A new strategy for MS/MS data acquisition applying multiple data dependent experiments on Orbitrap mass spectrometers in non-targeted metabolomic applications
Abstract The annotation and identification of metabolites is a current bottleneck in non-targeted metabolomics studies. Although accurate measurement of m/z is applied routinely in UPLC–MS applications to putatively annotate metabolites, the acquisition of MS/MS or MS n data is required to deduce structural information, further reducing the chemical search-space and providing greater confidence in metabolite annotation by comparison to mass spectral databases. Here we propose an innovative new strategy for data dependent acquisition (DDA) for on-line MS/MS data acquisition in parallel t...
Source: Metabolomics - December 19, 2014 Category: Biology Source Type: research

I spy with my little eye something beginning with … ‘H’
(Source: Metabolomics)
Source: Metabolomics - December 18, 2014 Category: Biology Source Type: research

KLK1 and ZG16B proteins and arginine–proline metabolism identified as novel targets to monitor atherosclerosis, acute coronary syndrome and recovery
In conclusion, two novel urinary panels of proteins and metabolites are here for the first time shown related to atherosclerosis, ACS and patient’s recovery. (Source: Metabolomics)
Source: Metabolomics - December 14, 2014 Category: Biology Source Type: research

An interactive cluster heat map to visualize and explore multidimensional metabolomic data
Abstract Heat maps are a commonly used visualization tool for metabolomic data where the relative abundance of ions detected in each sample is represented with color intensity. A limitation of applying heat maps to global metabolomic data, however, is the large number of ions that have to be displayed and the lack of information provided about important metabolomic parameters such as m/z and retention time. Here we address these challenges by introducing the interactive cluster heat map in the data-processing software XCMS Online. XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed t...
Source: Metabolomics - December 12, 2014 Category: Biology Source Type: research

Are ant feces nutrients for plants? A metabolomics approach to elucidate the nutritional effects on plants hosting weaver ants
Abstract Weaver ants (genus Oecophylla) are tropical carnivorous ant species living in high numbers in the canopies of trees. The ants excrete copious amounts of fecal matter on leaf surfaces, and these feces may provide nutrients to host trees. This hypothesis is supported by studies of ant-plant interactions involving other ant species that have demonstrated the transfer of nutrients from ants to plants. In this 7-months study, a GC–MS-based metabolomics approach along with an analysis of total nitrogen and carbon levels was used to study metabolic changes in ant-hosting Coffea arabica plants compared with...
Source: Metabolomics - December 9, 2014 Category: Biology Source Type: research

Comprehensive analysis of alterations in lipid and bile acid metabolism by carbon tetrachloride using integrated transcriptomics and metabolomics
Abstract Understanding mechanisms of liver injury can enable better preclinical testing and clinical management of patients. Carbon tetrachloride (CCl4), used extensively as a model hepatotoxicant, induces lipid perturbation and increases in plasma bile acids (BAs). An integrated transcriptomics and metabolomics approach was employed to investigate CCl4-induced alterations in lipid and BA metabolism. Sprague–Dawley rats were treated orally with corn oil, 50 (low dose, LD) or 2,000 mg CCl4/kg/d (high dose, HD). Animals were sacrificed at 6, 24 or 72 h. Terminal blood was collected for clinical chem...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Population-based nutrikinetic modeling of polyphenol exposure
Abstract The beneficial health effects of fruits and vegetables have been attributed to their polyphenol content. These compounds undergo many bioconversions in the body. Modeling polyphenol exposure of humans upon intake is a prerequisite for understanding the modulating effect of the food matrix and the colonic microbiome. This modeling is not a trivial task and requires a careful integration of measuring techniques, modeling methods and experimental design. Moreover, both at the population level as well as the individual level polyphenol exposure has to be quantified and assessed. We developed a strategy to qu...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

