Charge Enhancement of Single-Stranded DNA in Negative Electrospray Ionization Using the Supercharging Reagent Meta-nitrobenzyl Alcohol

Charge enhancement of single-stranded oligonucleotide ions in negative ESI mode is investigated. The employed reagent, meta-nitrobenzyl alcohol (m-NBA), was found to improve total signal intensity (I_tot), increase the highest observed charge states (z_high), and raise the average charge states (z_avg) of all tested oligonucleotides analyzed in negative ESI. To quantify these increases, signal enhancement ratios (SER_1%) and charge enhancement coefficients (CEC_1%) were introduced. The SER_1%, (defined as the quotient of total oligonucleotide ion abundances with 1 % m-NBA divided by total oligonucleotide abundance without m-NBA) was found to be greater than unity for every oligonucleotide tested. The CEC_1% values (defined as the average charge state in the presence of 1 % m-NBA minus the average charge state in the absence of m-NBA) were found to be uniformly positive. Upon close inspection, the degree of charge enhancement for longer oligonucleotides was found to be dependent upon thymine density (i.e., the number and the location of phospho-thymidine units). A correlation between the charge enhancement induced by the presence of m-NBA and the apparent gas-phase acidity (largely determined by the sequence of thymine units but also by the presence of protons on other nucleobases) of multiply deprotonated oligonucleotide species, was thus established. Ammonium cations appeared to be directly involved in the m-NBA supercharging mechanism, and their role seems to be consistent with previously postulated ESI mechanisms describing desorption/ionization of single-stranded DNA into the gas phase.

Characterization of an Electron Ionization Source Trap Operating in the Presence of a Magnetic Field Through Computer Simulation

We explore the feasibility of conducting electron ionization (EI) in a radio-frequency (rf) ion source trap for mass spectrometry applications. Electrons are radially injected into a compact linear ion trap in the presence of a magnetic field used essentially to lengthen the path of the electrons in the trap. The device can either be used as a stand-alone mass spectrometer or can be coupled to a mass analyzer. The applied parallel magnetic field and the oscillating rf electric field produced by the trap give rise to a set of coupled Mathieu equations of motion. Via numerical simulations, electron trajectories are studied under varying intensities of the magnetic field in order to determine the conditions that enhance ion production. Likewise, the dynamic behavior of the ions are investigated in the proposed EI source trap and the fast Fourier transform FFT formalism is used to obtain the frequency spectrum from the numerical simulations to study the motional frequencies of the ions which include combinations of the low-frequency secular and the high-frequency micromotion with magnetron and cyclotron frequencies. The dependence of these motional frequencies on the trapping conditions is examined and particularly, the limits of applying a radial magnetic field to the EI ion trap are characterized.

New mass spectrometric approaches to structural analysis in mixtures

Structural analysis of minor components in mixtures is a vital requirement in the development of any pharmaceutical compound. Mass spectrometry is uniquely able to give this kind of information on the trace amounts of material present as minor impurities in a drug substance. In this study we show that a combination of mass spectrometric analysers with different characteristics is an even more powerful approach with a higher chance of establishing a potential structure. In particular the advent of analysers capable of accurate mass measurement on small amounts of material has enabled structures to be proposed in situations where previously no real conclusions could be made. Copyright 1999 John Wiley & Sons, Ltd.     

Rational matrix approximation with a priori error bounds for non-symmetric matrix Riccati equations with analytic coefficients

In this paper the exact solution of the non-symmetric matrixRiccati equation with analytic coefficients is approximatedby a rational matrix function with a prefixed accuracy. Thisrational matrix function is locally defined as the exact solutionof a Riccati problem with matrix polynomial coefficients obtainedby truncation of the Taylor expansions of the matrix coefficientsof the original problem.     

Topoisomer Differentiation of Molecular Knots by FTICR MS: Lessons from Class II Lasso Peptides

Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminal macrolactam ring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collision-induced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECD spectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c•/z from c/z•) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions ( b￠_n ^· ) \left( {b{\prime}_n^{ \bullet }} \right) . We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z• and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture.     

Heparin-like glycosaminoglycan/amine salt-bridge interactions: a new potential tool for HLGAGs analysis using mass spectrometry

Characterization of glycosaminoglycans poses a challenge for current analytical techniques, as they are highly acidic, polydisperse and heterogeneous compounds. The purpose of this study is the separation and analysis of a partially depolymerized heparin-like glycosaminoglycan by on-line ion-pairing reversed-phase high-performance liquid chromatography/electrospray mass spectrometry. The gas-phase behavior of two synthesized glycosaminoglycans has been investigated. Dibutylamine was found to be the best suited ion-pairing reagents for mass spectrometry analysis. The optimized ion-pairing conditions provide reproducible and easily interpretable electrospray mass spectra in both negative and positive ESI modes. The glycosaminoglycans are detected as a non-covalent complex with amines. In fact, the observed ionic species and their gas-phase dissociation under CID conditions revealed the presence of salt bridge interactions in the gas phase.     

Synthesis and inclusion properties study of some mono 6-amino ??-cyclodextrin dimers bridged by N,N-succinyldiamide linkers

Methylated and partially methylated cyclodextrin homo- and heterodimers linked by diamidosuccinic bridges were synthesised and their inclusion properties were evaluated using NMR and isothermic microcalorimetric measurements ITC. The selective binding of ligands, such as bisadamantyl derivatives, to the cavities of unprotected cyclodextrin dimers showed the equimolar formation of bidendate inclusion complexes (2:2, two ligand guest to two cavities host).     

Combined compact difference method for solving the incompressible Navier–Stokes equations

This paper presents a numerical method for solving the two‐dimensional unsteady incompressible Navier–Stokes equations in a vorticity–velocity formulation. The method is applicable for simulating the nonlinear wave interaction in a two‐dimensional boundary layer flow. It is based on combined compact difference schemes of up to 12th order for discretization of the spatial derivatives on equidistant grids and a fourth‐order five‐ to six‐alternating‐stage Runge–Kutta method for temporal integration. The spatial and temporal schemes are optimized together for the first derivative in a downstream direction to achieve a better spectral resolution. In this method, the dispersion and dissipation errors have been minimized to simulate physical waves accurately. At the same time, the schemes can efficiently suppress numerical grid‐mesh oscillations. The results of test calculations on coarse grids are in good agreement with the linear stability theory and comparable with other works. The accuracy and the efficiency of the current code indicate its potential to be extended to three‐dimensional cases in which full boundary layer transition happens. Copyright © 2011 John Wiley & Sons, Ltd.     

Gold‐ and Platinum‐Catalyzed Cycloisomerization of Enynyl Esters versus Allenenyl Esters: An Experimental and Theoretical Study

Ester‐way to heaven : Unexpected formation of bicyclo[3.1.0]hexene 4 was the main focus of combined experimental and theoretical studies on the Au‐catalyzed cycloisomerization of branched dienyne 1 (see scheme), which provided better understanding of the mechanistic details governing the cyclization of enynes bearing a propargylic ester group.

     

The use of desorption/ionization on porous silicon mass spectrometry for the detection of negative ions for fatty acids

The study of low molecular weight compounds by matrix-assisted laser desorption/ionization (MALDI) is difficult because of the presence of ions originating from the matrix in the low-m/z range. In order to resolve these problems, new matrix-free approaches were developed based on laser desorption/ionization from the surface of various materials such as graphite and porous silicon. Our work involves the use of 'desorption ionization on porous silicon mass spectrometry' (DIOS-MS) in the negative ion mode to study fatty acid compounds. The potential of the DIOS-MS technique is shown and an insight into the ionization mechanism provided.