Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics

The application of gas chromatography–mass spectrometry (GC–MS) to the ‘global’ analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project’s (METAbolomics for Plants Health and OutReach: http://www.meta-phor.eu/) priorities towards robust technology development, a GC–MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GC×GC–TOF/MS was compared with 1 dimensional GC–TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise

Micro-pyrolysis of technical lignins in a new modular rig and product analysis by GC-MS/FID and GC x GC-TOFMS/FID

A new offline-pyrolysis rig has been designed to allow multifunctional experiments for preparative and analytical purposes. The system conditions can be set and monitored, e.g. temperature, its gradients and heat flux. Some special features include ( I) high heating rates up to 120 degrees C/s with pyrolysis temperatures up to 850 degrees C at variable pyrolysis times and (2) the selection of different atmospheres during pyrolysis. A complete mass balance of products and reactants (gas, liquids and solids) by gravimetric methods and sequential chromatographic analyses was obtained. The pyrolytic behaviour and the decomposition products of lignin-related compounds were studied under different conditions: heating rates (from 2.6 degrees C/s up to 120 degrees C/s), pyrolysis temperatures at 500 degrees C and 800 degrees C in different atmospheres (N(2), H(2), and mixtures of N(2) and acetylene). Kraft lignin, soda lignin, organosolv lignin, pyrolytic lignin from pine bio-oil, residues from biomass hydrolysis and fermentation were studied. The obtained pyrolysis products were classified into three general groups: coke, liquid phase and gas phase (volatile organic compounds (VOC) and permanent gases). The liquid fraction was analysed by GCMS/FID. In addition, comprehensive two-dimensional CC was applied to further characterise the liquid fraction. VOCs were semi-quantified by a modified headspace technique using GC-MS/FID analysis. The micro-pyrolysis rig proved to be an efficient and useful device for complex pyrolysis applications. (C) 2008 Elsevier B.V. All rights reserved

Comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry for the forensic study of cadaveric volatile organic compounds released in soil by buried decaying pig carcasses

NoThis article reports on the use of comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC × GC–TOFMS) for forensic geotaphonomy application. Gravesoil samples were collected at various depths and analyzed for their volatile organic compound (VOC) profile. A data processing procedure was developed to highlight potential candidate marker molecules related to the decomposition process that could be isolated from the soil matrix. Some 20 specific compounds were specifically found in the soil sample taken below the carcass and 34 other compounds were found at all depths of the gravesoil samples. The group of the 20 compounds consisted of ketones, nitriles, sulfurs, heterocyclic compounds, and benzene derivatives like aldehydes, alcohols, ketones, ethers and nitriles. The group of the 34 compounds consisted of methyl-branched alkane isomers including methyl-, dimethyl-, trimethyl-, tetramethyl-, and heptamethyl-isomers ranging from C12 to C16. A trend in the relative presence of these alkanes over the various layers of soils was observed, with an increase in the amount of the specific alkanes when coming from the carcass to the surface. Based on the specific presence of these methyl-branched alkanes in gravesoils, we created a processing method that applies a specific script to search raw data for characteristic mass spectral features related to recognizable mass fragmentation pattern. Such screening of soil samples for cadaveric decomposition signature was successfully applied on two gravesoil sites and clearly differentiates soils at proximity of buried decaying pig carcasses from control soils

Continuous fraction collection of gas chromatographic separations with parallel mass spectrometric detection applied to cell-based bioactivity analysis

We describe the development and evaluation of a GC-MS fractionation platform that combines high-resolution fraction collection of full chromatograms with parallel MS detection. A y-split at the column divides the effluent towards the MS detector and towards an inverted y-piece where vaporized trap solvent is infused. The latter flow is directed outside the GC oven allowing subsequent condensation and stepwise collection of liquid fractions with trapped analytes on a 384-well plate. For study and optimization of the effluent split ratio, restriction capillaries of different lengths and diameters were evaluated. For a wide range of settings, local pressures were monitored during fractionation to assess the influence of MS vacuum and trap solvent infusion on the GC system stability. The platform performance was evaluated by GC-MS analysis and continuous fractionation of an n-alkane mixture followed by GC analysis of each fraction. Comparison of the on-line recorded and fraction-reconstructed chromatogram showed the GC separation is maintained during fractionation. Multiple fractionation cycles of the n-alkane sample on the same 384-well plate yielded a reconstructed chromatogram which was highly similar to that of a single analysis, demonstrating the high repeatability. The applicability of the GC-MS-fractionation platform for bioactivity screening was investigated by applying the AR-Ecoscreen reporter gene bioassay on fractions obtained after analysis of standard solutions and dust samples containing the anti-androgenic compounds vinclozolin and p,p’-DDE

Optimal endobronchial tool sizes for targeting lung lesions based on 3D modeling

Background For patients with suspicious lung lesions found on chest x-ray or CT, endo/trans- bronchial biopsy of the lung is the preferred method for obtaining a diagnosis. With the addition of new screening programs, a higher number of patients will require diagnostic biopsy which will prove even more challenging due to the small size of lesions found with screening. There are many endobronchial tools available on the market today and a wide range of new tools under investigation to improve diagnostic yield. However, there is little information available about the optimal tool size required to reach the majority of lesions, especially peripheral ones. In this manuscript we investigate the percentage of lesions that can be reached for various diameter tools if the tools remain inside the airways (i.e. endobronchial biopsy) and the distance a tool must travel “off-road” (or outside of the airways) to reach all lesions. Methods and findings To further understand the distribution of lung lesions with respect to airway sizes and distances from the airways, six 3D models of the lung were generated. The airways were modeled at two different respiratory phases (inspiration and expiration). Three sets of 1,000 lesions were randomly distributed throughout the lung for each respiratory phase. The simulations showed that the percentage of reachable lesions decreases with increasing tool diameter and decreasing lesion diameter. A 1mm diameter tool will reach <25% of 1cm lesions if it remains inside the airways. To reach all 1cm lesions this 1mm tool would have to navigate through the parenchyma up to 8.5mm. CT scans of 21 patient lesions confirm these results reasonably well. Conclusions The smaller the tool diameter the more likely it will be able to reach a lung lesion, whether it be for diagnostic biopsy, ablation, or resection. However, even a 1mm tool is not small enough to reach the majority of small (1-2cm) lesions. Therefore, it is necessary for endobronchial tools to be able to navigate through the parenchyma to reach the majority of lesions.Medical Instruments & Bio-Inspired Technolog

Distance a tool must travel off-road to reach a lesion in simulated model 1.

<p>The lines represent the average and standard deviations of the model. The black dots are the lesions measured from the CT scans.</p