Online coupling of high-resolution chromatography with extreme UV photon activation tandem mass spectrometry: Application to the structural investigation of complex glycans by dissociative photoionization

The activation of ions by extreme-energy photons (XUV) produced by a synchrotron radiation beamline is a powerful method for characterizing complex glycans using tandem mass spectrometry (MS). As previously described, this activation method leads to rich fragmentation spectra with many structurally valuable cross-ring cleavages while maintaining labile modifications on the glycan structures. However, until now, the tandem MS event was too long to be compatible with liquid chromatography elution times. In this work, the duty cycle of the activation and detection of fragments was shortened, and the background signal on the spectra was drastically reduced. Both improvements allowed, for the first time, the successful coupling of a UHPLC system to XUV-activated tandem MS. The approach was used to characterize a complex mixture of oligo-porphyrans, which are a class of highly sulfated oligosaccharides, in a fully automated way. Due to an enhanced dynamic range and an increased sensitivity, some hypothetical structures of low abundance have been unequivocally confirmed in this study and others have been revised. Some previously undescribed species of oligo-porphyrans that exhibit lateral branching have been fully resolved. This work contributes to the scarce knowledge of the structure of porphyrans in red algae and pushes the current capacities of XUV-activation tandem MS by demonstrating the possibility of a direct coupling with UHPLC. This study will considerably broaden the applicability and practicality of this method in many fields of analytical biology.     

Distance dependency and minimum amino acid alphabets for decoy scoring potentials

The validity and accuracy of a proposed tertiary structure of a protein can be assessed in several ways. Scoring such a structure by a knowledge‐based potential is a well‐known approach in molecular biophysics, an important task in structure prediction and refinement, and a key step in several experiments on protein structures. Although several parameterizations for such models have been derived over the course of time, improvements in accuracy by explicitly using continuous distance information have not been suggested yet. We close this methodological gap by formulating the parameterization of a protein structure model as a linear program. Optimization of the parameters was performed using amino acid distances calculated for the residues in topology rich 2830 protein structures. We show the capability of our derived model to discriminate between native structures and decoys for a diverse set of proteins. In addition, we discuss the effect of reduced amino acid alphabets on the model. In contrast to studies focusing on binary contact schemes (without considering distance dependencies and proposing five symbols as optimal alphabet size), we find an accurate protein alphabet size to contain at least five symbols, preferably more, to assure a satisfactory fold recognition capability. © 2012 Wiley Periodicals, Inc.     

Are liquid chromatography/electrospray tandem quadrupole fragmentation ratios unequivocal confirmation criteria?

Multiple reaction monitoring (MRM) ratios as provided by tandem mass spectrometers are used to confirm positive residue findings (e.g. veterinary drugs or pesticides). The Commission Decision 2002/657/EEC defines tolerance levels for MRM ratios, which are intended to prevent the reporting of false positives. This paper reports findings where blank sample extracts have been spiked by a drug (difloxacin) and the corresponding measured MRM ratios significantly deviated from MRM ratios observed in matrix‐free solution. The observation was explained by the formation of two different [M+H]⁺ analyte ions within the electrospray ionization (ESI) interface. These two ions vary only by the site of analyte protonation. Since they are isobaric, they are equally transmitted through the first quadrupole, but are differently fragmented in the collision chamber. The existence of two isobaric ions was deduced by statistical data and the observation of a doubly charged analyte ion. It was hypothesized that the combined presence of [M+H]⁺ and [M+2H]²⁺ implies the existence of two different singly charged ion species differing only by the site of protonation. Low‐ and high‐energy interface‐induced fragmentation was performed on the samples. The surviving precursor ion population was mass selected and again fragmented in the collision chamber. Equal product ion spectra would be expected. However, very different product ion spectra were observed for the two interface regimes. This is consistent with the assumption that the two postulated isobaric precursor ions show different stability in the interface. Hence the abundance ratio among the two types of surviving precursor ions will shift and change the resulting product ion spectra. The existence of the postulated singly charged ions with multiple chargeable sites was finally confirmed by successful ion mobility separation. Copyright © 2009 John Wiley & Sons, Ltd.     

Factorization and cutting planes for completely positive matrices by copositive projection

We consider the problem of projecting a matrix onto the cones of copositive and completely positive matrices. As this can not be done directly, we use polyhedral approximations of the cones. With the help of these projections we obtain a technique to compute factorizations of completely positive matrices. We also describe a method to determine a cutting plane which cuts off an arbitrary matrix from the completely positive (or copositive) cone.     

