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Quadrupole Ion Trap (quadrupole + ion_trap)
Terms modified by Quadrupole Ion Trap Selected AbstractsEffect of instrument tuning on the detectabilityof biopolymers in electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2003Herbert Oberacher Abstract Electrospray ionization mass spectrometry of multiply charged biopolymer ions of different molecular size revealed a strong influence of tuning parameters on their detectability in quadrupole ion trap and triple quadrupole mass spectrometers. Hence, after optimizing the ion optical parameters with the signal of the 4, charge state of (dT)24 (low charge state tuning), a tenfold increase in the signal-to-noise ratio for a mixture of oligodeoxythymidylic acids (n = 12,18) was obtained compared with the results achieved with tune parameters optimized with a synthetic 80-mer oligodeoxynucleotide. By contrast, a detection limit in the upper femtomole region could only be reached for a 104-mer oligodeoxynucleotide utilizing the 24, charge state of the 80-mer (high charge state tuning). The same effect was observed for proteins investigated in the positive ion mode using low and high charge states of cytochrome c and carbonic anhydrase, respectively, for instrument tuning. By comparing the settings for low and high charge state tuning, it became obvious that the most significant difference was observed in the potential applied to the heated metal capillary used to transfer ions from the atmospheric pressure to the vacuum region of the ion source. Taking advantage of the optimized tuning procedure, the molecular mass of a 61 base pair product of polymerase chain reaction was accurately determined by electrospray ionization mass spectrometry on-line interfaced to ion-pair reversed-phase high-performance liquid chromatography. Copyright © 2003 John Wiley & Sons, Ltd. [source] Solvation of acylium fragment ions in electrospray ionization quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2001Ziqiang Guan Abstract In electrospray ionization (ESI) quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometry, certain fragment ions (e.g. acylium ions) generated either during the ion transportation process (in the source interface region) or in the ion trap are found to undergo ion,molecule reactions with ESI solvent molecules (water, acetonitrile and aliphatic alcohols) to form adduct species. These unexpected solvated fragment ions severely complicate the interpretation of mass spectrometic data. High-resolution accurate mass measurements are important in establishing the elemental compositions of these adduct species and preventing erroneous data interpretation. Copyright © 2001 John Wiley & Sons, Ltd. [source] Negative and positive ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and positive ion nano-electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus speciesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2001Gerold Bacher Abstract A general approach for the detailed characterization of sodium borohydride-reduced peptidoglycan fragments (syn. muropeptides), produced by muramidase digestion of the purified sacculus isolated from Bacillus subtilis (vegetative cell form of the wild type and a dacA mutant) and Bacillus megaterium (endospore form), is outlined based on UV matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) quadrupole ion trap (QIT) mass spectrometry (MS). After enzymatic digestion and reduction of the resulting muropeptides, the complex glycopeptide mixture was separated and fractionated by reversed-phase high-performance liquid chromatography. Prior to mass spectrometric analysis, the muropeptide samples were subjected to a desalting step and an aliquot was taken for amino acid analysis. Initial molecular mass determination of these peptidoglycan fragments (ranging from monomeric to tetrameric muropeptides) was performed by positive and negative ion MALDI-MS using the thin-layer technique with the matrix ,-cyano-4-hydroxycinnamic acid. The results demonstrated that for the fast molecular mass determination of large sample numbers in the 0.8,10 pmol range and with a mass accuracy of ±0.07%, negative ion MALDI-MS in the linear TOF mode is the method of choice. After this kind of muropeptide screening often a detailed primary structural analysis is required owing to ambiguous data. Structural data could be obtained from peptidoglycan monomers by post-source decay (PSD) fragment ion analysis, but not from dimers or higher