bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of phosphopeptides from protein digests using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and nanoelectrospray quadrupole time‐of‐flight mass spectrometry
Authors: Ma Yuliang , Lu Yun , Zeng Huiqing , Ron David , Mo Wenjun , Neubert Thomas A. 
Published: August 2002

AbstractA two‐step mass spectrometric method for characterization of phosphopeptides from peptide mixtures is presented. In the first step, phosphopeptide candidates were identified by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) based on their higher relative intensities in negative ion MALDI spectra than in positive ion MALDI spectra. The detection limit for this step was found to be 18 femtomoles or lower in the case of unfractionated in‐solution digests of a model phosphoprotein, β‐casein. In the second step, nanoelectrospray tandem mass (nES‐MS/MS) spectra of doubly or triply charged precursor ions of these candidate phosphopeptides were obtained using a quadrupole time‐of‐flight (Q‐TOF) mass spectrometer. This step provided information about the phosphorylated residues, and ruled out nonphosphorylated candidates, for these peptides. After [32P] labeling and reverse‐phase high‐performance liquid chromatography (RP‐HPLC) to simplify the mixtures and to monitor the efficiency of phosphopeptide identification, we used this method to identify multiple autophosphorylation sites on the PKR‐like endoplasmic reticulum kinase (PERK), a recently discovered mammalian stress‐response protein. Copyright © 2001 John Wiley & Sons, Ltd.
Electrospray ionization with ambient pressure ion mobility separation and mass analysis by orthogonal time‐of‐flight mass spectrometry
Authors: Steiner Wes E. , Clowers Brian H. , Fuhrer Katrin , Gonin Marc , Matz Laura M. , Siems William F. , Schultz Albert J. , Hill Herbert H. 
Published: August 2002

AbstractRapid screening and identification of drug and other mixtures are possible using a novel ambient pressure high‐resolution ion mobility (APIMS) orthogonal reflector time‐of‐flight mass spectrometer (TOFMS). Departing ions from the APIMS drift tube traversed a pressure interface between the APIMS and TOFMS where they were subjected to numerous gas collisions that could produce selective fragmentation. By increasing the accelerating field in the pressure interface region, the ions generated using water‐cooled electrospray ionization (ESI) underwent collision‐induced dissociation (CID). Mixtures of ESI ions were separated by APIMS based on their respective size‐to‐charge (s/z) ratios while CID and analysis of mass‐to‐charge (m/z) ratios occurred in the pressure interface and TOFMS. Product ions that were formed in this pressure interface region could be readily assigned to precursor ions by matching the mobility drift times. This process was demonstrated by the examination of a mixture of amphetamines and the resulting fragmentation patterns of the mobility‐separated precursor ion species [M + H]+. Copyright © 2001 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric observation of a peptide triplet induced by thermal cleavage of cystine
Authors: Kim Jong‐Seo , Kim Hie‐Joon 
Published: August 2002

AbstractHeat‐induced (90 °C, 30 min) β‐elimination of a cystine residue leads to cleavage of a disulfide bond and produces a set of three peptides with a cysteine residue, a thiocysteine residue (+32Da), and a dehydroalanine residue (−34Da). This characteristic feature was observed from somatostatin and insulin by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Mass spectrometric observation of this triplet is useful in identifying the presence of a cystine residue in a peptide, and could assist mass spectrometric identification of the peptide from a database. Copyright © 2001 John Wiley & Sons, Ltd.
Gas‐phase ion chemistry of Glu/Met systems
Authors: Wincel H. , Fokkens R. H. 
Published: August 2002

