MULTI-FUNCTIONAL MBIT FOR PEPTIDE TANDEM MASS SPECTROMETRY

Isobaric tags have been widely used for the identification and quantification of proteins in mass spectrometry-based proteomics. The mass-balanced, H-1/H-2 isotope-coded dipeptide tag (MBIT) is a multifunctional isobaric tag based on N-acetyl-Ala-Ala dipeptide containing an amine-reactive linker that conjugates the tag to the primary amines of proteolytic peptides. MBITs provide a pair of isotope-coded quantitation signals separated by 3Da, which enables 2-plex quantification and identification of proteins in the 15-250fmol range. Various MBITs diversified at the N-acetyl group or at the side chain of the first alanine provide a pair of bs ions as low-mass quantitation signals in a distinct mass window. Thus, a combination of different MBITs allows multiplex quantification of proteins in a single liquid chromatography-mass spectrometry experiment. Unlike other isobaric tags, MBITs also offer a pair of ys ions as high-mass quantitation signals in a noise-free region, facilitating protein quantification in quadrupole ion trap mass spectrometers. Uniquely, b(S) ions, forming N-protonated oxazolone, undergo unimolecular dissociation and generate the secondary low-mass quantitation signals, a(S) ions. The yield of a(S) ions derived from b(S) ions can be used to measure the temperature of b(S) ions, which enables a reproducible acquisition of the peptide tandem mass spectra. Thus, MBITs enable multiplexed quantitation of proteins and the concurrent measurement of ion temperature using b(S) and a(S) signal ions as well as the isobaric protein quantitation in resonance-type ion trap using y(S) (complement of b(S)) signal ions. This review provides an overview of MBITs with a focus on the multi-functionality that has been successfully demonstrated in the peptide tandem mass spectrometry. (c) 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 209-218, 2015.X1141Ysciescopu

Energy- and Time-Dependent Branching to Competing Paths in Coupled Unimolecular Dissociations of Chlorotoluene Radical Cations

The energy- and time-dependent branching to the competing dissociation paths are studied by theory for coupled unimolecular dissociations of the o-, m-, and p-chlorotoluene radical cations to C7H7+ (benzylium and tropylium). There are four different paths to C7H7+, three to the benzylium ion and one to the tropylium ion, and all of them are coupled together. The branching to the multiple paths leads to the multiexponential decay of reactant with the branching ratio depending on both internal energy and time. To gain insights into the multipath branching, we study the detailed kinetics as a function of time and internal energy on the basis of ab inito/RRKM calculations. The number of reaction steps to C7H7+ is counted for each path. Of the three isomers, the meta mostly goes through the coupling, whereas the para proceeds with little or no coupling. In the beginning, some reactants with high internal energy decay fast to the benzylium ion without any coupling and others rearrange to the other isomers. Later on all three isomers dissociate to the products via long-lived intermediates. Thus, the reactant shows a multiexponential decay and the branching ratio varies with time as the average internal energy decreases with time. The reciprocal of the effective lifetime is taken as the rate constant. The resulting rate-energy curves are in line with experiments. The present results suggest that the coupling between the stable isomers is thermodynamically controlled, whereas the branching to the product is kinetically controlled.X1111Ysciescopu

