. There was no phase decomposition of hydroxyapatite, although the crystallinity and grain size were different. The ability of resulting structure to support osteoblastic cells culture was tested in vitro. Cells were evenly distributed on exterior surfaces and grew into the internal channels of scaffolds. To exploit the ability of this technique, anatomically shaped femoral supracondylar scaffolds with 300-800 μm interconnected channels were produced and characterized.
Reproduction of fretting wear at the stem—cement interface in total hip replacement
Authors: Brown L , Zhang H , Blunt L , Barrans S
Published: December 2007

The stem-cement interface experiences fretting wear in vivo due to low-amplitude oscillatory micromotion under physiological loading, as a consequence it is considered to play an important part in the overall wear of cemented total hip replacement. Despite its potential significance, in-vitro simulation to reproduce fretting wear has seldom been attempted and even then with only limited success. In the present study, fretting wear was successfully reproduced at the stem-cement interface through an in-vitro wear simulation, which was performed in part with reference to ISO 7206-4: 2002. The wear locations compared well with the results of retrieval studies. There was no evidence of bone cement transfer films on the stem surface and no fatigue cracks in the cement mantle. The cement surface was severely damaged in those areas in contact with the fretting zones on the stem surface, with retention of cement debris in the micropores. Furthermore, it was suggested that these micropores contributed to initiation and propagation of fretting wear. This study gave scope for further comparative study of the influence of stem geometry, stem surface finish, and bone cement brand on generation of fretting wear.
Frequency-based reliability Pareto optimum design of proportional-integral-derivative controllers for systems with probabilistic uncertainty
Authors: Nariman-Zadeh N , Jamali A , Hajiloo A
Published: December 2007

A reliability-based approach for the Pareto optimum design of proportional-integral-derivative (PID) controllers for systems with probabilistic uncertainty is presented. In this way, some non-dominated optimum PID controllers in the Pareto sense are found using four non-commensurable objective functions in frequency domain based on stochastic behaviour of a system with parametric uncertainties. Such conflicting objective functions are namely the probability of instability, the probability of failure to a desired frequency response, the variability of frequency response about deterministic behaviour, and the value of degree of stability from the Nyquist diagram's percentiles. The first three objective functions have to be minimized whilst the last has to be maximized simultaneously. It is shown that multi-objective Pareto optimization of such robust PID controllers using a recently developed diversity-preserving mechanism genetic algorithm unveils some very important and informative trade-offs among those objective functions. Consequently, some optimum PID controllers can be compromised and chosen from the Pareto frontiers.
Analysis of wood surface waviness with a two-image photometric stereo method
Authors: Jackson M , Yang D , Parkin R
Published: December 2007

This paper describes a two-image photometric stereo (PS) method for analysis of surface waviness on planed wood products. This method is based on an assumption that the wood surface is a Lambertian surface. In addition, owing to the fact that surface waviness on planed wood is mainly composed of cutter marks, which fluctuate only in one dimension, three-dimensional surface topography can reasonably be represented by a two-dimensional surface profile. Accordingly, a surface waviness profile can be extracted from two images of the surface under specifically arranged illumination. Measurement results from the two-image PS method are compared with those from a laser profilometer. Comparison indicates a high correlation between the two methods.
Multicylinder engine pressure reconstruction using NARX neural networks and crank kinematics
Authors: Potenza R , Dunne J F , Vulli S , Richardson D , King P
Published: December 2007

A NARX neural network is adapted for cylinder pressure trace reconstruction on a multicylinder engine. Following a systematic study to establish the required NARX input information (using measured pressure traces and simulated crank kinematics), two fully recurrent training algorithms are developed and applied to real engine data. These include a back-propagation-through-time algorithm (BPTT) and an extended Kalman filter (EKF). For multi-cylinder engines, two cases are examined, both assuming crank kinematics is obtained from a single shaft-encoder fitted at the forward end of the crankshaft. In one case, a NARX model is constructed to provide an inverse relationship between the kinematics at the encoder location and the pressure trace in an arbitrary cylinder. In the second case, by transforming the kinematics (to emulate a local encoder), a different NARX model is constructed to relate the kinematics at the crank location of a particular cylinder to the corresponding pressure trace. The accuracy and efficiency of both NARX models is examined for application to a three-cylinder in-line DISI engine (in which pressure traces are measured on all cylinders). The paper shows that the computational requirements of training are substantial and, although the efficiency of the EKF algorithm is better than the BPTT, the fitting accuracies are similarly good. For generalization, however (to unseen data), neither method is yet sufficiently accurate (even for steady state engine operation) unless substantially more training data are used to achieve the target accuracy of ± 4 per cent. The overall conclusion of the paper is that the NARX model has the correct architecture for multicylinder pressure reconstruction.
Deactivation of a diesel oxidation catalyst due to exhaust species from rich premixed compression ignition combustion in a light-duty diesel engine
Authors: Northrop W F , Jacobs T J , Assanis D N , Bohac S V
Published: December 2007

