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Trap Mass Spectrometer (trap + mass_spectrometer)
Kinds of Trap Mass Spectrometer Selected AbstractsAn investigation of the homolytic saccharide cleavage of deprotonated flavonol 3- O -glycosides in a quadrupole ion trap mass spectrometerJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2008Barry D. Davis Abstract The trend in the extent of homolytic saccharide cleavage is reported for a series of deprotonated flavonol 3- O -glycosides upon collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer. The second-generation product ions from the primary [Y0], and [Y0, H],, product ions were also identified. It was determined that the structure of both the aglycon and the saccharide portions of the flavonoid glycoside are pivotal in inducing radical cleavage. In contrast to earlier work on this subject reported for a smaller group of flavonols, the correlation between the degree of B-ring hydroxylation and the extent of radical saccharide cleavage showed several notable exceptions in the present work. Homolytic cleavage was also investigated in the context of using tandem mass spectrometry to identify the aglycon portions of flavonoid glycosides. Copyright © 2008 John Wiley & Sons, Ltd. [source] Thin-layer chromatography/electrospray ionization triple-quadrupole linear ion trap mass spectrometry system: analysis of rhodamine dyes separated on reversed-phase C8 plates ,JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 7 2005Michael J. Ford Abstract The direct analysis of separated rhodamine dyes on reversed-phase C8 thin-layer chromatography plates using a surface sampling/electrospray emitter probe coupled with a triple-quadrupole linear ion trap mass spectrometer is presented. This report represents continuing work to advance the performance metrics and utility of this basic surface sampling electrospray mass spectrometry system for the analysis of thin-layer chromatography plates. Experimental results examining the role of sampling probe spray end configuration on liquid aspiration rate and gas-phase ion signal generated are discussed. The detection figures-of-merit afforded by full-scan, automated product ion and selected reaction monitoring modes of operation were examined. The effect of different eluting solvents on mass spectrum signal levels with the reversed-phase C8 plate was investigated. The combined effect of eluting solvent flow-rate and development lane surface scan rate on preservation of chromatographic resolution was also studied. Analysis of chromatographically separated red pen ink extracts from eight different pens using selected reaction monitoring demonstrated the potential of this surface sampling electrospray mass spectrometry system for targeted compound analysis with real samples. Copyright © 2005 John Wiley & Sons, Ltd. [source] High-resolution H/D exchange studies on the HET-s218,295 prion proteinJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2005Alexis Nazabal Abstract In a search for improved resolution of hydrogen/deuterium (H/D) exchange experiments analyzed by mass spectrometry (HXMS), we evaluated two methodologies for a detailed structural study of solvent accessibility in the case of the HET-s218,295 prion protein. For the first approach, after incubation in the deuterated solvent, aggregated HET-s218,295 was digested with pepsin and the generated peptides were analyzed by nanospray mass spectrometry in an ion trap, with and without collision-induced dissociation (CID). We compared deuterium incorporation in peptides as determined on peptide pseudomolecular ions and on b and y fragments produced by longer peptides under CID conditions. For both b and y fragment ions, an extensive H/D scrambling phenomenon was observed, in contrast with previous studies comparing CID-MS experiments and 1H NMR data. Thus, the spatial resolution of HXMS experiments could not be improved by means of MS/MS data generated by an ion trap mass spectrometer. In a second approach, the incorporation of deuterium was analyzed by MS for 76 peptides of the HET-s218,289 peptide mass fingerprint, and the use of shared boundaries among peptic peptides allowed us to determine deuteration levels of small regions ranging from one to four amino acids. This methodology led to evidence of highly protected regions along the HET-s218,295 sequence. Copyright © 2005 John Wiley & Sons, Ltd. [source] Using collision-induced dissociation with corrections for the ion number of degrees of freedom for quick comparisons of relative bonding strengthJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 11 2004Natalia Vinokur Abstract The number of degrees of freedom-dependent stability of ions and ion,neutral non-covalent complexes under collision-induced dissociation (CID) conditions was studied in a quadrupole ion trap mass spectrometer. It was found that the stability of ions as probed by energy-variable CID has a linear dependence on the total number of degrees of freedom for the ions (or ion,neutral complexes) with the same (or nearly the same) bonding energy. The slope of such a stability vs number of degrees of freedom dependence correlates with the binding energy. Proton-bound amine dimers display the lowest slope as they have weak bonds. Breaking covalent bonds will result in much greater slopes. In addition to the binding energy, the vibrational frequencies of the ion also affect