AbstractA combined chemical ionisation and tandem mass spectrometry (MS/MS) approach has been used for investigation of the gas‐phase ion chemistry of systems containing the amino acids Glu and Met, and the dipeptides γ‐Glu‐Met and Met‐Glu. The metastable fragmentation of the protonated dimer, (Glu)2H+, reveals an intracluster reaction leading to the elimination of the Glu residue. The main features of the ion‐molecule reactions observed in the systems containing Glu and Glu + Met can be described in terms of sequential adduct formation. The results obtained for the thermal dehydration of Glu were used to rationalise the formation of the proton‐bound structures (Glu − H2O)···H+··· (Glu − H2O) and (Glu − H2O)3·H+. The adduct ions, [(Glu − H2O) + H + Glu]+ and [(Glu − H2O) + H + Met]+, and further association products were also observed. The results lead to a reconsideration of the structural aspects proposed earlier for these species in the sense that they suggest that the systems correspond to a mixture of isomeric covalent and proton‐bound structures.The thermal effects on the decomposition of the neutral (γ‐Glu‐Met) and its protonated form, (γ‐Glu‐Met)H+, at m/z 279 were investigated, and dramatic changes in the MI spectra of the m/z 279 ion with temperature were found. A mechanistic explanation for the observed evolution of higher mass ion peaks in the mass spectra is developed. Copyright © 2001 John Wiley & Sons, Ltd.
Silver stain removal using H2O2 for enhanced peptide mass mapping by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Sumner Lloyd W. , Wolf‐Sumner Barbara , White Steven P. , Asirvatham Victor S. 
Published: August 2002

AbstractHydrogen peroxide solutions are reported for the removal of silver stain from proteins isolated in polyacrylamide gels. Removal of silver stain prior to in‐gel digestion is shown to enhance sensitivity and sequence coverage of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) peptide mass maps. The rate of silver removal using H2O2 is influenced by H2O2 concentration and increases with increasing pH. The presence of complexation reagents such as ammonia from mass spectrometry compatible ammonium bicarbonate solutions enhances the efficiency and speed of H2O2‐mediated silver removal. H2O2‐mediated silver removal using the described procedure does not appear to have any detrimental effects on proteins but is observed to produce a slightly elevated level of methionine oxidization over that usually observed in in‐gel tryptic digestion. Copyright © 2001 John Wiley & Sons, Ltd.
Microwave‐assisted protein staining: mass spectrometry compatible methods for rapid protein visualisation
Authors: Nesatyy Victor J. , Dacanay Andrew , Kelly John F. , Ross Neil W. 
Published: August 2002

AbstractThe effects of microwave irradiation on the staining of electrophoresed and electroblotted proteins have been assessed using currently available detection methods. Although the absorption of microwave radiation was found to be uneven, band intensity following microwave‐assisted protein staining (MAPS) was comparable and in some cases exceeded the intensity of the bands visualised by the original staining methods. It was found that microwave treatment drastically reduced the duration of the staining protocols for visualisation of the proteins separated by both one‐ and two‐dimensional electrophoresis. Application of MAPS methods did not affect peptide mass fingerprinting analysis by mass spectrometry and subsequent identification of the protein by database searching. The peptide mass maps corresponding to the proteins visualised using both the conventional and MAPS methods did not show significant difference in signal/noise ratio. Moreover, it appeared that microwave treatment of the gels resulted in the increased recovery of the peptides following in‐gel trypsin digestion. Briefly, microwave‐assisted protein staining methods were rapid, compatible with mass spectrometry and were equally effective on thin (0.75 mm) and thick (1.5 mm) gels (such as those used in 2D electrophoresis). Copyright © 2002 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.
Derivatization of small oligosaccharides prior to analysis by matrix‐assisted laser desorption/ionization using glycidyltrimethylammonium chloride and Girard's reagent T
Authors: Gouw Joost W. , Burgers Peter C. , Trikoupis Moschoula A. , Terlouw Johan K. 
Published: August 2002

