Use of ultra-performance liquid chromatography/time-of-flight mass spectrometry with nozzle-skimmer fragmentation for comprehensive quantitative analysis of secondary metabolites in Arabidopsis thaliana.

This study sought to develop techniques for LC/MS-based metabolomics and to verify that an MS/MS spectral tag (MS2T) could be used in practical secondary metabolite profiling. The retention time (RT), precursor ions, and fragment ions generated by nozzle-skimmer fragmentation were determined using ultra-performance liquid chromatography/time-of-flight mass spectrometry (UPLC/TOF-MS) and compared with the MS2T. A standard mix was analyzed with UPLC/TOF-MS under the same conditions as were used to construct the MS2T.

Application of supercritical fluid chromatography/mass spectrometry to lipid profiling of soybean.

A metabolomics technology for lipid profiling based on supercritical fluid chromatography (SFC) coupled with mass spectrometry (MS) was applied to analyze lipids of soybean. Principal component analysis (PCA) was used to discriminate twelve soybean cultivars according to their suitability for different processed foods such as natto, tofu, edamame, and nimame. By PCA assay, triacylglycerol (TAG) was found as the main variable for discrimination of soybean cultivars.

Metabolic profiling of β-cryptoxanthin and its fatty acid esters by supercritical fluid chromatography coupled with triple quadrupole mass spectrometry.

In this study, a high-throughput and high-sensitivity profiling system for β-cryptoxanthin (βCX) and β-cryptoxanthin fatty acid ester (βCXFA) was constructed by supercritical fluid chromatography (SFC) coupled with triple quadrupole mass spectrometry (QqQMS). βCX and nine βCXFAs were successfully separated within 20 min using a column packed with octadecylsilyl-bonded silica particles. The limit of detection was 540 fmol for the free form and 32-130 fmol for the esterified forms.

Serum metabolomics as a novel diagnostic approach for gastrointestinal cancer.

Conventional tumor markers are unsuitable for detecting carcinoma at an early stage and lack clinical efficacy and utility. In this study, we attempted to investigate the differences in serum metabolite profiles of gastrointestinal cancers and healthy volunteers using a metabolomic approach and searched for sensitive and specific metabolomic biomarker candidates. Human serum samples were obtained esophageal (n = 15), gastric (n = 11), and colorectal (n = 12) cancer patients and healthy volunteers (n = 12).

Systems biology in a commercial quality study of the Japanese Angelica radix: toward an understanding of traditional medicinal plants.

The commercial quality of Japanese Angelica radices -- Angelica acutiloba Kitagawa (Yamato-toki) and A. acutiloba Kitagawa var. sugiyama Hikino (Hokkai-toki) -- used in Kampo traditional herbal medicines, was studied by use of omics technologies.

Predication of Japanese green tea (Sen-cha) ranking by volatile profiling using gas chromatography mass spectrometry and multivariate analysis.

The sensory quality ranking of Japanese green tea (Sen-cha) was evaluated and predicted using volatile profiling and multivariate data analyses. The volatile constituents were extracted from tea infusion using vacuum hydrodistillation and analyzed using GC/MS. A quality of green tea could be discriminated to a high or low grade regarding the volatile profile by partial least squares discriminant analysis (PLS-DA).

Influences of methamphetamine-induced acute intoxication on urinary and plasma metabolic profiles in the rat.

Methamphetamine (MA) is an illicit psychostimulant, and its abuse has become an international public health problem. MA intoxication can cause life-threatening hyperthermia, renal and liver failure, cardiac arrhythmias, and neurological damage. To investigate the relationship between the underlying mechanism of such intoxication and metabolic networks, mass spectrometry-based metabolomics experiments were performed on Sprague-Dawley rats treated with MA at 10mgkg(-1)h(-1) for 4h.

Practical non-targeted gas chromatography/mass spectrometry-based metabolomics platform for metabolic phenotype analysis.

Gas chromatography coupled to mass spectrometry (GC/MS) is a core analytical method for metabolomics and has been used as a platform in non-targeted analysis, especially for hydrophilic metabolites. Non-targeted GC/MS-based metabolomics generally requires a high-throughput technology to handle a large volume of samples and an accumulated database (reference library) of the retention times and mass spectra of standard compounds for accurate peak identification. In this study, we provide a practical GC/MS platform and an auto peak identification technique that is not restricted to certain types of mass spectrometers.

Application of Fourier transform near-infrared spectroscopy to optimization of green tea steaming process conditions.

In this study, we constructed prediction models by metabolic fingerprinting of fresh green tea leaves using Fourier transform near-infrared (FT-NIR) spectroscopy and partial least squares (PLS) regression analysis to objectively optimize of the steaming process conditions in green tea manufacture. The steaming process is the most important step for manufacturing high quality green tea products. However, the parameter setting of the steamer is currently determined subjectively by the manufacturer.