the stability vs number of degrees of freedom behavior. Studying such a dependence of the CID stability in a system paves the way for direct relative binding energy comparisons. The application of this approach is demonstrated by testing the relative heme affinities of anti-malaria drugs and related compounds. Copyright © 2004 John Wiley & Sons, Ltd. [source] Rapid screening and characterization of drug metabolites using a new quadrupole,linear ion trap mass spectrometerJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2003Gérard Hopfgartner Abstract The application of a new hybrid RF/DC quadrupole,linear ion trap mass spectrometer to support drug metabolism and pharmacokinetic studies is described. The instrument is based on a quadrupole ion path and is capable of conventional tandem mass spectrometry (MS/MS) as well as several high-sensitivity ion trap MS scans using the final quadrupole as a linear ion trap. Several pharmaceutical compounds, including trocade, remikiren and tolcapone, were used to evaluate the capabilities of the system with positive and negative turbo ionspray, using either information-dependent data acquisition (IDA) or targeted analysis for the screening, identification and quantification of metabolites. Owing to the MS/MS in-space configuration, quadrupole-like CID spectra with ion trap sensitivity can be obtained without the classical low mass cutoff of 3D ion traps. The system also has MS3 capability which allows fragmentation cascades to be followed. The combination of constant neutral loss or precursor ion scan with the enhanced product ion scan was found to be very selective for identifying metabolites at the picogram level in very complex matrices. Owing to the very high cycle time and, depending on the mass range, up to eight different MS experiments could be performed simultaneously without compromising chromatographic performance. Targeted product ion analysis was found to be complementary to IDA, in particular for very low concentrations. Comparable sensitivity was found in enhanced product ion scan and selected reaction monitoring modes. The instrument is particularly suitable for both qualitative and quantitative analysis. Copyright © 2003 John Wiley & Sons, Ltd. [source] Determination of regioselectivity in ring opening of tert -butylaziridinones by a combination of 15N labeling and electrospray ionization-ion trap mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2002E. R. Talaty Abstract The ring opening of 1,3-di- tert -butylaziridinone by tert -butylamine and aniline was investigated by using electrospray ionization and collision-induced dissociation in an ion trap mass spectrometer in conjunction with 15N labeling of the two amine nucleophiles. Using the MSn capabilities of the ion trap instrument, we were able to monitor the retention of the 15N label through successive fragmentation steps. Both amines exhibited a remarkable degree of selectivity in that they both cleaved exclusively the 1,3-bond (the alkyl,nitrogen bond). This result is in contrast to that obtained previously with methylamine, which cleaved just the opposite bond, namely, the 1,2-bond (the acyl,nitrogen bond). These contrasting results could not have been predicted by previously published guidelines. Copyright © 2001 John Wiley & Sons, Ltd. [source] Analysis of phosphatase and tensin homolog tumor suppressor interacting proteins by in vitro and in silico proteomicsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2005David K. Crockett Abstract The phosphatase and tensin homolog (PTEN) tumor suppressor is a multifunctional protein deregulated in many types of cancer. To date, a comprehensive documentation of PTEN interacting proteins has not been performed. The goal of our study was to characterize the PTEN interactome using affinity pull-down and tandem mass spectrometry (MS/MS). Wild-type PTEN cDNA was inserted into pTRC-His2 vector to create a 6-His tagged protein, which was expressed in Escherichia coli. Lysate from a human lymphoma cell line was used in pull-down assays, utilizing affinity for nickel-agarose beads. Bound proteins were eluted with imidazole, digested and analyzed on an LCQ DecaXP ion trap mass spectrometer. The nickel affinity pull-down efficiency was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis. Acquired data were searched against the NCBI nr.fasta nonredundant protein database using the SEQUEST algorithm and screened using INTERACT and ProteinProphet. All experiments were performed in duplicate with 6-His- lacZ serving as control. A total of 79 proteins were identified in the wild-type 6-His-PTEN pull-down by MS/MS. We further validated a subset of the proteins present in the PTEN interactome by performing immunoprecipitation using an anti-PTEN antibody and establishing the presence of the proteins in the immunocomplex by Western blot analysis. A search of published PTEN interactions was also performed using Online Mendelian Inheritance in Man, Human Protein Reference Database, the IntAct Project database, and PubMed. This in silico analysis confirmed 42 out of 79 (53%) of the proteins identified by MS/MS. The remaining 37 proteins represent probable PTEN interactions not previously documented in public databases or reported in the literature. These results highlight the value of combining both in vitro biochemical approaches with in silico analyses for a comprehensive study of