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## GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates

Lohmann, Klaus Karl; von der Lieth, Claus-W.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
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In recent years, mass spectrometry has become the method of choice for high-sensitivity glycan identification. Currently, only a few tools assisting mass spectra interpretation are available. The web application GlycoFragment (www.dkfz.de/spec/projekte/fragments/) calculates all theoretically possible fragments of complex carbohydrates and aims to support the interpretation of mass spectra. GlycoSearchMS (www.dkfz.de/spec/glycosciences.de/sweetdb/ms/) compares each peak of a measured mass spectrum with the calculated fragments of all structures contained in the SweetDB database. The best-matching spectra and the associated structures are displayed in order of decreasing similarity. Since both algorithms work very efficiently, they are well suited to be used for automatic identification of series of mass spectra of complex carbohydrates.

## Formation and reactions of negative ions relevant to chemical ionization mass spectrometry. I. Cl mass spectra of organic compounds produced by F− reactions

Tiernan, T. O.; Chang, C.; Cheng, C. C.
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.11%
A systematic study of the negative-ion chemical ionization mass spectra produced by the reaction of F− with a wide variety of organic compounds has been accomplished. A time-of-flight mass spectrometer fitted with a modified high pressure ion source was employed for these experiments. The F− reagent ion was generated from CF3H or NF3, typically at an ion source pressure of 100 μm. In pure NF3, F− is the major ion formed and constitutes more than 90% of the total ion intensity. While F− is also the major primary ion formed in pure CF3H, it undergoes rapid ion-molecule reactions at elevated source pressures, yielding (HF)nF− (n = 1−3) ions, which makes CF3H less suitable as a chemical ionization reagent gas. Among the organic compounds investigated were carboxylic acids, ketones, aldehydes, esters, alcohols, phenols, halides, nitriles, nitrobenzene, ethers, amines and hydrocarbons. An intense (M − 1)− ion was observed in the F− chemical ionization mass spectra of carboxylic acids, ketones, aldehydes and phenols. Alcohols yield only (M + F)− ions upon reaction with F−. A weaker (M + F)− ion was also detected in the F− chemical ionization spectra of carboxylic acids, aldehydes, ketones and nitriles. The F− chemical ionization mass spectra of esters...

## “Lossless” compression of high resolution mass spectra of small molecules

Blanckenburg, Bo; van der Burgt, Yuri E. M.; Deelder, André M.; Palmblad, Magnus
Fonte: Springer US Publicador: Springer US
Tipo: Artigo de Revista Científica
EN
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Fourier transform ion cyclotron resonance (FTICR) provides the highest resolving power of any commercially available mass spectrometer. This advantage is most significant for species of low mass-to-charge ratio (m/z), such as metabolites. Unfortunately, FTICR spectra contain a very large number of data points, most of which are noise. This is most pronounced at the low m/z end of spectra, where data point density is the highest but peak density low. We therefore developed a filter that offers lossless compression of FTICR mass spectra from singly charged metabolites. The filter relies on the high resolving power and mass measurement precision of FTICR and removes only those m/z channels that cannot contain signal from singly charged organic species. The resulting pseudospectra still contain the same signal as the original spectra but less uninformative background. The filter does not affect the outcome of standard downstream chemometric analysis methods, such as principal component analysis, but use of the filter significantly reduces memory requirements and CPU time for such analyses. We demonstrate the utility of the filter for urinary metabolite profiling using direct infusion electrospray ionization and a 15 tesla FTICR mass spectrometer.

## ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging

Ma, Ze-Qiang; Chambers, Matthew C.; Ham, Amy-Joan L.; Cheek, Kristin L.; Whitwell, Corbin W.; Aerni, Hans-Rudolf; Schilling, Birgit; Miller, Aaron W.; Caprioli, Richard M.; Tabb, David L.
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
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In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools. Despite recent improvements in identification algorithms, a significant number of high quality spectra remain unidentified for various reasons. Here we present ScanRanker, an open-source tool that evaluates the quality of tandem mass spectra via sequence tagging with reliable performance in data from different instruments. The superior performance of ScanRanker enables it not only to find unassigned high quality spectra that evade identification through database search, but also to select spectra for de novo sequencing and cross-linking analysis. In addition, we demonstrate that the distribution of ScanRanker scores predicts the richness of identifiable spectra among multiple LC-MS/MS runs in an experiment, and ScanRanker scores assist the process of peptide assignment validation to increase confident spectrum identifications. The source code and executable versions of ScanRanker are available from http://fenchurch.mc.vanderbilt.edu.

## Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

Diament, Benjamin; Noble, William Stafford
Tipo: Artigo de Revista Científica
EN
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Computational analysis of mass spectra remains the bottleneck in many proteomics experiments. SEQUEST was one of the earliest software packages to identify peptides from mass spectra by searching a database of known peptides. Though still popular, SEQUEST performs slowly. Crux and TurboSEQUEST have successfully sped up SEQUEST by adding a precomputed index to the search, but the demand for ever-faster peptide identification software continues to grow. Tide, introduced here, is a software program that implements the SEQUEST algorithm for peptide identification and that achieves a dramatic speedup over Crux and SEQUEST. The optimization strategies detailed here employ a combination of algorithmic and software engineering techniques to achieve speeds up to 170 times faster than a recent version of SEQUEST that uses indexing. For example, on a single Xeon CPU, Tide searches 10,000 spectra against a tryptic database of 27,499 C. elegans proteins at a rate of 1,550 spectra per second, which compares favorably with a rate of 8.8 spectra per second for a recent version of SEQUEST with index running on the same hardware.

## Peptide Identification by Database Search of Mixture Tandem Mass Spectra*

Wang, Jian; Bourne, Philip E.; Bandeira, Nuno
Fonte: The American Society for Biochemistry and Molecular Biology Publicador: The American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
EN
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In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision.

## High Mass Accuracy Phosphopeptide Identification Using Tandem Mass Spectra

Fonte: Hindawi Publishing Corporation Publicador: Hindawi Publishing Corporation
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46%
Phosphoproteomics is a powerful analytical platform for identification and quantification of phosphorylated peptides and assignment of phosphorylation sites. Bioinformatics tools to identify phosphorylated peptides from their tandem mass spectra and protein sequence databases are important part of phosphoproteomics. In this work, we discuss general informatics aspects of mass-spectrometry-based phosphoproteomics. Some of the specifics of phosphopeptide identifications stem from the labile nature of phosphor groups and expanded peptide search space. Allowing for modifications of Ser, Thr, and Tyr residues exponentially increases effective database size. High mass resolution and accuracy measurements of precursor mass-to-charge ratios help to restrict the search space of candidate peptide sequences. The higher-order fragmentations of neutral loss ions enhance the fragment ion mass spectra of phosphorylated peptides. We show an example of a phosphopeptide identification where accounting for fragmentation from neutral loss species improves the identification scores in a database search algorithm by 50%.

## mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra

Niedermeyer, Timo H. J.; Strohalm, Martin
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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46.03%
Natural or synthetic cyclic peptides often possess pronounced bioactivity. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and the complex fragmentation patterns observed. Even though several software tools for cyclic peptide tandem mass spectra annotation have been published, these tools are still unable to annotate a majority of the signals observed in experimentally obtained mass spectra. They are thus not suitable for extensive mass spectrometric characterization of these compounds. This lack of advanced and user-friendly software tools has motivated us to extend the fragmentation module of a freely available open-source software, mMass (http://www.mmass.org), to allow for cyclic peptide tandem mass spectra annotation and interpretation. The resulting software has been tested on several cyanobacterial and other naturally occurring peptides. It has been found to be superior to other currently available tools concerning both usability and annotation extensiveness. Thus it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides.

## Effects of Growth Medium on Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectra: a Case Study of Acetic Acid Bacteria

Wieme, Anneleen D.; Spitaels, Freek; Aerts, Maarten; De Bruyne, Katrien; Van Landschoot, Anita; Vandamme, Peter
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
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The effect of the growth medium used on the matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectra generated and its consequences for species and strain level differentiation of acetic acid bacteria (AAB) were determined by using a set of 25 strains. The strains were grown on five different culture media that yielded a total of more than 600 mass spectra, including technical and biological replicates. The results demonstrate that the culture medium can have a profound effect on the mass spectra of AAB as observed in the presence and varying signal intensities of peak classes, in particular when culture media do not sustain optimal growth. The observed growth medium effects do not disturb species level differentiation but strongly affect the potential for strain level differentiation. The data prove that a well-constructed and robust MALDI-TOF mass spectrometry identification database should comprise mass spectra of multiple reference strains per species grown on different culture media to facilitate species and strain level differentiation.