oligomers and not with the necessary sensitivity. Multistage collision-induced dissociation (CID) experiments performed on an nESI-QIT instrument were found to be the superior method for structural characterization of not only monomeric but also of dimeric and trimeric muropeptides. Up to MS4 experiments were sometimes necessary to obtain unambiguous structural information. Three examples are presented: (a) CID MSn (n = 2,4) of a peptidoglycan monomer (disaccharide-tripeptide) isolated from B. subtilis (wild type, vegetative cell form), (b) CID MSn (n = 2,4) of a peptidoglycan dimer (bis-disaccharide-tetrapentapeptide) obtained from a B. subtilis mutant (vegetative cell form) and (c) CID MS2 of a peptidoglycan trimer (a linear hexasaccharide with two peptide side chains) isolated from the spore cortex of B. megaterium. All MSn experiments were performed on singly charged precursor ions and the MS2 spectra were dominated by fragments derived from interglycosidic bond cleavages. MS3 and MS4 spectra exhibited mainly peptide moiety fragment ions. In case of the bis-disaccharide-tetrapentapeptide, the peptide branching point could be determined based on MS3 and MS4 spectra. The results demonstrate the utility of nESI-QIT-MS towards the facile determination of the glycan sequence, the peptide linkage and the peptide sequence and branching of purified muropeptides (monomeric up to trimeric forms). The wealth of structural information generated by nESI-QIT-MSn is unsurpassed by any other individual technique. Copyright © 2001 John Wiley & Sons, Ltd. [source] Analysis of S -adenosylmethionine and related sulfur metabolites in bacterial isolates of Pseudomonas aeruginosa (BAA-47) by liquid chromatography/electrospray ionization coupled to a hybrid linear quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 21 2009Tommaso R. I. Cataldi A comprehensive and highly selective method for detecting in bacterial supernatants a modified sulfur nucleoside, S -adenosyl-L-methionine (SAM), and its metabolites, i.e., S -adenosylhomocysteine (SAH), adenosine (Ado), 5,-deoxy-5,-methylthioadenosine (MTA), adenine (Ade), S -adenosyl-methioninamine (dcSAM), homocysteine (Hcy) and methionine (Met), was developed. The method is based on reversed-phase liquid chromatography with positive electrospray ionization (ESI+) coupled to a hybrid linear quadrupole ion trap (LTQ) and 7-T Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). A gradient elution was employed with a binary solvent of 0.05,M ammonium formate at pH 4 and acetonitrile. The assay involves a simultaneous cleanup of cell-free bacterial broths by solid-phase extraction and trace enrichment of metabolites with a 50-fold concentration factor by using immobilized phenylboronic and anion-exchange cartridges. While the quantitative determination of SAM was performed using stable-isotope-labeled SAM-d3 as an internal standard, in the case of Met and Ade, Met- 13C and Ade- 15N2 were employed as isotope-labeled internal standards, respectively. This method enabled the identification of SAM and its metabolites in cell-free culture of Pseudomonasaeruginosa grown in Davis minimal broth (formulation without sulphur organic compounds), with routine sub-ppm mass accuracies (,0.27,±,0.68,ppm). The resulting contents of SCSS -SAM, SS -dcSAM, MTA, Ado and Met in the free-cell supernatant of P. aeruginosa was 56.4,±,2.1,nM, 32.2,±,2.2,nM, 0.91,±,0.10,nM, 19.6,±,1.2,nM and 1.93,±,0.02,µM (mean,±,SD, n,=,4 extractions), respectively. We report also the baseline separation (Rs ,1.5) of both diastereoisomeric forms of SAM (SCSS and SCRS) and dcSAM (SS and RS), which can be very useful to establish the relationship between the biologically active versus the inactive species, SCSS/SCRS and SS/RS of SAM and dcSAM, respectively. An additional confirmation of SAM-related metabolites was accomplished by a systematic study of their MS/MS spectra. Copyright © 2009 John Wiley & Sons, Ltd. [source] Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 10 2009King Wai Lau Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument-specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupole-time-of-flight and quadrupole ion trap instruments. Specifically, quadrupole-time-of-flight tandem mass spectra show a significant under-representation of N-terminal b-type fragments in comparison to quadrupole ion trap product ion spectra. Energy-resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b-type ions are significantly less stable than their y-type N-terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole-time-of-flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies. 