protein-protein interactions. [source] Assigning glucose or galactose as the primary glycosidic sugar in 3- O -mono-, di- and triglycosides of kaempferol using negative ion electrospray and serial mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 19 2009Geoffrey C. Kite Kaempferol 3- O - , -glucopyranoside, kaempferol 3- O - , -galactopyranoside and higher glycosides of these two flavonoids with , -rhamnose at C-2 and/or C-6 of the primary sugar were studied by negative ion electrospray ionisation and serial mass spectrometry in a three-dimensional (3D) ion trap mass spectrometer. Kaempferol 3- O - , -glucopyranoside and kaempferol 3- O - , -rhamnopyranosyl(1,6)- , -glucopyranoside could be distinguished from their respective galactose analogues by differences in the ratio of the radical aglycone ion [Y0 , H],, to the rearrangement aglycone ion Y following MS/MS of the deprotonated molecules. Kaempferol 3- O -rhamnopyranosyl(1,2)- , -glucopyranoside and kaempferol 3- O - , -rhamnopyranosyl(1,2)[, -rhamnopyranosyl(1,6)]- , -glucopyranoside could be distinguished from their respective galactose analogues by differences in the product ion spectra of the [(M , H) , rhamnose], ion following serial mass spectrometry. In the triglycoside, it was deduced that this ion resulted from the loss of the rhamnose substituted at 2-OH of the primary sugar by observing that MS/MS of deprotonated kaempferol 3- O - , -glucopyranosyl(1,2)[, -rhamnopyranosyl(1,6)]- , -glucopyranoside showed the loss of glucose and not rhamnose. Thus the class of sugar (hexose, deoxyhexose, pentose) at C-2 and C-6 of the primary sugar can be determined. These observations aid the assignment of kaempferol 3- O -glycosides, having glucose or galactose as the primary glycosidic sugar, in LC/MS analyses of plant extracts, and this can be done with reference to only a few standards. Copyright © 2009 John Wiley & Sons, Ltd. [source] Coupling of ion-molecule reactions with liquid chromatography on a quadrupole ion trap mass spectrometerRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2008Yuriy Pyatkivskyy We report for the first time a coupling of gas-phase ion-molecule reactions with chromatographic separations on a quadrupole ion trap mass spectrometer. The interface was accomplished by using a pulsed valve for the introduction of a volatile neutral into the ion trap. The pulsed valve controller is synchronized with the mass spectrometer software. The setup requires some minor modifications to the vacuum system of the commercial quadrupole ion trap but most of the modifications are external to the mass spectrometer. Two applications of this interface are described: differentiation between two phosphoglucose positional isomers and detection of a phosphopeptide in a peptide mixture. Both applications are using the reactivity of trimethoxyborate towards a phosphate moiety in the negative ion mode. The detection of phosphopeptides hinges on our findings that non-phosphorylated peptide anions do not react with trimethoxyborate. This LC/MS detection can be easily visualized in terms of selected reaction monitoring. Copyright © 2008 John Wiley & Sons, Ltd. [source] Compound-specific stable carbon isotope ratios (,13C values) of the halogenated natural product 2,3,3,,4,4,,5,5,-heptachloro-1,-methyl-1,2,-bipyrrole (Q1)RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 20 2006Walter Vetter Compound-specific isotope analysis using gas chromatography interfaced to isotope ratio mass spectrometry (GC/IRMS) was applied for the determination of ,13C values of the marine halogenated natural product 2,3,3,,4,4,,5,5,-heptachloro-1,-methyl-1,2,-bipyrrole (Q1). The ,13C value of a lab-made Q1 standard (,34.20,±,0.27,) was depleted in 13C by more than 11, relative to the residues of Q1 in dolphin blubber from Australia and skua liver from Antarctica. This clarified that the synthesized Q1 was not the source for Q1 in the biota samples. However, two Australian marine mammals showed a large variation in the ,13C value, which, in our experience, was implausible. Since the GC/IRMS system was connected to a conventional ion trap mass spectrometer by a post-column splitter, we were able to closely inspect the peak purity of Q1 in the respective samples. While the mass spectra of Q1 did not indicate any impurity, a fronting peak of PCB 101 was identified in one sample. This interference falsified the ,13C value of the respective sample. Once this sample was excluded, we found that the ,13C values of the remaining samples, i.e. liver of Antarctic brown skua (,21.47,±,1.47,) and blubber of Australian melon-headed whale (,22.80,±,0.33,), were in the same order. The standard deviation for Q1 was larger in the skua samples than in the standard and the whale blubber sample. This was due to lower amounts of skua sample available. It remained unclear if the Q1 residues originate from the same producer and location. Copyright © 2006 John Wiley & Sons, Ltd. [source] Unimolecular dissociation of protonated trans -1,4-diphenyl-2-butene-1,4-dione in the gas phase: rearrangement versus simple cleavageRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 17 2006Lianming Wu Fragmentation mechanisms of trans -1,4-diphenyl-2-butene-1,4-dione were studied using a variety of mass spectrometric techniques. The major fragmentation pathways occur by various rearrangements by loss of H2O, CO, H2O and CO, and CO2. The other