AbstractIn matrix‐assisted laser desorption/ionization (MALDI) analyses of small oligosaccharides a very large increase in sensitivity (by a factor of 1000) may be obtained by introducing a quaternary ammonium center (‘quaternization’). Such a quaternary ammonium center may be introduced into the saccharide by reaction with commercially available glycidyltrimethylammonium chloride (GTMA), or by using Girard's reagent T (Naven and Harvey, Rapid Commun. Mass Spectrom. 1996; 10: 829). GTMA reacts with alcohol functionalities, whereas Girard's reagent T is specific for aldehyde and keto groups. Thus reducing saccharides can be derivatized by both GTMA and Girard's reagent T. For example, glucose or cellobiose having a stock concentration of 3 × 10−5 M (5 µg/mL) produces no sugar‐derived signals in conventional MALDI, but their quaternized derivatives, also at 3 × 10−5 M, yield intense signals, with the matrix‐derived signals only being weak. Similar results were obtained for glucosamine. Non‐reducing saccharides as well as sugar alcohols can be derivatized using GTMA; thus, although sucrose, raffinose and sorbitol do not react with Girard's reagent T, they all produce intense signals after derivatization with GTMA. An example of the application of these derivatization reactions is provided by the analysis of oligosaccharides in beer. Copyright © 2002 John Wiley & Sons, Ltd.
Analysis of protein ions in the range 3000–12000 Th under partial (no discharge) atmospheric pressure chemical ionization conditions using ion trap mass spectrometry
Authors: Cristoni Simone , Bernardi Luigi Rossi , Biunno Ida , Guidugli Federico 
Published: August 2002

AbstractA new approach, based on the use of atmospheric pressure chemical ionization ion trap mass spectrometry (APCI‐ITMS), but without a corona discharge, was investigated for application to creating and monitoring protein ions. It must be emphasized that APCI is not usually used in protein analysis. In order to verify the applicability of the proposed method to the analysis of proteins, two standard proteins (horse cytochrome c and horse myoglobin) were analyzed. A mixture of the two proteins was also analyzed showing that this novel approach, based on the use of APCI, can be used in the analysis of protein mixtures. Copyright © 2002 John Wiley & Sons, Ltd.
Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis
Authors: Sørensen Helle Aagaard , Sperotto Maria Maddalena , Petersen Marianne , Keşmir Can , Radzikowski Louise , Jacobsen Susanne , Søndergaard Ib 
Published: August 2002

AbstractThe performance of matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry with neural networks in wheat variety classification is further evaluated.1 Two principal issues were studied: (a) the number of varieties that could be classified correctly; and (b) various means of pre‐processing mass spectrometric data. The number of wheat varieties tested was increased from 10 to 30. The main pre‐processing method investigated was based on Gaussian smoothing of the spectra, but other methods based on normalisation procedures and multiplicative scatter correction of data were also used. With the final method, it was possible to classify 30 wheat varieties with 87% correctly classified mass spectra and a correlation coefficient of 0.90. Copyright © 2002 John Wiley & Sons, Ltd.
Centrifugal Bioreactors and Their Application in Remediation
Authors: Herman Heath H. , Lin Weimin , Petrecca Peter J. , Herman Tod M. , Bates Christopher , Simmons Robert , Houghton John 
Published: August 2002

AbstractA new approach to the maintenance of large microbial populations for bioremediation purposes has been
developed in which a centrifugal bioreactor is used to immobilize microbial populations at extremely high
density. The cells are ordered into a three‐dimensional array through which wastewater or groundwater
volumes may be flowed, unimpeded by frits or screens. The process methodology is independent of the type, shape,
or viability of the individual cells immobilized and, thus, may be adapted to many different bioremediation
needs. The utilization of this new process has been explored for three different types of remediation: the
removal of heavy metals from wastewater, the aerobic degradation of
methyl‐tert‐butyl ether (MTBE), and the anaerobic reduction of nitrate
to nitrogen gas. This article discusses the use of centrifugal bioreactors and their application in remediation.
© 2001 John Wiley & Sons, Inc.
Field Trial of Biosparging with Oxygen for Bioremediation of Volatile Organic Compounds
Authors: Sperry Kenneth L. , Stanley Christian , Kay James 
Published: August 2002