Low-temperature premixed-charge compression ignition (PCI) can significantly reduce both nitric oxide and nitrogen dioxide (NO x) and particulate matter emissions in compression ignition engines through a range of engine operating conditions. Exhaust hydrocarbons and carbon monoxide can be removed with a diesel oxidation catalyst (DOC). Although PCI normally utilizes a globally fuel-lean mixture, it is independent of equivalence ratio provided that local combustion temperatures are sufficiently low. A more fuel-rich PCI mode of operation could be useful in exhaust after-treatment strategies such as providing carbon monoxide and hydrocarbons for regeneration of a lean NO x trap (LNT). In a previous study, it was found that a rich PCI strategy deactivates a platinum-based DOC within seconds and may allow excessive harmful emissions to be passed into the environment.

This study attempts to quantify the effects of different species representative of those found in rich PCI exhaust on a platinum-based DOC in a background of exhaust from an engine operating in a lean PCI regime. Excess carbon monoxide, propane, propylene, and methane were injected in varying concentrations while catalyst outlet temperature, carbon monoxide, and hydrocarbon conversion were measured for a period of 200 s. Of the injected species, it is shown that propylene has the greatest deactivation effect on the catalyst followed by carbon monoxide, both in terms of time and concentration. Propane is found not to deactivate the catalyst even in very globally fuel-rich conditions whereas methane acts as an inert gas over the catalyst in the temperature range of interest. It is concluded from the study that high concentrations of carbon monoxide do not act alone in the poisoning process for the rich PCI condition. The presence of some partial oxidation products such as unsaturated hydrocarbons can also have an adverse effect on DOC performance.
Continuous regeneration of an electrically heated diesel particulate trap
Authors: Arai M , Saito M , Mitsuyama Y
Published: December 2007

A wall-flow type diesel particulate trap using electrostatic field (E-DPT) was proposed to remove soot particles exhausted from diesel engines. This device was capable of trapping soot particles by electrostatic effect by applying a direct current electric field between two electro-plates separated by 1.5 mm. Soot trapped on the plates formed bridges of soot clusters in a narrow space between the electro-plates and it was burned by Joule heating owing to the direct electrification through the bridges. When the applied voltage to the E-DPT was lower than the critical value ( Ep = 200 V), only the soot accumulation was observed. Its accumulation mechanism looked like a kind of electrostatic precipitator, and soot burning caused by the electrification through soot bridges was observed at higher applied voltages at 250-300 V. When soot accumulation and burning were balanced, a stable operation of E-DPT at 60-80 per cent removal efficiency was attained. An analysis of the experimental data on soot removal efficiency, power consumption, and heat balance during steady operation showed that the E-DPT developed is a potential system for practical application to actual diesel engines.
Soft and hard computing approaches for real-time prediction of currents in a tide-dominated coastal area
Authors: Charhate S B , Deo M C , Kumar V Sanil
Published: December 2007

The prediction of tidal currents in the coastal region on a real-time or online basis is useful in taking operation- and planning-related decisions such as towing of vessels and monitoring of oil slick movements. Currently, however, this is done in offline mode on the basis of the statistical method of harmonic analysis involving fitting of harmonic functions to measured data. Alternatively, numerical solutions of hydrodynamic models can also provide spatial and temporal information on currents. Owing to the complex real sea conditions, such methods may not always yield satisfactory results. This paper discusses a few alternative approaches based on the soft computing tools of artificial neural networks (ANNs) and genetic programming (GP), as well as the hard mathematical approaches of stochastic and statistical methods. The suggested schemes use only a univariate time series of currents to forecast their future values. The measurements of coastal currents made at two locations in the Gulf of Khambhat along the west coast of India have been analysed. The current predictions over a time step of 20 min, a few hours, and a day at the specified locations were carried out. It was found that the soft computing schemes of GP and ANN performed better than the traditional hard technique of harmonic analysis in the present application. This work should initiate more application of GP in coastal engineering. Addressing the problem of current predictions in real-time mode based on analysis of observed time series of ocean currents is a specialty of this work.
A Novel TTF-based Electron-donor with Imidazole-annelation Having Hydrogen-bonding and Proton-transfer Abilities
Authors: Morita Yasushi , Yamamoto Yosuke , Yakiyama Yumi , Murata Tsuyoshi , Nakasuji Kazuhiro
Published: December 2007

A TTF derivative with an imidazole-annelation having hydrogen-bond and proton-donor/acceptor abilities was newly synthesized. The donor formed a two-dimensional structure by hydrogen-bonds and π stacks in the crystal. The imidazole-annelation increased the electron-donating ability of the donor.
Lewis Base Catalyzed 1,3-Dithiane Addition to Carbonyl Compounds Using 2-Trimethylsilyl-1,3-dithiane
Authors: Michida Makoto , Mukaiyama Teruaki
Published: December 2007