## Interpretation and Deconvolution of Nanodisc Native Mass Spectra

Marty, Michael T.; Zhang, Hao; Cui, Weidong; Gross, Michael L.; Sligar, Stephen G.
Tipo: Artigo de Revista Científica
EN
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Nanodiscs are a promising system for studying gas-phase and solution complexes of membrane proteins and lipids. We previously demonstrated that native electrospray ionization allows mass spectral analysis of intact Nanodisc complexes at single lipid resolution. This report details an improved theoretical framework for interpreting and deconvoluting native mass spectra of Nanodisc lipoprotein complexes. In addition to the intrinsic lipid count and charge distributions, Nanodisc mass spectra are significantly shaped by constructive overlap of adjacent charge states at integer multiples of the lipid mass. We describe the mathematical basis for this effect and develop a probability-based algorithm to deconvolute the underlying mass and charge distributions. The probability-based deconvolution algorithm is applied to a series of dimyristoylphosphatidylcholine Nanodisc native mass spectra and used to provide a quantitative picture of the lipid loss in gas-phase fragmentation.

## Studies in the mass spectra of perfluoroaromatic derivatives of phosphorus and some selected transition metals

Jones, Timothy R. B.
Fonte: Brock University Publicador: Brock University
Tipo: Electronic Thesis or Dissertation
ENG
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The mass spectra and fragmentation of a variety of fluoroaromatic compounds of Group V and some selected transition elements are discussed in some detail, aided by data from metastable defocussed experiments. Results of ,studies on the coupling reaction using unstable organotitanium chloride intermediate species are reported. The preparation of some 5-substituted octafluorodibenzophospho1es is also discussed. Rearrangements under electron bombardment resulting in the loss of heteroatom-fluoride fragments are discussed in the light of presently accepted mechanisms for these processes as are rearrangements observed in compounds involving thionophosphoryl bonds ( p=s ).

## Mass spectral studies of some pentafluorophenyl derivatives of group V /|nby Andrew Tanner Rake. -- 260 St. Catharines, Ont. : [s. n.],

Rake, Andrew Tanner.
Fonte: Brock University Publicador: Brock University
Tipo: Electronic Thesis or Dissertation
ENG
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The mass spectra of compounds of t he series (C6F5 )3-n MP~ (n = 1,2,3, M = P and As ), (C6F5>3Sb, Ph) Sb and (C6F5 )2SbPh have been studied in detail and the important modes of fragmentation were e1ucidated, a ided by metastable ions. Various trends attributed to the central atom and or the . substituent groups have been noted and, where applicable, compared to recent studies on related phenyl and pentafluorophenyl compounds of groups IV and V. The mass spectra of fluorine containing organometallic compounds exhibit characteristic migrations of fluorine to t he central atom, giving an increasing abundance of MF+, MF2+' and RMF+ (R = Ph or C6F5) ions on descending the group_ The mass spectra of pentafluorophenyl , antimony, and arsenic compounds show a greater fragmentation of the aromatic ring than those of phosphorus. The mixed phenyl pentafluorophenyl derivatives show a characteristic pattern depending on the number of phenyl grm.lps present but show t he general characteristics of both the tris(phenyl) and tris(pentafluorophenyl) compounds. The diphenyl pentafluorophenyl der ivatives show the loss of biphenyl ion as the most import ant step, the los s of phenyl t o give the i on PhMC6F5 + being of secondary importance. The ...

## Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

Edwards, Nathan J
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.01%
Peptide identification by tandem mass spectrometry is the dominant proteomics workflow for protein characterization in complex samples. Traditional search engines, which match peptide sequences with tandem mass spectra to identify the samples' proteins, use protein sequence databases to suggest peptide candidates for consideration. Although the acquisition of tandem mass spectra is not biased toward well-understood protein isoforms, this computational strategy is failing to identify peptides from alternative splicing and coding SNP protein isoforms despite the acquisition of good-quality tandem mass spectra. We propose, instead, that expressed sequence tags (ESTs) be searched. Ordinarily, such a strategy would be computationally infeasible due to the size of EST sequence databases; however, we show that a sophisticated sequence database compression strategy, applied to human ESTs, reduces the sequence database size approximately 35-fold. Once compressed, our EST sequence database is comparable in size to other commonly used protein sequence databases, making routine EST searching feasible. We demonstrate that our EST sequence database enables the discovery of novel peptides in a variety of public data sets.