AbstractXpert Design & Diagnostics, LLC (XDD), & Conestoga‐Rovers and Associates
(CRA) conducted a biosparging field trial at a Superfund site in New Jersey. The biosparging field
trial proved that biosparging with oxygen was very effective in promoting the biological destruction of benzene.
The approximately 265‐day period of oxygen injection successfully reduced benzene concentrations by
several orders of magnitude, or even to non‐detect values, at least 40 feet from the point of injection.
Through co‐precipitation of arsenic with oxidized iron, biosparging also effectively reduced total
concentrations of arsenic and iron in groundwater. Based on the results of the biosparging field trial, the
final remedy for the site has been amended to include the use of biosparging technology as an alternative to
groundwater pumping and aboveground treatment in select locations. © 2001 John Wiley & Sons,Inc.
Full‐scale in‐situ biobarrier demonstration for containment and treatment of MTBE
Authors: Miller Karen D. , Johnson Paul C. , Bruce Cristin L. 
Published: August 2002

AbstractThe Naval Facilities Engineering Service Center (NFESC), Arizona State University, and Equilon
Enterprises LLC are partners in an innovative Environmental Security Technology Certification Program cleanup
technology demonstration designed to contain dissolved MTBE groundwater plumes. This full‐scale
demonstration is being performed to test the use of an oxygenated biobarrier at Naval Base Ventura County, in Port
Hueneme, California. Surprisingly, few cost‐effective in‐situ remedies are known for the cleanup of
MTBE‐impacted aquifers, and remediation by engineered in‐situ biodegradation was thought to be an
unlikely candidate just a few years ago. This project demonstrates that MTBE‐impacted groundwater can be
remediated in‐situ through engineered aerobic biodegradation under natural‐flow conditions. With
respect to economics, the installation and operation costs associated with this innovative biobarrier system are
at least 50 percent lower than those of a conventional pump and treat system. Furthermore, although it has been
suggested that aerobic MTBE biodegradation will not occur in mixed MTBE‐BTEX dissolved plumes, this project
demonstrates otherwise. The biobarrier system discussed in this article is the largest of its kind ever
implemented, spanning a dissolved MTBE plume that is over 500 feet wide. This biobarrier system has achieved an
in‐situ treatment efficiency of greater than 99.9 percent for dissolved MTBE and BTEX concentrations.
Perhaps of greater importance is the fact that extensive performance data has been collected, which is being used
to generate best‐practice design and cost information for this biobarrier technology. © 2001 John
Wiley & Sons, Inc.
‘Norwalk‐like viruses’ as a cause of foodborne disease outbreaks
Authors: Parashar Umesh D. , Monroe Stephan S. 
Published: August 2002

AbstractWhile outbreaks of foodborne disease remain an important public health concern, their aetiology is not identified in a majority of instances. In targeted studies, the application of newly developed molecular assays has demonstrated that a large proportion of these outbreaks may be caused by the ‘Norwalk‐like viruses’ (NLV), a genus of genetically related viruses belonging to the family Caliciviridae. NLV outbreaks associated with consumption of faecally contaminated oysters are frequently reported and can best be controlled by preventing contamination of oyster‐harvesting waters. Infectious foodhandlers are another frequent source of contamination, and such transmission can be minimised by exclusion of ill foodhandlers and the maintenance of strict personal hygiene. Molecular assays have greatly refined the epidemiological investigation of foodborne NLV outbreaks, allowing the linking of outbreaks in different locations and permitting the identification of the virus in the implicated vehicle. The development of simpler and more sensitive assays and their use on a broader scale will assist in defining the true burden of foodborne NLV outbreaks and improve strategies for their prevention and control. Copyright © 2001 John Wiley & Sons, Ltd.
Robust adaptive trajectory tracking independent of models for robotic manipulators
Authors: Chen Qijun , Chen Huitang , Wang Yuejuan , Woo Pengyung 
Published: August 2002

AbstractThis article proposes a robust adaptive trajectory control scheme for robotic trajectory tracking under uncertainties. The control scheme is globally exponentially convergent without the knowledge of the robotic dynamics and is simple in structure with a small computation. It can make the trajectory error convergent to an arbitrary small region. Lyapunov approach is used to analyze the stability and the robustness of this control scheme. Experiments on a two‐link direct‐drive robotic manipulator verify the validity of the proposed control scheme. © 2001 John Wiley & Sons, Inc.
Comparison of abdominal‐wall stretching between basic and enhanced laparoscopic instruments
Authors: Wittchen Jonathan D. , Podhorodeski Ron P. 
Published: August 2002