1,3-Dithiane addition to various aldehydes and ketones using 2-trimethylsilyl-1,3-dithiane in the presence of a catalytic amount of a Lewis base such as tetrabutylammonium phenoxide (PhONn-Bu4) proceeds smoothly to afford the corresponding α-hydroxy dithiane compounds in good to high yields under mild conditions.
Intermediate-range Order in Mesoporous Silicas Investigated by a High-energy X-ray Diffraction Technique
Authors: Wakihara Toru , Fan Wei , Kohara Shinji , Ogura Masaru , Sankar Gopinathan , Okubo Tatsuya
Published: December 2007

We perform a high-energy X-ray diffraction study comparing bulk amorphous silica with MCM-41 and SBA-15 that are representative mesoporous silicas prepared in basic and acidic conditions, respectively. It is revealed that mesoporous silicas, especially SBA-15, have less ordered structures and contain larger fractions of three- and four-membered rings than does bulk amorphous silica.
Quasi-solid Polymer Electrolytes Based on Polyacrylonitrile and Plasticizers for Indoline Dye Sensitized Solar Cells of Efficiency 5.3%
Authors: Ileperuma Oliver A , Kumara G R Asoka , Murakami Kenji
Published: December 2007

Fabrication of quasi-solid solar cells based on nanostructured TiO2 sensitized by the organic dye indoline is reported here. The electrolyte is based on polyacrylonitrile polymer with ethylene carbonate and propylene carbonate as plasticizers incorporating tetrabutylammonium iodide (0.70 M) and iodine (0.14 M). A conversion efficiency of 5.3% was achieved under AM 1.5 irradiation (100 mW cm−2).
Deuteration and Dimerization of Acetylene with a Nieuwland Catalyst in Deuterium Oxide
Authors: Tachiyama Takashi , Yoshida Makoto , Aoyagi Tatsuhiro , Fukuzumi Shunichi
Published: December 2007

Efficient deuteration and dimerization of acetylene have been readily attained in deuterium oxide with a Nieuwland catalyst which is practically used for dimerization of acetylene.
Separation of AmIII from EuIII Using an Improved System of Flow-counterbalanced Capillary Electrophoresis
Authors: Mori Tomotaka , Ishii Yasuo , Hayashi Kazunori , Yanaga Makoto , Satoh Isamu , Suganuma Hideo
Published: December 2007

Separation of 241AmIII from 152,154EuIII was carried out using an improved system of flow-counterbalanced capillary electrophoresis in a thiocyanate medium. In this system, EuIII was electrophoresed in the opposite direction to AmIII due to a combination of (1) the difference in the moving velocities of EuIII and AmIII, and (2) a constant flow in the capillary caused by a difference in the water levels of the inlet and outlet of the sample solution.
One-step Synthesis of Dibutyl Furandicarboxylates from Galactaric Acid
Authors: Taguchi Yoichi , Oishi Akihiro , Iida Hiroshi
Published: December 2007

Dibutyl 2,5-furandicarboxylate (2) and dibutyl 2,3-furandicarboxylate (3) were synthesized using one step from galactaric acid and 1-butanol. Sulfuric acid, p-toluenesulfonic acid, and heteropolyacids were good catalysts for the reaction. The reaction time was dependent on the amount of the catalyst, but the final yields of the main product, 2 remained unchanged.
Synthesis of Staudinger-type Molecular Probe for Catch-and-release Purification of the Binding Protein for Potassium Isolespedezate, a Leaf-closing Substance of Leguminous Plant
Authors: Fujii Tomohiko , Kato Nobuki , Iwakura Izumi , Manabe Yoshiyuki , Ueda Minoru
Published: December 2007

We synthesized azide-containing photoaffinity probe 1 based on the structure of potassium isolespedezate. This probe can be used for catch-and-release-mechanism purification of binding protein for 1: photo-crosslinking with 1 gave azide-labeled receptor which can be captured by phosphane-linked gel matrix by the Staudinger ligation. After washing the gel, the caught binding protein can be released by the reductive cleavage of disulfide bond in 1. This process can be used as a convenient method for the purification of binding protein for bioactive natural product.
Rearrangement and Fragmentation of Isomeric C4H5O Anions upon Collision Activation: A Combined Experimental and ab Initio Study
Authors: Dua Suresh , Bowie John H. , Hevko John M.
Published: December 2007