fragmentation pathways via simple alpha cleavages were also observed but accounted for the minor dissociation channels in both a two-dimensional (2-D) linear ion trap and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The elimination of CO2 (rather than CH3CHO or C3H8), which was confirmed by an exact mass measurement using the Q-TOF instrument, represented a major fragmentation pathway in the 2-D linear ion trap mass spectrometer. However, the elimination of H2O and CO becomes more competitive in the beam-type Q-TOF instrument. The loss of CO is observed in both the MS2 experiment of m/z 237 and the MS3 experiment of m/z 219 but via the different transition states. The data suggest that the olefinic double bond in protonated trans -1,4-diphenyl-2-butene-1,4-dione plays a key role in stabilizing the rearrangement transition states and increasing the bond dissociation (cleavage) energy to give favorable rearrangement fragmentation pathways. Copyright © 2006 John Wiley & Sons, Ltd. [source] Ultra-fast tandem mass spectrometry scanning combined with monolithic column liquid chromatography increases throughput in proteomic analysisRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 14 2006Mariola Batycka Liquid chromatography combined with electrospray ionization mass spectrometry (LC/ESI-MS) has been used successfully for the characterization of biomolecules in proteomics in the last few years. This methodology relied largely on the use of reversed-phase chromatography, in particular C18-based resins, which are suitable for separation of peptides. Here we show that polymeric [polystyrene divinylbenzene] monolithic columns can be used to separate peptide mixtures faster and at a higher resolution. For 500,fmol bovine serum albumin, up to 68% sequence coverage and Mascot Mowse scores of >2000 were obtained using a 9,min gradient on a monolithic column coupled to an ion trap mass spectrometer with ultra-fast MS/MS scan rates. In order to achieve similar results using C18 columns, it was necessary to extend gradient times to 30,min. In addition, we demonstrate the utility of this approach for the analysis of whole Escherichia coli cell lysates by one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) in combination with LC/MS/MS using 4,min gradients on monolithic columns. Our results indicate higher throughput capabilities of monolithic columns (3-fold gain in time or more) for conventional proteomics applications, such as protein identification and high sequence coverage usually required for detection of post-translational modifications (PTMs). Further optimization of sensitivity and quality of sequence information is discussed, in particular when combined with mass spectrometers that have very fast MS-MS/MS switching and scanning capabilities. Copyright © 2006 John Wiley & Sons, Ltd. [source] Potentials of ion trap collisional spectrometry for liquid chromatography/electrospray ionization tandem mass spectrometry determination of buprenorphine and nor -buprenorphine in urine, blood and hair samplesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2006Donata Favretto A liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method has been developed for the analysis of buprenorphine (BUP) and nor -buprenorphine (NBUP) in biological fluids. Analytes are isolated from urine and blood, after addition of d4 -buprenorphine (d4 -BUP) as internal standard, by solid-phase extraction. Preparation of hair involves external decontamination, mechanical pulverization, overnight incubation in acidic medium, and neutralization prior to extraction. Enzymatic hydrolysis with , -glucuronidase may be performed to distinguish between free and total BUP. Chromatographic separation is accomplished by gradient elution on a cyanopropyl 2.1,×,150,mm column. Positive ion ESI and MS analyses are carried out in an ion trap mass spectrometer. The use of this mass analyzer allows effective collisional experiments to be performed on ESI-generated MH+ species. Abundant product ions are produced, which can be monitored together with precursor ions without losing sensitivity. Thus, assay selectivity is definitely increased with respect to LC/ESI-MS/MS methods in which only precursor ions are monitored. The method has good linearity (calibration curves were linear in the range 0.1,10,ng/mL in urine and blood, in the range 10,160,pg/mg in hair) and limits of detection of 0.05,ng/mL for both BUP and NBUP in blood and urine samples, of 4,pg/mg for both analytes in hair. Both intra- and inter-assay precision and accuracy were satisfactory at three concentrations studied: relative standard deviations were <13.7% in urine, <17.3% in blood, <17.8% in hair; percent deviation of the mean from the true value was always <10.5% in urine and blood, <16.1% in hair. The method can be used to determine both analytes in the urine and hair of drug addicts on replacement therapy, and in post-mortem blood specimens when there is suspicion of drug-related death. Copyright © 2006 John Wiley & Sons, Ltd. [source] Ultra-performance liquid chromatography coupled to linear ion trap mass spectrometry for the identification of drug metabolites in biological samplesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2006G. J. Dear The coupling of ultra-performance liquid chromatography, operating at elevated pressures, to a linear ion trap mass spectrometer provides a high-performance