AbstractIn laparoscopic surgery, access to the patient's abdomen is gained by using an instrument, consisting of a 300–400 mm long stem with attached tool, inserted through a cannula mounted in the patient's abdominal wall. Sliding of the stem relative to the cannula and rotation of the stem about its longitudinal axis are the only motions not constrained by the abdominal wall. These limited‐motion capabilities necessitate abdominal‐wall stretching for full‐spatial tool displacements. Abdominal‐wall stretching is potentially damaging to the patient and fatiguing to the surgeon. Minimization of stretching is shown to be possible by the addition of a single revolute joint to the basic instrument. The motions allowed by the stem and cannula, the additional joint, and the abdominal wall result in a kinematically redundant system; i.e., an infinite number of joint displacements exist to achieve a desired tool position and orientation (desired tool pose). An optimization technique is applied to determine the minimum stretching for desired tool poses. Elimination of stretching is shown to be possible by the addition of two revolute joints to the basic instrument. Displacement models for the basic and enhanced instruments are found using concepts of manipulator kinematics. Forward and inverse displacement solutions for the instruments are found. The inverse displacement solutions are used to compare the amount of stretching required by each instrument. The stretching is highest for the basic instrument. The instrument with one additional joint produces stretching that is always less than or equal to that of the basic instrument. The instrument with two additional joints eliminates the need for stretching. © 2001 John Wiley & Sons, Inc.
Effects of pool formation and flash flooding on relative abundance of young‐of‐year flannelmouth suckers in the Paria River, Arizona
Authors: Thieme Michele L. , M𝒸ivor Carole C. , Brouder Mark J. , Hoffnagle Timothy L. 
Published: August 2002

AbstractFlannelmouth sucker, Catostomus latipinnis, a fish endemic to the Colorado River basin in the western United States, appears to experience poor recruitment to adult size in the Colorado River, downstream of Glen Canyon Dam. Lack or impermanence of rearing areas for young‐of‐year (YOY) fish is hypothesized to be the problem. Knowing the importance of tributary mouths as rearing areas in other river systems, we studied use of the mouth of the Paria River, a tributary of the Colorado River, by YOY flannelmouth suckers, and the availability of rearing area in the mouth at different flow levels in the Colorado River in 1996 and 1997. We also examined the relationship between flash floods in the Paria River and catch‐per‐unit‐effort (CPUE) of YOY in the Paria River between 1991 and 1996.Maximum mean daily discharge in the Paria River was inversely correlated with CPUE of YOY flannelmouth suckers (Spearman Rho=−0.9856, p=0.0003) during their critical rearing period (15 March–30 June). Thus, it appears that YOY flannelmouth suckers rear longer in the Paria River in years when flash flooding is minimal.Recruitment of YOY flannelmouth suckers at the Paria River may also be improved by enhancing pool formation during spring and summer rearing seasons. YOY flannelmouth sucker was captured in a pool created by high Colorado River flows (≥336 m3/s) that inundated the mouth of the Paria River during spring and summer, 1996. In 1997, high flows (about 550–750 m3/s) in the Colorado River during winter and spring initially inundated the Paria River and formed a pool in the mouth. However, these high flows eventually caused 0.5–1.0 m of suspended sediment from the incoming Paria River to deposit in the mouth. Thus, despite higher flows than 1996, the slackwater area formed only occasionally in 1997. Differences in pool formation between 1996 and 1997 demonstrate that pool formation cannot be inferred solely from Colorado River flows. Copyright © 2001 John Wiley & Sons, Ltd.
Some applications of the q‐Rice formula
Authors: Prodinger Helmut 
Published: August 2002

AbstractWe evaluate alternating sums involving q‐binomial coefficients using a contour integration technique. In this way, we rederive very easily some results due to Van Hamme, Uchimura (simplified!), Dilcher, Andrews, Crippa, and Simon. © 2001 John Wiley & Sons, Inc. Random Struct. Alg., 19: 552–557, 2001