Statistical methods for comparing comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry results: Metabolomic analysis of mouse tissue extracts

Shellie, Robert A.; Welthagen, Werner; Zrostlı́ková, Jitka; Spranger, Joachim; Ristow, Michael; Fiehn, Oliver; Zimmermann, Ralf

doi:10.1016/j.chroma.2005.05.088

Cited by 136 publications

(96 citation statements)

References 19 publications

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“…This procedure reduced the size of the output tables presenting the same numbers of peaks and enriched in OS-specific volatiles. These peak matrices, as already documented by several authors (Shellie et al, 2005;Hagan et al, 2007;Kusano et al, 2007;Tu et al, 2007), were suitable for univariate and multivariate statistical analyses (Figs. 3-7), after correction for false positives resulting from the alignment procedure.…”

Section: Nontargeted Functional Analysis Of Gcxgc-tofms Datamentioning

confidence: 70%

“…As discussed previously by Shellie et al (2005), the comparison feature embedded in the LECO ChromaToF software helped in aligning the different peak lists. This required the comparison of each individual chromatogram with a unique reference matrix in order to obtain output tables with the same numbers of peaks.…”

Section: A Stepwise Preprocessing Of Volatile Blendsmentioning

confidence: 99%

“…These qualities were exemplified by the 5-to 10-fold increase in the signal-to-noise ratio of a series of commonly emitted volatiles that we compared with the results from one-dimensional analyses performed with the same instrument (data not shown). The approach was found to be reliable and accurate for the automated processing of a large number of samples using parameters based on the recommendations described by Shellie et al (2005) and preliminary analyses performed with standard compounds (Fig. 2; Supplemental Table S2).…”

Section: Nontargeted Functional Analysis Of Gcxgc-tofms Datamentioning

confidence: 99%

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Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphigidae) and Its Natural Host Nicotiana attenuata. VIII. An Unbiased GCxGC-ToFMS Analysis of the Plant's Elicited Volatile Emissions

2009

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Treating wounds in Nicotiana attenuata leaves with Manduca sexta oral secretions (W1OS) mimics most changes elicited by M. sexta herbivory, but an unbiased analysis of the effect of the different OS constituents on volatile emissions is lacking. We used two-dimensional gas chromatography/time-of-flight (GCxGC-ToF) mass spectrometry combined with multivariate statistics to parse volatiles into regulatory patterns. Volatiles released by wounding alone and by the alkalinity of OS were assessed by applying a buffer known to mimic the pH-mediated changes of OS elicitation (pectin methyl esterase activation and methanol release). The activities of fatty acid amino acid conjugates, well-known elicitors of antiherbivore defenses, and of 2-hydroxyoctadecatrienoic acid, a newly discovered signal in OS, were determined. Approximately 400 analytes were detected after deconvolution and alignment of GCxGC data; 35 volatiles were significantly regulated upon W1OS. Two-thirds of these were specifically regulated by OS, being either amplified (most terpenoids and certain hexenylesters) or strongly repressed (many short-chain alcohols and some aromatic and hexenylester derivatives). Fatty acid amino acid conjugates played a central role in this pattern of regulation, since they induced the emission of half of OS-elicited volatiles and inhibited the production of almost all OS-repressed volatiles; 2-hydroxyoctadecatrienoic acid influenced emission of trans-a-bergamotene, while other unknown OS constituents amplified hexenylester production. We conclude that the complex bouquet of herbivory-elicited volatiles results from the complex modulations of the wound response by diverse cues found in OS. This work also underscores the value of ultra-high-resolution GCxGC-ToF analysis combined with the nontargeted mining of the resulting data.

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Section: Nontargeted Functional Analysis Of Gcxgc-tofms Datamentioning

confidence: 70%

Section: A Stepwise Preprocessing Of Volatile Blendsmentioning

confidence: 99%

Section: Nontargeted Functional Analysis Of Gcxgc-tofms Datamentioning

confidence: 99%

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Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphigidae) and Its Natural Host Nicotiana attenuata. VIII. An Unbiased GCxGC-ToFMS Analysis of the Plant's Elicited Volatile Emissions