system suitable for drug metabolite characterisation. This system demonstrates improved chromatographic efficiency and sensitivity and at the same time provides diagnostic MSn data often critical for metabolite structural assignment. The linear ion trap was capable of dealing with the high chromatographic efficiencies and hence narrow peak widths associated with 1.7,µm particle-packed column separations. Polarity switching and data-dependent MSn data were generated with ease, and applied to the identification of metabolites found in human plasma. Copyright © 2006 John Wiley & Sons, Ltd. [source] A comparison of the electron ionization and electrospray behaviour of some N,N,-disubstituted hexahydropyrimidinesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2006Liliana R. Orelli The behaviour of some N,N,-disubstituted hexahydropyrimidines, a class of naturally occurring compounds of biological and biomedical interest, has been studied in both electron ionization (EI) and electrospray ionization (ESI) modes coupled with collisional experiments (ESI-MSn). In both techniques, the [M,H]+ ions are highly abundant, even if their formation is generated by two different mechanisms, i.e. H. loss from the M+. species in the case of EI and hydride (H,) abstraction from the molecules in the case of ESI. Furthermore, due to the low, step-by-step internal energy deposition typical of collisional experiments performed in an ion trap mass spectrometer, different fragment ions were observed in EI and ESI-MSn collisions. In both cases, the ions can be related to the original structure and allow us to identify the positions in which the different substituents are present. Copyright © 2006 John Wiley & Sons, Ltd. [source] Ion motion in the rectangular wave quadrupole field and digital operation mode of a quadrupole ion trap mass spectrometer,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 1 2006L. Ding A quadrupolar electric field driven by a rectangular wave voltage can be used for mass-selective storage and analysis. The ion motion in such an electric field is derived, and the stability of ions is presented in the a-q diagram that is commonly used for sinusoidal wave quadrupole mass spectrometry in association with the solution of the Mathieu equation. The pseudo-potential well is discussed in an approximation that leads to the relation of secular frequency to operating parameters. A scheme for a digital ion trap mass spectrometer is described, based on this theory. An ion optics simulation was performed to check the theory of resonant ejection, and to prove the feasibility of the mass scan method for a practical ion trap of such geometry. Copyright © 2005 John Wiley & Sons, Ltd. [source] An integrated strategy for identification and relative quantification of site-specific protein phosphorylation using liquid chromatography coupled to MS2/MS3RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 24 2005Florian Wolschin Reversible and differential multisite protein phosphorylation is an important mechanism controlling the activity of cellular proteins. Here we describe a robust and highly selective approach for the identification and relative quantification of site-specific phosphorylation events. This integrated strategy has three major parts: visualisation of phosphorylated proteins using fluorescently stained polyacrylamide gels, determination of the phosphorylation site(s) using automatic MS3 triggered by the loss of phosphoric acid, and relative quantification of phosphorylation by integrating MS2 - and MS3 -extracted ion traces using a fast-scanning, linear ion trap mass spectrometer. As a test case, recombinant sucrose-phosphate synthase (SPS) from Arabidopsis thaliana (At5g1110) was used for identification and quantification of site-specific phosphorylation. The identified phosphorylation site of the actively expressed protein coincides with the major regulatory in vivo phosphorylation site in spinach SPS. Site-specific differential in vitro phosphorylation of native protein was demonstrated after incubation of the recombinant protein with cold-adapted plant leaf extracts from A. thaliana, suggesting regulatory phosphorylation events of this key enzyme under stress response. Copyright © 2005 John Wiley & Sons, Ltd. [source] Isomer differentiation by combining gas chromatography, selective self-ion/molecule reactions and tandem mass spectrometry in an ion trap mass spectrometerRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 10 2003Hui-Fen Wu This study presents a novel, simple and rapid procedure for isomer differentiation by combining gas chromatography (GC), a selective self-ion/molecule reaction (SSIMR) and tandem mass spectrometry (MS/MS) in an ion trap mass spectrometer (ITMS). SSIMR product ions were produced from four isomers. For aniline, SSIMR induces the formation of the molecular ion, [M+H]+, [M+CH]+, adduct ions of fragments ([M+F]+, where F represents fragment ions) and [2MH]+. 