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] Gas-phase fragmentation of half- and first-generation polyamidoamine dendrimers by electrospray mass spectrometry using a quadrupole ion trapRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 3 2008Thomas J.-C. Polyamidoamine (PAMAM) dendrimers are nanopolymers that can bind with biomolecules such as DNA, drugs or proteins. In order to study these complexes, we first fragmented half- and first-generation PAMAM, G0.5 and G1, respectively, using a quadrupole ion trap (QIT) equipped with an electrospray ionisation source. For both G0.5 and G1 we observed a series of impurities that only can stem from synthesis defects and that are principally due to missing branches and intramolecular cyclisations. Fragmentations of G1 showed regularity in the product ions. These ions result from the loss of 60,Da, obtained by an intramolecular cyclisation, and from the loss of 114,Da, obtained by a four-centred hydrogen transfer or a retro-Michael reaction. The fragmentations stemmed either from competitive or from consecutive reactions, even though resonant fragmentation QIT was used. It is shown that the principal fragmentation reaction is a retro-Michael rearrangement for both G1 and G0.5. In addition, by fragmenting totally deuterated [G1-d28]Na+ we were able to establish fragmentation pathways. Copyright © 2008 John Wiley & Sons, Ltd. [source] Capillary liquid chromatography/atmospheric-pressure matrix-assisted laser desorption/ionisation ion trap mass spectrometry: a comparison with liquid chromatography/matrix-assisted laser desorption/ionisation time-of-flight and liquid chromatography/electrospray ionisation quadrupole time-of-flight for the identification of tryptic peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2006Colin S. Creaser The atmospheric-pressure matrix-assisted laser desorption/ionisation quadrupole ion trap (AP-MALDI-QIT) analysis of tryptic peptides is reported following capillary liquid chromatographic (LC) separation and direct analysis of a protein digest. Peptide fragments were identified by peptide mass fingerprinting from mass spectrometric data and sequence analysis obtained by tandem mass spectrometry of the principal mass spectral peaks using a data-dependent scanning protocol. These data were compared with those from mass spectrometric analysis using capillary LC/MALDI-time-of-flight (TOF) and capillary LC/electrospray ionisation (ESI)-quadrupole TOF. For all three configurations the resulting data were searched against the MSDB database, using MASCOT and the sequence coverage compared for each technique. Complementary data were obtained using the three techniques. Copyright © 2006 John Wiley & Sons, Ltd. [source] Can radical cations of the constituents of nucleic acids be formed in the gas phase using ternary transition metal complexes?,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2005Sheena Wee Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) of ternary transition metal complexes of [M(L3)(N)]2+ (where M,=,copper(II) or platinum(II); L3,=,diethylenetriamine (dien) or 2,2,:6,,2,-terpyridine (tpy); N,=,the nucleobases: adenine, guanine, thymine and cytosine; the nucleosides: 2,deoxyadenosine, 2,deoxyguanosine, 2,deoxythymine, 2,deoxycytidine; the nucleotides: 2,deoxyadenosine 5,-monophosphate, 2,deoxyguanosine 5,-monophosphate, 2,deoxythymine 5,-monophosphate, 2,deoxycytidine 5,-monophosphate) was examined as a means of forming radical cations of the constituents of nucleic acids in the gas phase. In general, sufficient quantities of the ternary complexes [M(L3)(N)]2+ could be formed for MS/MS studies by subjecting methanolic solutions of mixtures of a metal salt [M(L3)X2] (where M,=,Cu(II) or Pt(II); L3,=,dien or tpy; X,=,Cl or NO3) and N to ESI. The only exceptions were thymine and its derivatives, which failed to form sufficient abundances of [M(L3)(N)]2+ ions when: (a) M,=,Pt(II) and L3,=,dien or tpy; (b) M,=,Cu(II) and L3,=,dien. In some instances higher oligomeric complexes were formed; e.g., [Pt(tpy)(dG)n]2+ (n,=,1,13). Each of the ternary complexes [M(L3)(N)]2+ was mass-selected and then subjected to collision-induced dissociation (CID) in a quadrupole ion trap. The types of fragmentation reactions observed for these complexes depend on the nature of all three components (metal, auxiliary ligand and nucleic acid