Die Berechnung der induzierten Ladung

One of the main aspects of statistical mechanics is that the properties of a thermodynamics state point do not depend on the choice of the statistical ensemble. It breaks down for small systems e.g. single molecules. Hence, the choice of the statistical ensemble is crucial for the interpretation of single molecule experiments, where the outcome of measurements depends on which variables or control parameters, are held fixed and which ones are allowed to fluctuate. Following this principle, this thesis investigates the thermodynamics of a single polymer pulling experiments within two different statistical ensembles. The scaling of the conjugate chain ensembles, the fixed end-to-end vector (Helmholtz) and the fixed applied force (Gibbs), are studied in depth. This thesis further investigates the ensemble equivalence for different force regimes and polymer-chain contour lengths. Using coarse-grained molecular dynamic simulations, i.e. Langevin dynamics, the simulations were found to complement the theoretical predictions for the scaling of ensemble difference of Gaussian chains in different force-regimes, giving special attention to the zero force regime. After constructing Helmholtz and Gibbs conjugate ensembles for a Gaussian chain, two different data sets of thermodynamic states on the force-extension plane, i.e. force-extension curves, were generated. The ensemble difference is computed for different polymer-chain lengths by using force-extension curves. The scaling of the ensemble difference versus relative polymer-chain length under different force regimes has been derived from the simulation data and compared to theoretical predictions. The results demonstrate that the Gaussian chain in the zero force limit generates nonequivalent ensembles, regardless of its equilibrium bond length and polymer-chain contour length. Moreover, if polymers are charged in confinement, coarse-graining is problematic, owing to dielectric interfaces. Hence, the effect of dielectric interfaces must be taken into account when describing physical systems such as ionic channels or biopolymers inside nanopores. It is shown that the effect of dielectrics is crucial for the dynamics of a biopolymer or an ion inside a nanopore. In the simulations, the feasibility of an efficient and accurate computation of electrostatic interactions in the presence of an arbitrarily shaped dielectric domain is challenging. Several solutions for this problem have been previously proposed in the literature such as a density functional approach, or transforming problem at hand into an algebraic problem ( Induced Charge Computation (ICC) ) and boundary element methods. Even though the essential concept is the same, which is to replace the dielectric interface with a polarization charge density, these approaches have been analyzed and the ICC algorithm has been implemented. A new superior boundary element method has been devised utilizing the force computation via the Particle-Particle Particle-Mesh (P3M) method for periodic geometries (ICCP3M). This method has been compared to the ICC algorithm, the algebraic solutions, and to density functional approaches. Extensive numerical tests against analytically tractable geometries have confirmed the correctness and applicability of developed and implemented algorithms, demonstrating that the ICCP3M is the fastest and the most versatile algorithm. Further optimization issues are also discussed in obtaining accurate induced charge densities. The potential of mean force (PMF) of DNA modelled on a coarsed-grain level inside a nanopore is investigated with and without the inclusion of dielectric effects. Despite the simplicity of the model, the dramatic effect of dielectric inclusions is clearly seen in the observed force profile.Eines der wichtigsten Ergebnisse der statistischen Mechanik ist, dass unterschiedliche statistische Ensembles dieselben thermodynamischen Zustände erzeugen. Dieses Prinzip gilt nicht notwendigerweise für kleine Systeme, wie zum Beispiel einzelne Moleküle oder ein einzelnes Polymer. Deshalb ist die Wahl des statistischen Ensembles von entscheidender Bedeutung für die Interpretation von Einzelmolekülexperimenten ( im Englischen "Single Molecule Experiment" (SME) ), denn das Ergebnis der Messung hängt davon ab, welche Variablen oder Kontrollparameter festgehalten werden und welche fluktuieren können. Ausgehend von diesem Problem haben wir Zugexperimente an einem einzigen Polymer in zwei verschiedenen Ensembles durchgeführt und den thermodynamischen Limes (Anzahl der Polymersegmente wächst gegen unendlich) untersucht. Wir haben zwei konjugierte Ensembles, nämlich das, in dem der End-zu-End Abstand (Helmholtz) festgehalten wurde, mit dem, wo wir die Kraft (Gibbs) festgehalten haben, gründlich und auf verschiedene Arten verglichen. Wir haben den Ensemble-Unterschied als Funktion der Anzahl der Polymersegmente in unterschiedlichen Zugkraftbereichen mittels Molekulardynamik Simulationen untersucht, wobei wir eine Langevin Dynamik benutzt haben. Die untersuchten Messgrössen waren die Bestimmung von sogenannten Kraft-Dehnungskurven, wie sie auch in AFM Experimenten gemessen werden. Diese Kurven wurden für zwei verschieden Gauss Ketten verschiedenster Polymerlänge durchgeführt, einmal mit verschwindender Bondlänge und einmal mit Bondlänge eins. Aufgrund unserer Simulationen konnten wir zeigen, das sowohl Gauss-Ketten mit endlicher, wie auch verschwindender Bondlänge für den Bereich verschwindender Zugkraft einen endlichen Ensembleunterschied besitzen, der nicht von der Kettenlänge abhängt. Dieses Phänomen wurde bereits vor 20 Jahren von R. Neumann beschrieben. Trotz der relativ einfachen Argumente von Neumann gibt es bis heute noch Arbeiten, die diesen Sachverhalt entweder anzweifeln oder verkehrt darstellen. Wir hoffen, durch diesen Teil der Arbeit den Sachverhalt zufriedenstellend aufgeklärt zu haben. Im zweiten Teil der Arbeit behandeln wir geladen Polymere unter einem räumlichen Einschluss. Dies können zum Beispiel Ionen in schmalen Kanälen sein (Ionenkanäle), oder DNA in Nanoporen. In vergröberten Simulationen werden geladene Polymere immer in einem dielektrischen Kontinuum dargestellt. Wasser hat eine relative dielektrische Konstante von 80 bei Raumtemperatur, die dann in dieses Model als Parameter gesteckt wird. Wenn feste Grenzflächen vorhanden sind, haben diese meist niedrige dielektrische Konstanten ($\approx 2$). Diese Grenzflächen haben grosse Auswirkungen auf die elektrostatischen Wechselwirkungen. In den Simulationen ist es wichtig, diese Effekte korrekt *und schnell* zu berechnen. Deshalb haben wir einen effizienten und präzisen Algorithmus entwickelt, der genau dies bewerkstelligt. In der Literatur wurden mehrere Möglichkeiten vorgeschlagen, wie dieses Problem für Simulationen lösbar sein sollte, wie zum Beispiel Dichtefunktionalmethoden, Umwandlung des Problems in ein algebraisches Problem (Induced Charge Computation, ICC) oder die Randelement Methode. Das wesentliche Konzept besteht darin, die Polarisationsladung auf dem dielektrischen Rand so zu bestimmen, dass die dielektrischen Randbedingungen erfüllt werden. Wir haben den ICCP3M Algorithmus entwickelt, dessen Kernstück darin besteht, den P3M Algorithmus zur Bestimmung der induzierten Ladung auf den Randelementen zu benutzen. Durch diesen Trick lässt sich die Ladungsberechnung in CPU Zeit $\mathscr{O}(Nlog N)$, wobei $\mathscr{O}(N)$ die Anzahl der Ladungen im System ist, durchführen. Wir haben den Algorithmus innerhalb des Espresso Programmpakets implementiert und optimiert. Im letzten Teil der Arbeit wurde das Potential der mittleren Kraft einer vergröberten DNA innerhalb einer Nanopore untersucht, wobei wir die Unterschiede zwischen korrekter Behandung der dielektrischen Ränder und der Ignorierung derselben quantifiziert haben. Trotz seiner Einfachheit zeigt unser Modell den dramatischen Einfluss, den die dielektrischen Ränder auf die gemessene efffektive Kraft und das Potential der mittleren Kraft ausüben

