Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species

In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected.     

In-vial pyrolysis (PyroVial) with pre- and post-sample treatment combined with different chromatographic techniques

A new generic pyrolysis unit (PyroVial) is presented. Pyrolysis is carried out in a 2 mL autosampler vial placed in a XYZ robot for automated pyrolysis as well as for pre- and post-pyrolysis treatment of the sample. Analysis of the volatiles is performed by headspace analysis while the semi- and non-volatiles are extracted from the pyrolysate with an organic solvent. The features of the PyroVial are such that all chromatographic techniques can be applied. The pyrolysis unit is discussed in terms of its technical features and its performance is illustrated with applications including conventional pyrolysis, in situ and post-pyrolysis derivatization, reaction pyrolysis and catalytic cracking.     

Unusual odd-electron fragments from even-electron protonated prodiginine precursors using positive-ion electrospray tandem mass spectrometry

Reports of anticancer and immunosuppressive properties have spurred recent interest in the bacterially produced prodiginines. We use electrospray tandem mass spectrometry (ES-MS/MS) to investigate prodigiosin, undecylprodiginine, and streptorubin B (butyl-meta-cycloheptylprodiginine) and to explore their fragmentation pathways to explain the unusual methyl radical loss and consecutive fragment ions that dominate low-energy collision-induced dissociation (CID) mass spectra. The competition between the formation of even-electron ions and radical ions is examined in detail. Theoretical calculations are used to optimize the structures and calculate the energies of both reactants and products using the Gaussian 03 program. Results indicate that protonation occurs on the nitrogen atom that initially held no hydrogen, thus allowing formation of a pseudo-seven-membered ring that constitutes the most stable ground state [M + H](+) structure. From this precursor, experimental data show that methyl radical loss has the lowest apparent threshold but, alternatively, even-electron fragment ions can be formed by loss of a methanol molecule. Computational modeling indicates that methyl radical loss is the more endothermic process in this competition, but the lower apparent threshold associated with methyl radical loss points to a lower kinetic barrier. Additionally, this characteristic and unusual loss of methyl radical (in combination with weaker methanol loss) from each prodiginine is useful for performing constant neutral loss scans to quickly and efficiently identify all prodiginines in a complex biological mixture without any clean-up or purification. The feasibility of this approach has been proven through the identification of a new, low-abundance prodigiosin analog arising from Hahella chejuensis.     

Temperature program optimization by computer simulation for the capillary GC analysis of fatty acid methyl esters on biscyanopropyl siloxane phases

The selectivity of capillary columns coated with biscyanopropyl siloxane stationary phases for the separation of fatty acid methyl esters has been optimized by means of computer-assisted column temperature optimization software. Temperature programming rates yielding the highest resolution in the shortest analysis time were selected for split, splitless, and on-column injection operated in the constant pressure and pressure programmed modes.     

A stability result using the matrix norm to bound the permanent

We prove a stability version of a general result that bounds the permanent of a matrix in terms of its operator norm. More specifically, suppose A is an n × n matrix over C (resp. R), and let P denote the set of n × n matrices over C (resp. R) that can be written as a permutation matrix times a unitary diagonal matrix. Then it is known that the permanent of A satisfies |per(A)| ≤ ||A|| ⁿ ₂ with equality iff A/||A||₂ ∈ P (where ||A||₂ is the operator 2-norm of A). We show a stability version of this result asserting that unless A is very close (in a particular sense) to one of these extremal matrices, its permanent is exponentially smaller (as a function of n) than ||A|| ⁿ ₂. In particular, for any fixed α, β > 0, we show that |per(A)| is exponentially smaller than ||A|| ⁿ ₂ unless all but at most αn rows contain entries of modulus at least ||A||₂(1?β).