The 3,4-epoxybutoxide anion on collisional activation in the gas phase forms an intermediate ion complex (vinyl ethylene oxide, HO−) which eliminates water by two competitive pathways, viz. (i) by the HO− ion deprotonating the neutral to produce a vinylethylene oxide anion deprotonated on the ring adjacent to the vinyl substituent: this anion then ring opens to give −CH2–CO–CH=CH2 and (ii) by the HO− ion deprotonating at the ring methylene group to give a cyclic anion which ring opens to yield −CH2–CH=CH–CHO. In contrast, when vinyl ethylene oxide is allowed to react with HO− in the source of the mass spectrometer, deprotonation occurs mainly, if not exclusively, at the ring methylene position (as shown by deuterium labelling) to yield the anion −CH2–CH=CH–CHO. The two ring-opening processes have been investigated using theoretical studies at the MP2 Fc/6-31+G(d) level of theory.
A Practical Protocol for the Reduction of Disulfide Bonds in Proteins Prior to Analysis by Mass Spectrometry
Authors: Scigelova Michaela , Green Philip S. , Giannakopulos Anastassios E. , Rodger Alison , Crout David H.G. , Derrick Peter J.
Published: December 2007

Aquick, simple applicable protocol for the reduction of protein disulfide bonds for the purposes of mass spectrometry has been established. The method utilises the chemical reducing agent dithiothreitol. Proteins with various numbers of disulfide bonds per molecule were chosen for the study to demonstrate the general applicability of the method. The results obtained under controlled conditions (concentration of reagents, pH, temperature) showed that a five-minute treatment at 70°C with 10 mM dithiothreitol in 5 mM ammonium acetate buffer pH 5.5 was sufficient for complete reduction of disulfide bonds in all investigated proteins (α-lactalbumin, lysozyme, ribonuclease, oxytocin and wheat germ agglutinin). The progress of disulfide bond reduction was observed by electrospray ionisation and Fourier transform ion cyclotron resonance mass spectrometry. Circular dichroism was used to monitor conformational changes of reduced proteins and of their unreduced counterparts undergoing the same heat treatment.
Letter: Calibration of Electrospray Mass Spectrometers with rccc-2,8,14,20-Tetra-n-Octyl-5,11,17,23-Tetrahydroxyresorc[4]Arene in the High Mass Range up to m/z 6000
Authors: Letzel Matthias C. , Agena Ceno , Mattay Jochen
Published: December 2007

rccc-2,8,14,20-Tetra- n-octyl-5,11,17,23-tetrahydroxyresorc[4]arene has the property to form cluster ions in both positive- and negative-ion mode with good intensity without the addition of any modifiers such as cesium. These cluster ions may be used for the calibration of electrospray mass spectrometers in the mass range up to m/z 6000.
The Formation of Protonated Dimethyl Ether from the Metastable Molecular Ions of 1-Methoxy-2-Propanol, CH3OCH2CH(OH)CH3
Authors: Nakajima Satoshi , Asakawa Tatsuki , Sekiguchi Osamu , Tajima Susumu , Nibbering Nico M.M.
Published: December 2007

The unimolecular metastable decomposition of 1-methoxy-2-propanol, CH3OCH2CH(OH)CH3 (mol. wt. 90) induced by electron ionization, has been investigated by use of mass-analyzed ion kinetic energy (MIKE) spectrometry and D-labeling in conjunction with thermochemical data. In the metastable time window, the molecular ions decompose almost exclusively into ions at m/z 47 [i.e. protonated dimethyl ether, CH3O+(H)CH3] by the loss of a C2H3O radical species following a double hydrogen atom transfer (DHT). Until now, only one DHT mechanism has been proposed, involving and accounting for the loss of an acetyl radical, C2H3O. In the present study it is shown that more DHT mechanisms are operative, leading to the losses of isomeric C2H3O radicals. The results obtained are best explained by the formation of the key intermediate ion–molecule complexes [CH3OCH3+•, CH3CHO] and [CH3OCH3, CH2=C(H)OH+•] following unimolecular metastable dissociation of the molecular ion. Subsequent hydrogen atom abstraction channels by CH3OCH3+• in the former complex and proton abstraction channels by CH3OCH3 in the latter complex lead eventually to the formation of protonated dimethyl ether with m/z 47.
Gas-Phase Conformation Can Have an Influence on Peptide Fragmentation
Authors: Griffiths William J. , Jonsson Andreas P.
Published: December 2007

In the post-genomic era, mass spectrometry is destined to fulfil a central role in biomedical research, and it is in the area of protein identification that mass spectrometry is now most rapidly expanding. An important identification method is to subject a protein to proteolysis and determine the resulting peptide masses and/or primary structure. From such determinations proteins can be identified. Tandem mass spectrometry (MS/MS) is used to determine primary structure and, for high-throughput identification, computer-based automated strategies are a prerequisite. Computer programs are available for such identifications, where simulated MS/MS spectra of amino acid sequences within a database are generated and compared to experimental spectra. Such algorithms take into account empirical rules for peptide fragmentation, rather than specific gas-phase ion chemistry. For example, fragmentation of each peptide bond is usually considered to be equally facile. In reality, this is not the case. Gas-phase ion chemistry bears an important role in determining the abundance of fragment ions in MS/MS spectra. In this communication, the gas-phase ion chemistry responsible for the facile cleavage between Gln and Gly residues is investigated, particularly in relation to Proline Rich Protein-1.
Improved Accuracy in the Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Determination of the Molecular Mass of Cyanogen Bromide Fragments of Proteins by Post-Cleavage Reaction with Tris(Hydroxymethyl)Aminomethane
Authors: Compagnini A. , Cunsolo V. , Foti S. , Saletti R.
Published: December 2007