Protomers of Benzocaine: Solvent and Permittivity Dependence

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid, which finds an application as a local anesthetic (LA), is found to adopt in its protonated form at least two populations of distinct structures in the gas phase and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization (ESI) process. Here we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry (IM-MS) to yield gas-phase IR spectra of simultaneously m/z and drift-time resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species - the N- and O-protonated form. Density functional theory (DFT) calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation has been suggested

New analytical approach for distinguishing biomolecular topologies using ion mobility spectrometry-mass spectrometry

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Advances in Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)-Based Techniques for Elucidating Higher-Order Protein Structures

Despite its great success in the field of proteomics, mass spectrometry has limited use for determining structural details of peptides, proteins, and their assemblies. Emerging ion mobility spectrometry-mass spectrometry has enabled us to explore the conformational space of protein ions in the gas phase, and further combinations with the gas-phase ion spectroscopy and the colli- sion-induced unfolding have extended its abilities to elucidating the secondary structure and local details of conformational transi- tions. This review will provide a brief introduction to the combined approaches of IMS-MS with gas-phase ion infrared spectroscopy or collision-induced unfolding and their most recent results that successfully revealed higher-order structural details.11Nscopuskc

Formation Mechanism of Alkali Halide Cluster Ion During the Electrospray Ionization

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Li+ and Li+I−Li+ Ions Solvated by 1,4-dioxane: An Ion Mobility Spectrometry-Mass Spectrometry Study

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Formation of Stable Chiral-Selective Serine/Glucose Complex Anion with a Chloride in the Gas Phase

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Untangling pathways of RNA hairpins in gaseous phase investigated using ion mobility spectrometry-mass spectrometry

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