constituent) and can be classified into: (i) a redox reaction which results in the formation of the radical cation of the nucleic acid constituent, N+.; (ii) loss of the nucleic acid constituent in its protonated form; and (iii) fragmentation of the nucleic acid constituent. Only the copper complexes yielded radical cations of the nucleic acid constituent, with [Cu(tpy)(N)]2+ being the preferred complex due to suppression, in this case, of the loss of the nucleobase in its protonated form. The yields of the radical cations of the nucleobases from the copper complexes follow the order of their ionization potentials (IPs): G (lowest IP),>,A,>,C,>,T (highest IP). Sufficient yields of the radical cations of each of the nucleobases allowed their CID reactions (in MS3 experiments) to be compared to their even-electron counterparts. Copyright © 2005 John Wiley & Sons, Ltd. [source] Investigation of cytolysin variants by peptide mapping: enhanced protein characterization using complementary ionization and mass spectrometric techniquesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2002Stanley M. Stevens Jr. Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) have been used in conjunction with time-of-flight (TOF) and quadrupole ion trap (IT) mass spectrometry, respectively, to analyze various cytolysin proteins isolated from the sea anemone Stichodactyla helianthus and digested by the protease trypsin. By employing different ionization methods, the subsequent changes in ionization selectivity for the peptides in the digested protein samples resulted in ion abundance variation reflected in the mass spectra. Upon investigation of this variation generated by the two ionization processes, it has been shown in this study that enhanced protein coverage (e.g., >95% for cytolysin III) can be achieved. Additionally, capillary and microbore reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with ESI mass spectrometry (MS) as well as flow injection analysis by nanoflow ESI-MS afforded the necessary limit of detection (LOD) for detailed structural information of the cytolysin proteins by tandem mass spectrometry (MS/MS) methods. It can be concluded that cytolysins II and III correspond to sticholysins I and II, that "cytolysin I" is a mixture of modified forms of cytolysins II and III, and that "cytolysin IV" is an incompletely processed precursor of cytolysin III. 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] Factors determining the performance of triple quadrupole, quadrupole ion trap and sector field mass spectrometer in electrospray ionization mass spectrometry.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2001The sequence coverage by fragment ions resulting from collision-induced dissociation in a triple stage quadrupole (TSQ) and a quadrupole ion trap (QIT) mass spectrometer of 10,20-mer oligonucleotides was investigated. While (a-B) and w ion series were the most abundant on both instruments, additional ion series of sequence relevance were preferably formed in the TSQ. Thus, a total number of 83 fragment ions were used to deduce the complete sequence of a 10-mer oligonucleotide of mixed sequence from a tandem mass spectrum recorded on the TSQ. The complete sequence was also encoded in the 28 fragments that were obtained from the QIT under comparable fragmentation conditions. Spectrum complexity increased considerably at the cost of signal-to-noise ratio upon fragmentation of a 20-mer oligonucleotide in the TSQ, whereas spectrum interpretation with longer oligonucleotides was significantly more straightforward in spectra recorded on the QIT. The extent of fragmentation had to be optimized by appropriate setting of collision energy and choice of precursor ion charge state in order to obtain full sequence coverage by fragments for de novo sequencing. Moreover, full sequence information was also dependent on base sequence because of the low tendency of backbone cleavage at thymidines. Tandem mass spectrometry on the QIT yielded redundant information that was successfully utilized to deduce the complete sequence of 20-mer oligonucleotides with high confidence. Copyright © 2001 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] Infrared Spectra of Protonated Uracil, Thymine and CytosineCHEMPHYSCHEM, Issue 15 2007Jean-Yves Salpin Dr. Abstract The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d,Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm,1 in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap. [source] | ||||||||||