Single-embryo metabolomics and systematic prediction of developmental stage in zebrafish.

Metabolites, the end products of gene expression in living organisms, are tightly correlated with an organism's development and growth. Thus, metabolic profiling is a potentially important tool for understanding the events that have occurred in cells, tissues, and individual organisms. Here, we present a method for predicting the developmental stage of zebrafish embryos using novel metabolomic non-target fingerprints of "single-embryos".

GC/MS based metabolomics: development of a data mining system for metabolite identification by using soft independent modeling of class analogy (SIMCA).

Background: The goal of metabolomics analyses is a comprehensive and systematic understanding of all metabolites in biological samples. Many useful platforms have been developed to achieve this goal. Gas chromatography coupled to mass spectrometry (GC/MS) is a well-established analytical method in metabolomics study, and 200 to 500 peaks are routinely observed with one biological sample.

A metabolomic approach to lung cancer.

Lung cancer is one of the most common cancers in the world, but no good clinical markers that can be used to diagnose the disease at an early stage and predict its prognosis have been found. Therefore, the discovery of novel clinical markers is required. In this study, metabolomic analysis of lung cancer patients was performed using gas chromatography mass spectrometry.

GABA metabolism pathway genes, UGA1 and GAD1, regulate replicative lifespan in Saccharomyces cerevisiae.

Many of the genes involved in aging have been identified in organisms ranging from yeast to human. Our previous study showed that deletion of the UGA3 gene-which encodes a zinc-finger transcription factor necessary for γ-aminobutyric acid (GABA)-dependent induction of the UGA1 (GABA aminotransferase), UGA2 (succinate semialdehyde dehydrogenase), and UGA4 (GABA permease) genes-extends replicative lifespan in the budding yeast Saccharomyces cerevisiae. Here, we found that deletion of UGA1 lengthened the lifespan, as did deletion of UGA3; in contrast, strains with UGA2 or UGA4 deletions exhibited no lifespan extension.

Sphingosine kinases and their metabolites modulate endolysosomal trafficking in photoreceptors.

Internalized membrane proteins are either transported to late endosomes and lysosomes for degradation or recycled to the plasma membrane. Although proteins involved in trafficking and sorting have been well studied, far less is known about the lipid molecules that regulate the intracellular trafficking of membrane proteins. We studied the function of sphingosine kinases and their metabolites in endosomal trafficking using Drosophila melanogaster photoreceptors as a model system.

Fluorescence-monitored zero dead-volume nanoLC-microESI-QIT-TOF MS for analysis of fluorescently tagged glycosphingolipids.

An analysis of the glycan processing event is of particular importance to understand the nontemplate dependent synthetic mechanism of the multiple glycosylation reactions taking place in the Golgi apparatus in connection with the post-translational modification of biomolecules. In our efforts to address the issue, we constructed an analysis platform using nano-liquid chromatography (LC), which also worked as a spray tip, with an optical-fiber-based blue (470 nm) light emitting diode (LED)-induced fluorescence (520 nm) detector coupled with a microelectrospray ionization (ESI)-quadrupole ion trap (QIT)-time of flight (TOF) mass spectrometer (MS). This system was designed to enable both quantitative and qualitative analyses of fluorescently tagged molecules such as BODIPY-tagged lactosylceramide.

GC-MS-based metabolomics reveals mechanism of action for hydrazine induced hepatotoxicity in rats.

Gas chromatography-mass spectrometry (GC-MS) has great advantages for analyzing organic/amino acids, which are often targets in efficacy and/or toxicity studies. Although GC-MS has been used for the detection of many metabolic disorders, applications of GC-MS-based metabolomics in pharmacology/toxicology are relatively underdeveloped. We intended to investigate applicability of a GC-MS-based metabolomics approach for toxicological evaluation, and tried to elucidate the mechanism of hydrazine-induced hepatotoxicity.

CDase is a pan-ceramidase in Drosophila.

Ceramidases catalyze the conversion of ceramide to sphingosine. They are acylaminohydrolases that catalyze the deacylation of the amide-linked saturated fatty acid from ceramide to generate sphingosine. They also catalyze the reverse reaction of ceramide biosynthesis using sphingosine and fatty acid.

Metabolite analysis by supercritical fluid chromatography.

Owing to its favorable properties, such as low viscosity and high diffusivity, a supercritical fluid can be used as the mobile phase in chromatography. Supercritical fluid chromatography (SFC) can provide high-speed and high-resolution separation. Since supercritical carbon dioxide (SCCO(2)), which is generally used as the mobile phase in SFC, is automatically emitted at room temperature, SFC is most commonly used as a preparative method.