In order to improve accuracy in the matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) determination of the molecular mass of CNBr fragments of proteins, the post-cleavage reaction of these fragments with tris(hydroxymethyl)amino methane was tested. Mixtures of homoserine and homoserine lactone peptide fragments originating from CNBr cleavage of cytochrome c, lysozyme and human serum albumin were used as model compounds. Reaction of these fragments with tris(hydroxymethyl) aminomethane converts quantitatively the homoserine lactone ending peptides into the corresponding amides, leaving unmodified the homoserine ending forms. Thus, pairs of fragments which differ by 103 Daare formed. In contrast to the unmodified CNBr mixtures of peptides, which, due to the overlap of the signals of the free homoserine and homoserine lactone forms, produce unresolved peaks in the high mass region of the MALDI spectra, these pairs of fragments give resolved peaks up to a mass doublet of 20,000 Da. This permits accurate determination of the molecular mass of the fragments. Using this procedure, differences lower than 5 Da with respect to the calculated values were obtained for the fragments examined.
Integrated System for High-Throughput Protein Identification Using a Microfabricated Device Coupled to Capillary Electrophoresis/Nanoelectrospray Mass Spectrometry
Authors: Li Jianjun , Tremblay Tammy-Lynn , Thibault Pierre , Wang Can , Attiya Said , Harrison D. Jed
Published: December 2007

An integrated microsystem providing rapid analyses of trace-level tryptic digests for proteomics application is presented. This modular microsystem includes an autosampler and a microfabricated device comprising a sample introduction port and an array of separation channels together with a low dead-volume facility enabling an interface to nanoelectrospray mass spectrometry. Sequential injection and separation of peptide standards and tryptic digests was achieved with a throughput of up to 30 samples per hour with less than 3% sample carryover. Replicate injections of peptide mixtures indicated that reproducibility of migration time was typically better than 2.3% relative standard deviation (RSD), whereas RSD values of 3.7–11.8% were observed on peak height. Mass spectral detection of sub-micromolar protein digests (< 7 fmol per injection) was achieved using a quadrupole/time-of-flight instrument in less than 2 min per sample with peak widths of 1.8–7.0 s. The analytical potential of this integrated device for the identification of gel-isolated proteins from Neisseria meningitidis immunotype L3 has been demonstrated using both peptide mass-fingerprint database searching and on-line tandem mass spectrometry.
Investigation of the Applicability of a Sequential Digestion Protocol Using Trypsin and Leucine Aminopeptidase M for Protein Identification by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry
Authors: Doucette Alan , Li Liang
Published: December 2007

An investigation into the applicability of a sequential digestion procedure involving endo- and exoprotease digestion of proteins is reported. The procedure involves the digestion of a protein sample with trypsin, yielding peptide fragments characteristic of the protein. The resulting mixture of peptide fragments is then subjected to N-terminal sequencing with leucine aminopeptidase M (LAP), with matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of the various digestion products. Several proteins in solution, as well as gel-extracted proteins, were subjected to this sequential enzyme digestion procedure. The results of these experiments reveal that LAP will preferentially cleave specific peptides of the trypsin-digested sample with high efficiency, while leaving other peptides undigested. Also, the length of the amino acid sequence tags that can be generated with this method is limited; the longest sequence tag generated from a single tryptic peptide was four amino acids, even though the digestion was allowed to proceed for long times. In the experiments, N-terminal digestion products were detected as early as two minutes, or as late as 90 minutes, following the addition of LAP to the sample. The method was shown to be effective for sub-picomole starting quantities of protein, although with some loss in digestion efficiency at lower concentrations of starting material. This method is useful in providing additional sequence information to increase the level of confidence in protein identification, as illustrated in the identification of bacterial proteins fractionated by HPLC. In some instances, this method can provide additional sequence information where post-source decay and nanospray mass spectrometry failed to generate fragment-ion spectra. This is illustrated by an example where the procedure was applied to a membrane protein, CD9, that had been isolated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Although the sequential digestion procedure requires more human intervention, it is a straightforward method and can be readily implemented.
Mass Spectrometric Characterization of Proteins Extracted from Jurkat T Cell Detergent-Resistant Membrane Domains
Authors: von Haller Priska D. , Donohoe Sam , Aebersold Ruedi , Watts Julian D. , Goodlett David R.
Published: December 2007