2 and 3-Picoline produce [M+H]+, [2MH]+ and [M+F]+, while 5-hexynenitrile produces [M+H]+, [M+F]+ and [2M+H]+ ions. The proposed method provides a relatively easy, rapid and efficient means of isomer differentiation via a SSIMR in the ITMS. Typically, isomer differentiation can be achieved within several minutes. The superiority of the SSIMR technique for isomer differentiation over electronic ionization (EI) is also demonstrated. Copyright © 2003 John Wiley & Sons, Ltd. [source] Reactivity of the NS2/3(907,1206)ASK4 protein with ,-mercaptoethanol studied by electrospray ion trap mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 20 2002Laura Orsatti The present work reports a mass spectrometric investigation of the NS2/3 protein, a protease from hepatitis C virus (HCV). During routine protein manipulation, in the presence of 100,mM ,-mercaptoethanol and under denatured conditions, the protein was unexpectedly modified at its cysteine residues, and the increased molecular weight corresponded to one molecule of ,-mercaptoethanol bound. The modified protein, once refolded, was found to be less active than the unmodified one. The aim of this work was to investigate whether the reactivity of cysteines with ,-mercaptoethanol involves one specific, highly reactive residue of the sequence, or if the modification is a random process. Liquid chromatography (LC) coupled on-line with an electrospray ion trap mass spectrometer was used to identify the modification sites. It was found that five cysteines out of nine had reacted with ,-mercaptoethanol, none of them showing a significantly higher reactivity than the others. 95% of sequence coverage was obtained. Copyright © 2002 John Wiley & Sons, Ltd. [source] Identification of 1-hydroxypyrene glucuronide in tissue of marine polychaete Nereis diversicolor by liquid chromatography/ion trap multiple mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2002Anders M. B. Giessing 1-Hydroxypyrene glucuronide is identified as the single major aqueous metabolite of the tetracyclic aromatic hydrocarbon pyrene, in tissue from a deposit-feeding marine polychaete, Nereis diversicolor. Identification was performed using an ion trap mass spectrometer fitted with an atmospheric pressure chemical ionization (APCI) probe and connected to a high-performance liquid chromatography/diode array detector (HPLC/DAD) system. Besides 1-hydroxypyrene, the 339-nm UV trace of tissue samples from pyrene-exposed worms showed only one dominant peak that could be related to pyrene metabolism. Negative APCI-MS of this supposed 1- hydroxypyrene conjugate gave a characteristic signal at m/z 429 corresponding to the molecular ion of 1-hydroxypyrene glucuronide plus eluent adducts ([M,,,H,+,2H2O],). Fragmentation pathways were studied by isolating the abundant ion at m/z 429 in the ion trap and performing multiple mass spectrometric experiments (MSn). The fragmentations observed were consistent with the proposed identification. Two low intensity LC peaks that could be related to pyrene metabolism by their DAD absorption spectra were also present in the 339-nm UV chromatogram of tissue samples. However, these peaks could not be identified by their mass spectra in negative ion mode due to ion suppression by very abundant co-eluting impurities. The present method shows that LC/MSn is a fast and useful analytical tool for identification of aqueous polycyclic aromatic hydrocarbon biotransformation products in samples from relatively small marine invertebrates with limited sample preparation. Copyright © 2002 John Wiley & Sons, Ltd. [source] Double resonance ejection in a micro ion trap mass spectrometerRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2002Jeremy Moxom Ion ejection from a cylindrical micro ion trap by resonance excitation of the secular motion is observed to be strongly dependent on the frequency of the secular motion at resonance. Both the intensity of the ion signal and the mass resolution of the resulting mass spectrum are increased when the ion secular frequency is approximately that of a nonlinear resonance of the trap. The resonances are attributed to electrical as well as geometrical considerations. Copyright © 2002 John Wiley & Sons, Ltd. [source] A new linear ion trap mass spectrometerRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 6 2002James W. Hager Characteristics of mass selective axial ion ejection from a linear quadrupole ion trap in the presence of an auxiliary quadrupole field are described. Ion ejection is shown to occur through coupling of radial and axial motion in the exit fringing fields of the linear ion trap. The coupling is efficient and can result in extraction of as much as 20% of the trapped ions. This, together with the very high trapping efficiencies, can yield high sensitivity mass spectral responses. The experimental apparatus is based on the ion path of a triple quadrupole mass spectrometer allowing either the q2 collision cell or the final mass analysis quadrupole to be used as the linear trap. Space charge induced distortions of the mass resolved features while using the pressurized q2 linear ion trap occur at approximately the same ion density as reported for conventional three-dimensional ion traps. These distortions are, however, much reduced for the lower pressure linear trap possibly owing to the proposed axial ejection mechanism that leads to ion ejection only for ions of considerable radial amplitude. RF heating due to the high ejection q -value and the low collision frequency may also contribute. Two hybrid RF/DC quadrupole-linear ion trap instruments are described that provide high sensitivity product ion scanning while operated in the linear ion trap mode while also retaining all conventional triple quadrupole scan modes such as precursor ion and neutral loss scan modes. Copyright © 2002 John Wiley & Sons, Ltd. [source] Characterisation and determination of indole alkaloids in frog-skin secretions by electrospray ionisation ion trap mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2002Stephen McClean The characterisation of selected indole alkaloids in a quadrupole ion trap mass spectrometer is presented. Fragmentation profiles for tryptamine, 5-hydroxytryptamine (5-HT), N,-methyl 5-hydroxytryptamine (N,-methyl 5-HT), N,,N,-dimethyl 5-hydroxytryptamine (bufotenine), N,,N,,N,-trimethyl 5-hydroxytryptamine (5-HTQ), and N,,N,-dimethyl 5-methoxytryptamine (5-MeODMT) are presented with proposed structures given for each product ion observed. Such MSn experiments can be used to differentiate the isobaric molecular ions of the compounds 5-HTQ (M+) and 5-MeODMT (MH+). The quantitative determination of certain indole alkaloids in the skin secretions of the Australian Golden Bell frog, Litoria aurea, by LC/ESI-ion trap MS is also presented. The concentrations of 5-HT, N,-methyl 5-HT and 5-HTQ were found to be 2.68, 0.26 and 0.54,µg per,mg of skin secretion, respectively. Copyright © 2002 John Wiley & Sons, Ltd. [source] Atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry of sulfonic acid derivatized tryptic peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2001T. Keough Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) and ion trap mass spectrometry have been used to study the fragmentation behavior of native peptides and peptide derivatives prepared for de novo sequencing applications. Sulfonic acid derivatized peptides were observed to fragment more extensively and up to 28 times more efficiently than the corresponding native peptides. Tandem mass spectra of native peptides containing aspartic or glutamic acids are dominated by cleavage on the C-terminal side of the acidic residues. This significantly limits the amount of sequence information that can be derived from those compounds. The MS/MS spectra of native tryptic peptides containing oxidized Met residues show extensive loss of CH3SOH and little sequence-specific fragmentation. On the other hand, the tandem mass spectra of derivatized peptides containing Asp, Glu and oxidized Met show much more uniform fragmentation along the peptide backbone. The AP-MALDI tandem mass spectra of some derivatized peptides were shown to be qualitatively very similar to the corresponding vacuum MALDI postsource decay mass spectra, which were obtained on a reflector time-of-flight instrument. However, the ion trap mass spectrometer offers several advantages for peptide sequencing relative to current reflector time-of-flight instruments including improved product ion mass measurement accuracy, improved precursor ion selection and MSn. These latter capabilities were demonstrated with solution digests of model proteins and with in-gel digests of 2D-gel separated proteins. Copyright © 2001 John Wiley & Sons, Ltd. [source] Liquid chromatography ion trap mass spectrometric analysis of oligosaccharides using permethylated derivativesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2001Jeannine Delaney Reversed phase liquid chromatography was combined with the multiple stage mass analysis capability of an ion trap mass spectrometer for the characterization of permethylated oligosaccharide mixtures. The new method was used to separate the components of an unlabeled permethylated maltooligomer ladder, a 2-aminobenzamide-labeled (2-AB) maltooligomer ladder, a complex mixture of 2AB-labeled bi- (B), tri- (T), and tetraantennary (Q) standards, and a mixture of recombinant glycoprotein carbohydrates from soluble CD4 with varying sialic acid (S) content. Using reversed phase HPLC, permethylated mixture components including , and , anomers were separated based on their structures. Fluorescent labeling with 2-aminobenzamide prior to permethylation was employed for off-line method development, but was not necessarily required for mass spectral analysis, as permethylation alone improved the ionization and fragmentation characteristics of the molecules. Antennae composition of permethylated derivatives was determined in MS2 where the fragmentation patterns of the Y- and B-ion series predominated, and then further evaluated in MS3, which provided additional information on branching obtained from A and X cross-ring fragmentation. Copyright © 2001 John Wiley & Sons, Ltd. [source] Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 7 2009Haiying Zhang Abstract Identification of drug metabolites by liquid chromatography/mass spectrometry (LC/MS) involves metabolite detection in biological matrixes and structural characterization based on product ion spectra. Traditionally, metabolite detection is accomplished primarily on the basis of predicted molecular masses or fragmentation patterns of metabolites using triple-quadrupole and ion trap mass spectrometers. Recently, a novel mass defect filter (MDF) technique has been developed, which enables high-resolution mass spectrometers to be utilized for detecting both predicted and unexpected drug metabolites based on narrow, well-defined mass defect ranges for these metabolites. This is a new approach that is completely different from, but complementary to, traditional molecular mass- or MS/MS fragmentation-based LC/MS approaches. This article reviews the mass defect patterns of various classes of drug metabolites and the basic principles of the MDF approach. Examples are