A stable limit law for recurrence times of the simple random walk on the two-dimensional integer lattice

We consider the random walk of a particle on the two-dimensional integer lattice starting at the origin and moving from each site (independently of the previous moves) with equal probabilities to any of the four nearest neighbors. When τ _i denotes the even number of steps between the (i ? 1)th and ith returns to the origin, we shall prove that the geometric mean of τ ₁ , . . . , τ _n divided by n ^π converges in distribution to some positive random variable having a logarithmic stable law. We also obtain a rate of this convergence and improve the asymptotic estimate of the tail probability of τ ₁ obtained by Erdos and Taylor (1960).     

Study of high-resolution mass spectrometry technology as a replacement for tandem mass spectrometry in the field of quantitative pesticide residue analysis

A validated LC/MS/MS-based multiresidue pesticide method was converted to an LC high-resolution MS single-stage Orbitrap platform. No changes regarding the cleanup and LC were made. Optimization of high-resolution MS-specific parameters and interface settings was kept at a minimum. The aim was to explore the capability of current Orbitrap technology to substitute for LC/MS/MS technology. The test included the quantitative performance (sensitivity, selectivity, linearity, accuracy, and precision) of some 240 analytes in three different matrixes. The LC/MS/MS instrumentation was operated at the edge of its technical limitations. A further extension of the number of analytes for LC/MS/MS would require the use of even narrower dwell times, significantly reducing sensitivity and reproducibility of measurement. No such limitations exist for the high-resolution technology. Similar performance was observed for both technologies. A current drawback of the high-resolution technology is the speed of data processing, which took significantly longer than for LC/MS/MS data due to the limited capabilities of the software.     

Nickel Tetracarbonyl as Starting Material for the Synthesis of NHC-stabilized Nickel(II) Allyl Complexes

A novel, useful in situ synthesis for NHC nickel allyl halide complexes [Ni(NHC)(η³-allyl)(X)] starting from [Ni(CO)₄], NHC and allyl halides is presented. The reaction of [Ni(CO)₄] with (i) one equivalent of the corresponding NHC and (ii) with an excess of the corresponding allyl chloride at room temperature leads with elimination of carbon monoxide to complexes of the type [Ni(NHC)(η³-allyl)(X)]. This approach was used to synthesize the complexes [Ni(tBu₂Im)(η³-H₂C -C (Me)-C H₂)(Cl)] ( 2 ), [Ni(iPr₂Im^Me)(η³-H₂C -C (Me)-C H₂)(Cl)] ( 3 ), [Ni(iPr₂Im)(η³-H₂C -C (Me)-C H₂)(Cl)] ( 4 ), [Ni(iPr₂Im)(η³-H₂C -C (H)-C (Me)₂)(Br)] ( 5 ), [Ni(Me₂Im^Me)(η³-H₂C -C (Me)-C H₂)(Cl)] ( 6 ), and [Ni(EtiPrIm^Me)(η³-H₂C -C (Me)-C H₂)(Cl)] ( 7 ). The complexes 1 to 7 were characterized using NMR and IR spectroscopy and elemental analysis, and the molecular structures are provided for 2 and 7 . The allyl nickel complexes 1 – 7 are stereochemically non-rigid in solution due to (i) NHC rotation about the nickel-carbon bond, (ii) allyl rotation about the Ni–η³-allyl axis and (iii) π–σ–π allyl isomerization processes. The allyl halide complexes can be methylated as was demonstrated by the methylation of a number of the complexes [Ni(NHC)(η³-allyl)(X)] with methylmagnesium chloride or methyllithium, which led to isolation of the complexes [Ni(Me₂Im)(η³-H₂C -C (Me)-C H₂)(Me)] ( 8 ), [Ni(tBu₂Im)(η³-H₂C -C (Me)-C H₂)(Me)] ( 9 ), [Ni(iPr₂Im^Me)(η³-H₂C -C (Me)-C H₂)(Me)] ( 10 ), [Ni(iPr₂Im)(η³-H₂C -C (Me)-C H₂)(Me)] ( 11 ), [Ni(iPr₂Im)(η³-H₂C -C (H)-C (Me)₂)(Me)] ( 12 ), and [Ni(EtiPrIm^Me)(η³-H₂C -C (Me)-C H₂)(Me)] ( 13 ). These complexes were fully characterized including X-ray molecular structures for 10 and 11 .