Plasma membranes of most cell types are thought to contain microdomains commonly referred to as lipid rafts, biochemically distinct from bulk plasma membrane and apparently enriched for proteins involved in signal transduction. In T cells, it is believed that lipid rafts aggregate at the site of T cell receptor engagement and act as foci for initiation of the signaling process. In order to gain insight into the possible functioning of lipid rafts, we applied microcapillary liquid chromatography-electrospray ionization-tandem mass spectrometry (μLC-ESI-MS/MS) methodologies to the identification of proteins which co-purified with lipid rafts. Following isolation of lipid rafts as Triton-insoluble, low-density membrane fractions from Jurkat T cells, tryptic digests were generated of electrophoretically-resolved, individual protein bands. Alternatively, avidin-affinity purification was used to isolate cysteine-containing peptides from total tryptic digests of unseparated lipid raft proteins following protein labeling with a cysteine-specific biotinylation reagent. In both cases, protein identifications were made by comparison of tandem mass spectra, generated by μLC-ESI-MS/MS, with both protein and DNA sequence databases using Sequest software. Proteins identified essentially fell into two groups: cytoskeletal proteins and proteins involved in signal transduction. These findings are discussed in light of the current understanding of both lipid-raft biology and signal transduction.
Detection and Localisation of Disulphide Bonds in a Synthetic Peptide Reproducing the Sequence 1–30 of Par j 1.0101 by Electrospray Ionisation Mass Spectrometry
Authors: Cunsolo Vincenzo , Foti Salvatore , Saletti Rosaria , Ceraulo Leopoldo , di Stefano Vita
Published: December 2007

The structural characterisation of a synthetic peptide reproducing the sequence 1–30 of Par j 1.0101, a major allergenic protein present in the pollen of Parietaria judaica, by combined use of chemical and enzymatic cleavage, reversed-phase high-performance liquid chromatography (RP-HPLC) and electrospray ionisation mass spectrometry (ESI-MS), is described. Direct ESI-MS of the synthetic peptide after reaction with methyl iodide showed that the product is a mixture of two peptides: one form in which two out of the four cysteine residues present in the sequence are oxidised and a minor amount of another form in which all the cysteines are fully reduced. It was ascertained, using the combined procedure described above and without prior separation of the two species, that the disulphide bond in the partially oxidised form is located between cysteines 29 and 30. These results show the usefulness of this approach for characterising synthetic peptides containing multiple cysteine residues in the sequence.
Gas Chromatography/Mass Spectrometry of Polyethylene Glycol Oligomers
Authors: Onigbinde Adebayo , Nicol Gordon , Munson Burnaby
Published: December 2007

Polyethylene glycol (PEG) oligomers, H(OC2H4O) nH, were analyzed by gas chromatography/mass spectrometry (GC/MS) for oligomers, n = 2–11, without indications of pyrolysis of the higher oligomers at oven temperatures of 330°C. The electron ionization (EI) mass spectra (70 eV and 12–14 eV) of these PEG oligomers contain only low molecular weight fragment ions and, essentially, no M+ ions. The low-voltage EI spectra contain more abundant high mass ions and allow easier identification of the PEG oligomers. The major fragment ions in all EI spectra are (C2H4O) xH+ at m/z 45, 89, 133 and 177. The base peak in the low-voltage spectra varies with molecular weight and suggests preferential cleavage at the second and third ether linkages. The relative molar sensitivities (70 eV EI) of PEG oligomers ( n = 1–6) are linear functions of molecular weight or polarizability ratios. The CH4 chemical ionization mass spectra of the PEG oligomers contain, predominantly, (C2H4O) xH+ ions at m/z 45, 89, 133 and 177. The relative abundances of MH+ ions vary markedly across the chromatographic peaks because these ions are formed predominantly by sample ion / sample molecule reactions. Proton transfer reactions from CH5+ and C2H5+ to the PEG oligomers are almost entirely dissociative. The i-C4H10 CI mass spectra of PEG oligomers contain MH+ as the base peaks. The relative abundances of MH+ ions do not vary significantly across the chromatographic peaks but do increase with increasing pressure of i-C4H10. The extent of decomposition of MH+ ions in i-C4H10 CI mass spectra increases with increasing molecular weight of the PEG oligomers. Relative molar sensitivities (CH4 CI and i-C4H10 CI) of PEG oligomers ( n = 1–6) are essentially the same linear functions of molecular weight ratio.
Complexation of Glycine by Atomic Metal Cations in the Gas Phase
Authors: Hoyau Sophie , Pélicier Jean-Pierre , Rogalewicz Françoise , Hoppilliard Yannik , Ohanessian Gilles
Published: December 2007