Contribution of mevalonate and methylerythritol phosphate pathways to polyisoprenoid biosynthesis in the rubber-producing plant Eucommia ulmoides oliver.

The biosynthetic origin of isopentenyl diphosphate in the polyisoprenoid biosynthesis of the rubber-producing plant Eucommia ulmoides Oliver was elucidated for the first time by feeding experiments using 13C-labeled isotopomers of (RS)-mevalonate, 1-deoxy-D-xylulose-3,4,5-triacetate, 2C-methyl-D-erythritol-1,2,3,4-tetraacetate, and pyruvate. After 13C-labeled isotopomers were fed to the young seedlings, the polyisoprenoid fractions were prepared and analyzed by 13C NMR. The NMR data showed that the isoprene units of polyisoprenoid derived from isopentenyl diphosphate, which was biosynthesized using both mevalonate and 1-deoxy-D-xylulose-5-phosphate in E.

Metabolomics-based systematic prediction of yeast lifespan and its application for semi-rational screening of ageing-related mutants.

Metabolomics - the comprehensive analysis of metabolites - was recently used to classify yeast mutants with no overt phenotype using raw data as metabolic fingerprints or footprints. In this study, we demonstrate the estimation of a complicated phenotype, longevity, and semi-rational screening for relevant mutants using metabolic profiles as strain-specific fingerprints. The fingerprints used in our experiments are profiled data consisting of individually identified and quantified metabolites rather than raw spectrum data.

Influences of biofluid sample collection and handling procedures on GC-MS based metabolomic studies.

Sample collection procedures of pharmacology and toxicology studies might have a great impact on interpretation of metabolomic study results. Characterization of range variation among sample collection methods is necessary to prevent misinterpretation, as is use of optimal methods in animal experiments to minimize biological/technical variation. Here, we investigated the influence of urine and plasma sample collection and handling procedures on GC-MS based metabolomic studies as follows: for urine, pooling period and tube conditions during collection; for plasma, sampling sites, anesthesia and anticoagulants.

AtNUDX6, an ADP-ribose/NADH pyrophosphohydrolase in Arabidopsis, positively regulates NPR1-dependent salicylic acid signaling.

Here, we investigated the physiological role of Arabidopsis (Arabidopsis thaliana) AtNUDX6, the gene encoding ADP-ribose (Rib)/NADH pyrophosphohydrolase, using its overexpressor (Pro35S:AtNUDX6) or disruptant (KO-nudx6). The level of NADH in Pro35S:AtNUDX6 and KO-nudx6 plants was decreased and increased, respectively, compared with that of the control plants, while the level of ADP-Rib was not changed in either plant. The activity of pyrophosphohydrolase toward NADH was enhanced and reduced in the Pro35S:AtNUDX6 and KO-nudx6 plants, respectively.

Pyrolysis GC-MS-based metabolite fingerprinting for quality evaluation of commercial Angelica acutiloba roots.

Metabolite fingerprinting was applied in the attempt to evaluate the quality of Angelica acutiloba dried roots (Yamato-toki). A pyrolyser coupled to a gas chromatography mass spectrometer (PY-GC-MS) was used to obtain higher chemical universality by analyzing whole compounds including high molecular weight metabolites. The machine was relatively fast and easy to use, with no sample preparation procedure required.

High-throughput and highly sensitive analysis method for polyisoprene in plants by pyrolysis-gas chromatography/mass spectrometry.

Natural polyisoprene is a biopolymer consisting of isoprene units (C(5)H(8)) that is used commercially in household, medical, and industrial materials. For the management of natural polyisoprene production, the selection of high-yield polyisoprene-producing trees, and an understanding of polyisoprene biosynthesis, a high-throughput and highly sensitive screening method for the quantification of polyisoprene is required. In this study, we examined pyrolysates from polyisoprenes, polyprenols, carotenoids, ubiquinone (CoQ-10), and sterols by pyrolysis gas chromatography/mass spectrometry (PyGC/MS) and determined that the amounts of isoprene and limonene released from polyprenols and polyisoprenes were dependent upon their molecular weights.

Metabolic turnover analysis by a combination of in vivo 13C-labelling from 13CO2 and metabolic profiling with CE-MS/MS reveals rate-limiting steps of the C3 photosynthetic pathway in Nicotiana tabacum leaves.

Understanding of the control of metabolic pathways in plants requires direct measurement of the metabolic turnover rate. Sugar phosphate metabolism, including the Calvin cycle, is the primary pathway in C(3) photosynthesis, the dynamic status of which has not been assessed quantitatively in the leaves of higher plants. Since the flux of photosynthetic carbon metabolism is affected by the CO(2) fixation rate in leaves, a novel in vivo (13)C-labelling system was developed with (13)CO(2) for the kinetic determination of metabolic turnover that was the time-course of the (13)C-labelling ratio in each metabolite.