given on the applications of the MDF technique to the detection of stable and chemically reactive metabolites in vitro and in vivo. Advantages, limitations, and future applications are also discussed on MDF and its combinations with other data mining techniques for the detection and identification of drug metabolites. Copyright © 2009 John Wiley & Sons, Ltd. [source] Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2008Julian Vasilescu Abstract We report a simple approach for determining ion score cutoffs that permit the confident identification of ubiquitinated proteins by tandem mass spectrometry (MS/MS). Initial experiments involving the analysis of gel bands containing multi-Ubiquitin chains with quadrupole time-of-flight and quadrupole ion trap mass spectrometers revealed that standard ion score cutoffs used for database searching were not sufficiently stringent. We also found that false positive and false negative rates (FPR and FNR) varied significantly depending on the cutoff scores used and that appropriate cutoffs could only be determined following a systematic evaluation of false positive rates. When standard cutoff scores were used for the analysis of complex mixtures of ubiquitinated proteins, unacceptably high FPR were observed. Finally, we found that FPR for ubiquitinated proteins are affected by the size of the protein database that is searched. These observations may be applicable for the study of other post-translational modifications. Copyright © 2007 John Wiley & Sons, Ltd. [source] Influence on mass-selective ion ejection of the phase difference between the drive r.f. and the axial modulation potentialsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2005G. Dobson Abstract The phase difference between the drive r.f. and the axial modulation potential is known to influence significantly the mass shift, and all commercial ion trap mass spectrometers use a fixed value for this difference. However, although this important parameter is partly responsible for the good precision achievable today in most commercial ion traps, little discussion on the variation of the phase difference between the drive r.f. and the axial modulation potential has appeared in the literature. We present here an examination of the influence of a low-level axial modulation potential superimposed by capacitive coupling between the electrodes. Low-level axial modulation potentials are used for certain analytical scans such as reverse scan or slow scan speeds. Such low-level potentials help to prevent deterioration of mass resolution due to, for example, the dissociation of the ions during their resonant ejection from the ion trap. Reverse and forward scans are used to illustrate the mass shift and change in resolution, caused by a change in the phase difference between the drive r.f. potential applied to the ring electrode and the axial modulation potential applied on an end-cap electrode, in electrospray ionization mass spectra. Copyright © 2005 John Wiley & Sons, Ltd. [source] Application of ion trap technology to liquid chromatography/mass spectrometry quantitation of large peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 9 2008Petia Shipkova Triple quadrupole mass spectrometers are generally considered the instrument of choice for quantitative analysis. However, for the analysis of large peptides we have encountered some cases where, as the data presented here would indicate, ion trap mass spectrometers may be a good alternative. In general, specificity and sensitivity in bioanalytical liquid chromatography/mass spectrometry (LC/MS) assays are achieved via tandem MS (MS/MS) utilizing collision-induced dissociation (CID) while monitoring unique precursor to product ion transitions (i.e. selected reaction monitoring, SRM). Due to the difference in CID processes, triple quadrupoles and ion traps often generate significantly different fragmentation spectra of product ion species and intensities. The large peptidic analytes investigated here generated fewer fragments with higher relative abundance on the ion trap as compared to those generated on the triple quadrupole, resulting in lower limits of detection on the ion trap. Copyright © 2008 John Wiley & Sons, Ltd. [source] Evaluation of axial DC offsets during scanning of a quadrupole ion trap for sensitivity improvementsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 9 2001Timothy Vaden In the normal operation of quadrupole ion trap mass spectrometers, approximately half of the trapped ions are ejected through the source endcap during a mass-selective instability scan. This reduces the sensitivity of the instrument by ,50%. In this preliminary study, a circuit was constructed that produced a dipolar DC offset on the axial modulation waveform to recover this lost ion current. A variable (0 to 10,V DC), positive and negative offset was applied to the source and detector endcap, respectively. This DC offset axially displaced the ion cloud toward the detector endcap increasing the probability of detection. Several compounds, including 11 pesticides, were evaluated. Sensitivity enhancements ranged from 13 to 97% (theoretical 100%). No spectral resolution problems were observed; however, a compound-dependent mass discrimination was observed in several cases. This mass discrimination problem is currently under investigation. Copyright © 2001 John Wiley & Sons, Ltd. [source] | ||||||||||