## Effect of protein stabilization on charge state distribution in positive- and negative-ion electrospray ionization mass spectra

Watt, Stephen J; Sheil, Margaret; Beck, Jennifer; Prosselkov, Pavel; Otting, Gottfried; Dixon, Nicholas
Tipo: Artigo de Revista Científica
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55.85%
Changes in protein conformation are thought to alter charge state distributions observed in electrospray ionization mass spectra (ESI-MS) of proteins. In most cases, this has been demonstrated by unfolding proteins through acidification of the solution. T

## Variational Analysis of Mass Spectra and Decay Constants for Ground State Pseudoscalar and Vector Mesons in Light-Front Quark Model

Choi, Ho-Meoyng; Ji, Chueng-Ryong; Li, Ziyue; Ryu, Hui-Young
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.1%
Using the variational principle, we compute mass spectra and decay constants of ground state pseudoscalar and vector mesons in the light-front quark model (LFQM) with the QCD-motivated effective Hamiltonian including the hyperfine interaction. By smearing out the Dirac delta function in the hyperfine interaction, we avoid the issue of negative infinity in applying the variational principle to the computation of meson mass spectra and provide analytic expressions for the meson mass spectra. Our analysis with the smeared hyperfine interaction indicates that the interaction for the heavy meson sector including the bottom and charm quarks gets more point-like. We also consider the flavor mixing effect in our analysis and determine the mixing angles from the mass spectra of $(\omega,\phi)$ and $(\eta,\eta')$. Our variational analysis with the trial wave function including the two lowest order harmonic oscillator basis functions appears to improve the agreement with the data of meson decay constants and the heavy meson mass spectra over the previous computation handling the hyperfine interaction as perturbation.; Comment: 5 figures. Added the flavor mixing effect in our analysis and determine the mixing angles from the mass spectra of (\omega...

## Jet Mass Spectra in Higgs + One Jet at NNLL

Jouttenus, Teppo T.; Stewart, Iain W.; Tackmann, Frank J.; Waalewijn, Wouter J.
Tipo: Artigo de Revista Científica
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The invariant mass of a jet is a benchmark variable describing the structure of jets at the LHC. We calculate the jet mass spectrum for Higgs plus one jet at the LHC at next-to-next-to-leading logarithmic (NNLL) order using a factorization formula. At this order, the cross section becomes sensitive to perturbation theory at the soft m_jet^2/p_T^jet scale. Our calculation is exclusive and uses the 1-jettiness global event shape to implement a veto on additional jets. The dominant dependence on the jet veto is removed by normalizing the spectrum, leaving residual dependence from non-global logarithms depending on the ratio of the jet mass and jet veto variables. For our exclusive jet cross section these non-global logarithms are parametrically smaller than in the inclusive case, allowing us to obtain a complete NNLL result. Results for the dependence of the jet mass spectrum on the kinematics, jet algorithm, and jet size R are given. Using individual partonic channels we illustrate the difference between the jet mass spectra for quark and gluon jets. We also study the effect of hadronization and underlying event on the jet mass in PYTHIA. To highlight the similarity of inclusive and exclusive jet mass spectra, a comparison to LHC data is presented.; Comment: 29 pages...

## Study of the $\pi\pi$ mass spectra in the process $e^+e^- \to \pi^+\pi^-\pi^0$ at $\sqrt[]{s} \simeq 1020$ MeV

Achasov, M. N.; Aulchenko, V. M.; Beloborodov, K. I.; Berdyugin, A. V.; Bogdanchikov, A. G.; Bozhenok, A. V.; Bukin, A. D.; Bukin, D. A.; Burdin, S. V.; Dimova, T. V.; Druzhinin, V. P.; Golubev, V. B.; Ivanchenko, V. N.; Ivanov, P. M.; Korol, A. A.; Koros
Tipo: Artigo de Revista Científica
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46.01%
The invariant mass spectra of the $\pi^+\pi^-$ and $\pi^\pm\pi^0$ pairs in the process $e^+e^- \to \pi^+\pi^-\pi^0$ were studied in the SND experiment at the VEPP-2M collider in the energy region $\sqrt[]{s} \simeq 1020$ MeV. These studies were based on about $0.5 \times 10^6$ experimental events. The spectra were analyzed in the framework of the vector meson dominance model. It was found that the experimental data can be described with $e^+e^- \to \rho\pi \to \pi^+\pi^-\pi^0$ transition only. Upper limit on the branching ratio of the $\phi(1020)\to\pi^+\pi^-\pi^0$ decay through intermediate states different from $\rho\pi$ was obtained at the 90 % confidence level: $B(\phi\to\pi^+\pi^-\pi^0)<6 \cdot 10^{-4}$. The $\rho$-meson mass and width which follow from the spectra analysis are $m_\rho=775.0\pm 1.3$ MeV, $\Gamma_\rho=150.4 \pm 3.0$ MeV. Neutral and charged $\rho$-mesons mass difference was found to equal $m_{\rho^\pm}-m_{\rho^0}=-1.3\pm2.3$ MeV. In the $\pi^+\pi^-$ mass spectrum the $\rho-\omega$ interference was seen at two standard deviations level.; Comment: 22 pages REVTEX and 19 figures