The interaction of glycine with 15 metal cations (M+ or M2+)in the gas phase has been studied by quantum chemical calculations. Three types of complexation have been considered: (i)chelation between nitrogen and the carbonyl oxygen, (ii)attachment to the carboxyl group of neutral glycine and (iii)attachment to the carboxylate group of zwitterionic glycine. It is found that the relative energies of these structures and, therefore, the nature of the lowest energy isomer, depend dramatically upon the metal ion. In several cases, metal ion attachment to glycine results in a switch from the neutral form (the most stable form of gaseous glycine)to the zwitterion (the most stable form of glycine in solution). This occurs with doubly-charged cations and, in some cases, with monocations. Several metal properties are invoked to explain these results: metal charge, size, electron affinity and polarizability. The role of metal–ion polarizability is illustrated by the computed geometries of M(CH3OH)2n+ complexes.
Halogen Counter-Ion Effect on the Dissociation of Monosaccharide—iron Complexes Generated by Electrospray Ionization Combined with an Ion Trap Mass Spectrometer
Authors: Carlesso V. , Fournier F. , Afonso C. , Tabet J.C.
Published: December 2007

A primary focus of research in our laboratory has been to determine the stereochemistry of four isomeric monosaccharides using the electrospray ionization/desorption mode combined with an ion trap mass spectrometer. α/β-Anomers of glucose, mannose, galactose and talose differ stereochemically at the C2 and C4 positions; previous work described an efficient system able to easily differentiate these four isomeric hexoses when combined with the iron(II)ion. This approach was based upon interaction between the sugar analyte and iron(II)yielding cationized [MFeIICl]+ monosaccharides which were then studied by sequential tandem mass spectrometry. The daughter ions of these clusters were produced using the resonant excitation mode and are characterized by variable rate constants related to the hydroxyl stereochemistry. When submitted to resonant excitation conditions, the [MFeIICl]+ cluster ions undergo processes that can be either stereospecific in certain cases or, more usually, kinetically controlled by stereochemical effects. It is, therefore, possible to distinguish stereoisomeric sugars by examining the variation in relative abundance of diagnostic fragment ions. The present work reports data on the influence of counter-ions associated with iron(II)(viz. FeCl2, FeBr2, FeI2 and FeF2) on desorbed species obtained by electrospray desorption/ionization. The cationized monomeric [MFeIIX]+ and dimeric [M2FeIIX]+ ions were studied by collision-induced dissociation (CID)to demonstrate a significant halogen effect from the resonant excitation experiments and on the extent of the differentiation of the diastereomers. The data presented demonstrate the influence of thermochemical properties (i.e. acidity and basicity), mainly related to the halide size, on the dissociation of cationic [MFeIIX]+ and [M2FeIIX]+ sugar–metal complexes in CID experiments. Only weak effects due to the halide were observed during desorption itself, when comparison of the latter cluster with the former shows a relatively enhanced desorption yield of the monomer with an iodide counter-ion. However, the more significant counter-ion effects concern the cationized dimeric species, which present spectacular product-ion abundance changes in CID spectra. In all cases, it has been possible to distinguish the diastereomers.
Structure, Thermochemistry and Reactivity of Protonated Glycolaldehyde
Authors: Bouchoux Guy , Penaud-Berruyer Florence , Bertrand William
Published: December 2007

Structures and relative energies of various conformers of the simplest sugar, glycolaldehyde, 1, and its protonated form, [1H]+, were investigated by ab initio molecular orbital calculations. The 298 K heats of formation of the most stable conformers, deduced from the atomization energies at the G2 level, are equal to Δ fH°(1) = −324.8 kJ mol−1 and Δ fH°[1H]+ = 426.0 kJ mol−1. The corresponding proton affinity value is PA(1) = 779.8 kJ mol−1, in perfect agreement with the experimental determination of 783.3 ± 3.8 kJ mol−1 obtained by the kinetic method. A gas-phase basicity value, GB(1), of 745–748 kJ mol−1 is also deduced from theory and experiment. The exclusive dissociation channel of protonated glycolaldehyde, [1H]+, is water loss which leads essentially to the acylium ion [CH3CO]+. The corresponding potential energy profile, investigated at the MP2/6–31G* level, reveals a route via a [CH3CO]+ / water complex after an energy determining step involving a simultaneous 1,2-hydrogen migration and C–O bond elongation. The critical energy of the reaction, evaluated at the G2(MP2,SVP)level, is 170 kJ mol −1 above the most stable conformation of the [1H]+ ion. The 298 K heats of formation of the three most stable [C2H3O]+ ions have been calculated at the G2 level: Δ fH°[CH3CO]+ = 655.0 kJ mol−1, Δ fH°[CH2COH]+ = 833.0 kJ mol−1, Δ fH°[c-CH2CHO]+ = 886.2 kJ mol−1.
Conformational Properties of α-Dendrotoxin Using Electrospray Mass Spectrometry
Authors: Belva Hélène , Lange Catherine , Segalas Isabelle
Published: December 2007

