GlycoMiner: a new software tool to elucidate glycopeptide composition

New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment.     

Modal resonant ultrasound spectroscopy for ferroelastics

Recent experimental and theoretical improvements of resonant ultrasound spectroscopy (RUS) are summarized to investigate elastic constants of phases in shape memory alloys. The proposed inversion procedure, described in this work, is particularly suitable to reliable evaluation of the temperature dependence of elastic constants of low-symmetry ferroelastic materials which may be strongly elastically anisotropic and tend to exist in twinned forms. The method is applicable even for the evaluation of single-crystal elastic constants from RUS measurements on microtwinned crystals, since it involves a homogenization algorithm based on the macroscopic deformation response of the layered structure. This potentially allows performing meaningful acoustic studies on samples with a general submicron-size layered structure.     

Chemical grafting of biphenyl self-assembled monolayers on ultrananocrystalline diamond

We have investigated the formation of self-assembled monolayers (SAMs) of 4'-nitro-1,1-biphenyl-4-diazonium tetrafluoroborate (NBD) onto ultrananocrystalline diamond (UNCD) thin films. In contrast to the common approach to modify diamond and diamond-like substrates by electrografting, the SAM was formed from the saturated solution of NBD in acetonitrile by pure chemical grafting. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), and near edge X-ray absorption fine structure spectroscopy (NEXAFS) have been used to verify the direct covalent attachment of the 4'-nitro-1,1-biphenyl (NB) SAM on the diamond substrate via stable C-C bonds and to estimate the monolayer packing density. The results confirm the presence of a very stable, homogeneous and dense monolayer. Additionally, the terminal nitro group of the NB SAM can be readily converted into an amino group by X-ray irradiation as well as electrochemistry. This opens the possibility of in situ electrochemical modification as well as the creation of chemical patterns (chemical lithography) in the SAM on UNCD substrates and enables a variety of consecutive chemical functionalization for sensing and molecular electronics applications.     

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D “heat map”, indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

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Covalent Labeling of Nucleosides with VIII‐ and VI‐Valent Osmium Complexes

Osmium tetroxide complexes with nitrogen ligands [Os(VIII)L] have been widely applied as probes of the DNA structure and as electroactive labels of DNA. Here we describe the electrochemical behavior of Os(VIII)2,2‐bipyridine (Os, bipy)‐base‐labeled nucleosides. We show that electroactive label can be introduced also in the nucleoside ribose residues using six‐valent osmium complex. Cyclic voltammograms of sugar‐Os(VI)‐modified ribosides are similar but not identical to those of the base‐modified ribosides. Our results showing the electroactivity of sugar modified ribosides pave the way to facile end‐labeling of RNA.     

Efficient Synthesis of Phosphono‐ and Phosphinoxidomethylated N‐Heterocycles under Solvent‐Free Microwave Conditions

Simple N‐heterocycles were converted to N‐phosphono‐ and phosphinoxidomethyl derivatives by a solvent‐free microwave‐assisted condensation of the heterocycle, paraformaldehyde, and diethylphosphite or diphenylphosphine oxide in a convenient and, in most cases, efficient way. In contrast to an earlier report, imidazole proved to be unreactive in this type of phospha‐Mannich reaction.     

Worst scenario method in homogenization. Linear case

The paper deals with homogenization of a linear elliptic boundary problem with a specific class of uncertain coefficients describing composite materials with periodic structure. Instead of stochastic approach to the problem, we use the worst scenario method due to Hlaváček (method of reliable solution). A few criterion functionals are introduced. We focus on the range of the homogenized coefficients from knowledge of the ranges of individual components in the composite, on the values of generalized gradient in the places where these components change and on the average of homogenized solution in some critical subdomain. This research was supported by grant No. 201/03/0570 of the Grant Agency of the Czech Republic.     

Electrospray ionization–tandem mass spectrometric study of fused nitrogen-containing ring systems

Four fused nitrogen-containing ring systems were investigated by electrospray ionization–tandem mass spectrometry: Pyridazino-indoles, pyridazino-quinolines, a pyrimido-quinoline derivative and pyrimido-cinnolines. Fragmentation patterns of these compounds are discussed and compared. Several characteristic cross-ring fragments were formed mainly on the pyridazine and pyrimidine rings of the ring systems. The connected Cl, NO₂, Me, Ph and more extended heterocyclic substituents influenced the fragmentation.     

Quantification of the electron beam damage of thin films

Owing to diverse possible mechanisms of the e-beam damage, some changes either in the crystalline structure, chemical composition or film thickness occur as the proper damage of the virgin state. Changes in the chemical bonds are often connected with some change in thickness or structure so that the other two are the most important items to be detected, preferably in real time of the electron-microscopical or electron-spectroscopical examination. We propose to measure the film thickness on the basis of the most probable energy loss due to the electron pass through the film and back, i.e. on the basis of the position of the broad background maximum in the electron spectra of stratified specimens. A change in crystallinity can be sensed through the elastic peak intensity. Placing a measurement window between these features in the energy scale and measuring the energy filtered background during the irradiation, we get a pronounced dependence of the signal on the dose which unambiguously reveals the damage limit in the form of a curve knee. In some cases, two stages of damage are detectable.     

Consecutive Reactions Observed Using Floated Collision Cells

Sequential processes occurring in one field-free region of a sector-type mass spectrometer were observed by floating the collision cell. This way four overall processes were identified; (a) both processes occurring outside the cell, (b) both processes inside the cell, (c) the first process outside and the second inside, and (d) the first inside, the second outside the cell. Positions of these peaks are derived and several examples are shown (for CsI clusters, benzophenone and nitrobenzene). This is a unique technique for distinguishing sequential and one-step processes like the (sequential) loss of two monomers and loss of a dimer from a supramolecular cluster.