## Monitoring and modeling of protein processes using mass spectrometry, circular dichroism, and multivariate curve resolution methods

Navea, Susana; Tauler Ferré, Romà; Juan, Anna de
Fonte: American Chemical Society Publicador: American Chemical Society
Tipo: Artículo Formato: 162 bytes; application/msword
ENG
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11 pages, 10 figures.-- PMID: 16841894 [PubMed].-- Printed version published Jul 15, 2006.; Mass spectrometry has recently become one of the major analytical tools to study biomolecular structure and function. Ionization techniques, such as electrospray ionization (ESI), desorb biomolecules from solution to the gas phase keeping practically intact their natural structure. ESI applied to a protein solution produces a mixture of multiply charged ions, the ion charge distribution of which depends on the oligomeric form (mass) and on the protein surface exposed (amount of accommodated charges) of the related protein conformation. ESI-MS provides an efficient way to monitor protein processes; however, the ionic contributions of the different protein conformations involved usually overlap, and the use of chemometric tools is necessary to unravel the information related to the pure conformations that the biomolecule adopts along the process. Multivariate curve resolution-alternating least squares applied to MS-monitored protein processes provides the concentration profiles associated with the different protein conformations occurring during the process and the related pure mass spectra. The concentration profiles, in this context, the ionic contributions...

## Invariant mass spectrum and alpha-n correlation function studied in the fragmentation of He-6 on a carbon target

Aleksandrov, D.; Aumann, T.; Axelsson, L.; Baumann, T.; García Borge, María José; Chulkov, L. V.; Cub, J.; Dostal, W.; Eberlein, B.; Elze, Th. W.; Emling, H.; Geissel, H.; Goldberg, V. Z.; Golovkov, M.; Grünschloß, A.; Hellström, M.; Holeczek, J.; H
Tipo: Artículo Formato: 720623 bytes; application/pdf
ENG
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13 pags, 5 figures.-- PACS nrs.: 24.60.−t; 25.70.Ef; 27.20.+n.; Momentum distributions and invariant mass spectra from the breakup of He-6 ions with an energy of 240 MeV/u interacting with a carbon target have been studied. The data were used to extract information about the reaction mechanism which is influenced by the structure of He-6. It is found that the dominant reaction mechanism is a two-step process: knock out of one neutron followed by the decay of the He-5 resonance. The shape of the (α+n) two-body invariant mass spectrum is interpreted as mainly reflecting the 5He ground state which is a J(π) = 3/2(-) resonance. However, no evidence for correlations between cu particles and neutrons is observed in the momentum widths of the distributions. It is demonstrated that a combined analysis of the two-body invariant mass spectrum and an appropriate correlation function may be used to determine the properties of the intermediate resonance.; This work was supported by the German Federal Minister for Education and Research (BMBF) under Contracts 06 DA 820, 06 OF 474 and 06 MZ 476 and by GSI via Hochschulzusammenarbeitsvereinbarungen under Contracts DARIK, OF ELK, MZ KRK and partly supported by the Polish Committee of Scientific Research under Contract PB2/P03B/113/09...

## Comparison of negative and positive ion electrospray ionization mass spectra of calmodulin and its complex with trifluoperazine

Watt, Stephen J; Oakley, Aaron; Sheil, Margaret; Beck, Jennifer
Fonte: John Wiley & Sons Inc Publicador: John Wiley & Sons Inc
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
56.07%
The protein calmodulin (apoCaM) undergoes a conformational change when it binds calcium. This structure of the protein (Ca4CaM) is a dumbbell-shaped molecule that undergoes a further profound conformational change on binding of the antipsychotic drug trifluoperazine (TFP). Experimental conditions were developed to prepare samples of apoCaM, Ca4CaM and Ca4CaM/TFP that were substantially free of sodium. The effects of the conformational changes of calmodulin on the charge-state distributions observed in positive ion and negative ion electrospray ionization (ESI) mass spectra were examined. Conversion of apoCaM into Ca4CaM was concomitant with a change in the negative ion ESI mass spectrum whereby the 16- ion was the most abundant ion observed for the apo form and the 8- ion was the most abundant for the complex. In contrast, in the positive ion ESI mass spectra of apoCaM and Ca4CaM, the most abundant species in each case was the 8+ ion. When a complex of Ca4CaM with TFP was prepared, the most abundant species was the 5+ ion. This is consistent with a conformational change of Ca4CaM that rendered some basic sites inaccessible to ionization in the ESI process. Using the same Ca4CaM/TFP mixture, no complex with TFP was observed in negative ion ESI mass spectra. These observations are discussed in the context of the structural changes that are known to occur in calmodulin...