2009

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“…Around 25% of all injections were done for quality control; however, the error rate for the extraction technique used here is unknown because the quantity of tissue biopsies was not large enough to do in-depth validation studies of the extraction technique. Nevertheless, this extraction technique was successfully used before for mouse tissues (38). Method error rates for mouse and plant tissues as well as blood plasma were found in the range of 5% to 25% relative SD, depending on the chemical structure of the metabolites.…”

Section: Discussionmentioning

confidence: 99%

Mass Spectrometry–Based Metabolic Profiling Reveals Different Metabolite Patterns in Invasive Ovarian Carcinomas and Ovarian Borderline Tumors

et al. 2006

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Metabolites are the end products of cellular regulatory processes, and their levels can be regarded as the ultimate response of biological systems to genetic or environmental changes. We have used a metabolite profiling approach to test the hypothesis that quantitative signatures of primary metabolites can be used to characterize molecular changes in ovarian tumor tissues. Sixty-six invasive ovarian carcinomas and nine borderline tumors of the ovary were analyzed by gas chromatography/time-of-flight mass spectrometry (GC-TOF MS) using a novel contamination-free injector system. After automated mass spectral deconvolution, 291 metabolites were detected, of which 114 (39.1%) were annotated as known compounds. By t test statistics with P < 0.01, 51 metabolites were significantly different between borderline tumors and carcinomas, with a false discovery rate of 7.8%, estimated with repeated permutation analysis. Principal component analysis (PCA) revealed four principal components that were significantly different between both groups, with the highest significance found for the second component (P = 0.00000009). PCA as well as additional supervised predictive models allowed a separation of 88% of the borderline tumors from the carcinomas. Our study shows for the first time that large-scale metabolic profiling using GC-TOF MS is suitable for analysis of fresh frozen human tumor samples, and that there is a consistent and significant change in primary metabolism of ovarian tumors, which can be detected using multivariate statistical approaches. We conclude that metabolomics is a promising high-throughput, automated approach in addition to functional genomics and proteomics for analyses of molecular changes in malignant tumors. (Cancer Res 2006; 66(22): 10795-804)

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“…In the 2004-2005 period, there was a significant interest towards the analysis of metabolites by using GC Â GC-ToF-MS (Sinha et al, 2004b,c;Hope et al, 2005b;Shellie et al, 2005;Welthagen et al, 2005). The analytical method appeared to be particularly suited, because the determination of volatile metabolites in a specific biological situation is a large task.…”

Section: Gradual Expansion: 2004-2006mentioning

confidence: 99%

Comprehensive two‐dimensional gas chromatography‐mass spectrometry: A review

Mondello

Tranchida

Dugo

et al. 2008

Mass Spectrometry Reviews

379

216

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Although comprehensive two-dimensional gas chromatography (GC Â GC) has been on the scene for more than 15 years, it is still generally considered a relatively novel technique and is yet far from being fully established. The revolutionary aspect of GC Â GC, with respect to classical multidimensional chromatography, is that the entire sample is subjected to two distinct analytical separations. The resulting enhanced separating capacity makes this approach a prime choice when GC analysts are challenged with highly complex mixtures. The combination of a third mass spectrometric dimension to a GC Â GC system generates the most powerful analytical tool today for volatile and semi-volatile analytes. The present review is focused on the rather brief, but not scant, history of comprehensive two-dimensional GC-MS: the first experiments were carried out at the end of the 1990s and, since then, the methodology has been increasingly studied and applied. Almost all GC Â GC-MS applications have been carried out by using either a time-of-flight or quadrupole mass analyzer; significant experiments relative to a variety of research fields, as well as advantages and disadvantages of the MS systems employed, are discussed. The principles, practical and theoretical aspects, and the most significant developments of GC Â GC are also described. #

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Statistical methods for comparing comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry results: Metabolomic analysis of mouse tissue extracts

Cited by 136 publications

References 19 publications

Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphigidae) and Its Natural Host Nicotiana attenuata. VIII. An Unbiased GCxGC-ToFMS Analysis of the Plant's Elicited Volatile Emissions

Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphigidae) and Its Natural Host Nicotiana attenuata. VIII. An Unbiased GCxGC-ToFMS Analysis of the Plant's Elicited Volatile Emissions

Mass Spectrometry–Based Metabolic Profiling Reveals Different Metabolite Patterns in Invasive Ovarian Carcinomas and Ovarian Borderline Tumors

Comprehensive two‐dimensional gas chromatography‐mass spectrometry: A review

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