To examine the conformation of α-dendrotoxin, charge state distributions (CSD)and hydrogen/deuterium (H/D)isotopic exchange using electrospray-ionization mass spectrometry [ES-MS] have been used. Here, it cannot be deduced from the CSDs that some basic residues are hidden in the core of the structure. At neutral pH, the CSDs reflect the equilibrium bulk solution exactly. Seven basic residues seem to be shielded from the solvent, according to calculations from the X-ray structure. But, under acidic conditions, the CSDs observed in mass spectra are not a true reflection of the equilibrium bulk solution, partly because of an increased intramolecular electrostatic effect with the gaseous ions. H/D exchange experiments show that three to seven hydrogens are involved in hydrogen bonds. The resistance to urea denaturation has also been investigated. Urea and 1,4-dithiothreitol (DTT)denaturation together lead to unfolded conformers. During this reduction of the bridges, it is observed that the Cys16–Cys40 and Cys32–Cys53 linkages are more accessible to the reducing agent than the Cys7–Cys57 linkage, which is very important by maintaining a compact fold.
De Novo Sequencing by Nano-Electrospray Multiple-Stage Tandem Mass Spectrometry of An Immune-Induced Peptide of Drosophila Melanogaster
Authors: Carte Nathalie , Cavusoglu Nukhet , Leize Emmanuelle , Van Dorsselaer Alain , Charlet Maurice , Bulet Philippe
Published: December 2007

To combat infection, the fruit fly Drosophila melanogaster responds by rapid synthesis of a series of immune-induced molecules reported as Drosophila immune-induced molecules (DIMs). Characterization of the primary structure of the DIMs is required to establish their exact function. In order to get such information, previous studies on the elucidation of primary structures of the DIMs were developed using a methodology combining matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), high-performance liquid chromatography (HPLC), enzymatic digestion and Edman degradation. Nevertheless, some of the DIMs were resistant to classical Edman sequencing. Therefore, mass spectrometry was used to characterize the primary structure of one of the DIMs, namely the N-blocked DIM13 peptide. The complete sequence of DIM13 was established by means of a strategy of nano-electrospray ionisation (ESI)combined with multiple-stage tandem mass spectrometry (MS n)and then was partially confirmed with a combination of enzymatic digestions and MALDI-MS analyses. Interestingly, most of the amino acid sequences have been determined using three-stage (MS3)and four-stage (MS4)tandem experiments, whereas classical tandem mass spectrometry (MS2)yielded only incomplete sequence information. Finally, DIM13 is a 23 amino acid peptide with a pyroglutamic modification at the N terminal position. This work illustrates the remarkable advantages of MS3 and MS4 compared with the MS2 experiment for de novo peptide sequencing. The use of nano-ESI also makes these experiments compatible with the low amount (picomolar level)of DIM13 peptide available for sequencing by ESI-MS n.
Structural Elucidation of Eighteen Cerebrosides from Holothuria Coronopertusa in a Complex Mixture by High-Energy Collision-Induced Dissociation of [M + Li]+ Ions
Authors: Hue Nathalie , Montagnac Alain , Païs Mary , Serani Laurent , Laprévote Olivier , Menou Jean-Louis , Debitus Cécile
Published: December 2007

Eighteen cerebrosides were detected in admixture from the sea cucumber Holothuria coronopertusa. Their structures have been established on the basis of liquid-secondary ion mass spectrometry (LSIMS)experiments. The collision-induced dissociation (CID)of the lithiated molecules ([M + Li]+)led to diagnostic fragment ions which were further identified by tandem mass spectrometry (MS/MS). In the present study, the combination of LSIMS as ionization mode and high-energy MS/MS analysis appears to be a very powerful method for the rapid analysis of unresolved mixtures of complex molecules.
Gas Chromatograhy-Tandem Mass Spectrometry Determination of 8-Iso-PGF2α, a Biomarker of in vivo Lipid Peroxidation, in Human Plasma and Urine
Authors: Richelle M. , Turini M.E. , Guidoux R. , Tavazzi I. , Métairon S. , Fay L.B.
Published: December 2007

The measurement of isoprostanes is a promising assay that is specific and sensitive enough to detect in vivo lipid peroxidation. We present here a gas chromatography-tandem mass spectrometry (GC/MS/MS)method that enables determination of 8-iso-prostaglandin F2α (8-iso-PGF2α)in human plasma and urine. After the addition of [2H4]-PGF2α as the internal standard to acidified plasma or urine, the samples are purified on C18 and silica cartridges, derivatised as pentafluorobenzyl esters, extracted with diethyl ether, purified on silica gel TLC plates and finally silylated. Then, 8-iso-PGF2α and its internal standard are measured by GC/MS/MS in selective-reaction monitoring mode using the transition [M −181]− to [M −181 – (3 × 90)]−. The detection limit of this method is 5 pg mL−1. Its application is presented in two situations of oxidative stress: in vitro low-density lipoprotein oxidation and in smokers. Measurement of urinary 8-iso-PGF2α levels provides a non-invasive in vivo index of free radical generation that appears not to be confounded by changes in diet.