A simultaneous extraction method for metabolome and lipidome and its application in cry1Ac and sck -transgenic rice leaf treated with insecticide based on LC–MS analysis
Abstract Abiotic stress caused by insecticide treatment is an interesting and challenging topic in plant research. Here a simultaneous extraction method with methyl tert-butyl ether for metabolomics and lipidomics analysis by using rapid resolution liquid chromatography quadrupole time-of-flight mass spectrometry was developed and validated. The extraction efficiency of lipidome and metabolome based on the current developed method showed an obvious improvement compared with literatures. About 300 metabolites were identified in rice leaf. Method validation was performed and analytical properties including the line...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Cross-platform comparative analyses of genetic variation in amino acid content in potato tubers
In this study, we used a diploid potato mapping population to explore the genetic basis of amino acid content. Hereto, we compared the use of one non-targeted and two targeted analytical approaches for amino acid analysis, allowing the evaluation of the robustness of amino acid quantification and the number and strength of detected quantitative trait locis (QTLs) across the different analytical platforms. Assessment of the three methodologies revealed a comparable detection of amino acids using non-targeted and targeted approaches. QTL detection across the different analytical platforms was similar, although slight differe...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Distinguishing between the metabolome and xenobiotic exposome in environmental field samples analysed by direct-infusion mass spectrometry based metabolomics and lipidomics
Abstract Environmental metabolomics is increasingly used to investigate organismal responses to complex chemical mixtures, including waste water effluent (WWE). In parallel, increasingly sensitive analytical methods are being used in metabolomics studies, particularly mass spectrometry. This introduces a considerable, yet overlooked, challenge that high analytical sensitivity will not only improve the detection of endogenous metabolites in biological specimens but also exogenous chemicals. If these often unknown xenobiotic features are not removed from the “biological” dataset, they will bias the ...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Metabolite profiling of polar steroid constituents in the Far Eastern starfish Aphelasterias japonica using LC–ESI MS/MS
Abstract Numerous polar steroids are characteristic metabolites of starfish which determine physiological activities of their extracts. The Far Eastern starfish Aphelasterias japonica is a rich source of different steroid glycosides and polyhydroxysteroids. For detailed analysis of complicated mixture of steroids from this species, isolated by solid-phase extraction, a liquid chromatography–electrospray tandem mass spectrometry (LC–ESI MS/MS) approach was selected and applied. The characteristic fragmentations in ESI MS/MS spectra of steroid glycosides allowed determining types of aglycones, presence ...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Metabolomic profiling of bronchoalveolar lavage fluids by isotope labeling liquid chromatography mass spectrometry: a promising approach to studying experimental asthma
Abstract Metabolomic analysis of bronchoalveolar lavage fluid (BALF) may help understand the pathophysiology of pulmonary diseases such as asthma. However, a major analytical challenge is that most metabolites in BALF are in low abundance and further diluted by the collection procedure. Here we report a sensitive metabolomic profiling method based on 12C-/13C-differential isotope dansylation that targets amine- and phenol-containing metabolites, solid phase extraction for analyte enrichment, and liquid chromatography Fourier transform ion cyclotron resonance-mass spectrometry (LC–FTICR-MS). This method dete...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Development of an NMR metabolomics-based tool for selection of flaxseed varieties
Abstract Flaxseed is an important source of lignans and ω-3 fatty acids, compounds which present interest in human health with many applications in food industry. It is therefore necessary to precisely know the metabolite content in flaxseed. A metabolomic approach using NMR was developed to achieve this goal. Due to particular characteristics of flaxseed (high level in oil, high amount in mucilage, and integration of the phenolics into a macromolecule), the extraction procedure had first to be optimized using an experimental design, based on the extraction time, in a water bath or an ultrasound bath, alkal...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Effect of cheese and butter intake on metabolites in urine using an untargeted metabolomics approach
Abstract Cheese intake has been shown to decrease total cholesterol and LDL cholesterol concentrations when compared to butter of equal fat content. An untargeted metabolite profiling may reveal exposure markers of cheese but may also contribute with markers which can help explain how the intake of cheese affects cholesterol concentrations. Twenty-three subjects collected 2 × 24 h urine samples after 6 weeks of cheese and 6 weeks of butter intake with equal amounts of fat in a cross-over intervention study. The samples were analyzed by UPLC-QTOF/MS. A two-step univariate data analy...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

A non-targeted metabolomics approach to evaluate the effects of biomass growth and chitosan elicitation on primary and secondary metabolism of Hypericum perforatum in vitro roots
Abstract Hypericum perforatum L. is a medicinal plant commonly used worldwide for the treatment of mild and moderate depression due to its wide range of bioactive compounds. H. perforatum regenerated roots have been proposed as an efficacious in vitro system to biosynthesize pharmaceutically useful secondary metabolites. In the present study, a metabolomic platform, which integrates an nuclear magnetic resonance (NMR)-based metabolic profiling and analysis of variance-simultaneous component analysis (ASCA), has been applied in order to characterize the changes of the primary and secondary metabolism o...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Investigating sources of variability in metabolomic data in the EPIC study: the Principal Component Partial R -square (PC-PR2) method
Abstract The key goal of metabolomic studies is to identify relevant individual biomarkers or composite metabolic patterns associated with particular disease status or patho-physiological conditions. There are currently very few approaches to evaluate the variability of metabolomic data in terms of characteristics of individuals or aspects pertaining to technical processing. To address this issue, a method was developed to identify and quantify the contribution of relevant sources of variation in metabolomic data prior to investigation of etiological hypotheses. The Principal Component Partial R-square (PC-PR2) m...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Biomarkers in renal cell carcinoma: a metabolomics approach
Abstract Since Otto Warburg, many studies have explored the unique metabolic phenotype of cancer cells highlighting the value and applicability of metabolomics in the oncology field, particularly in the development of cancer biomarkers. With respect to renal cell carcinoma (RCC), a metabolomics approach would own a great potential since urinary system is intimately connected with urine and, this biofluid, offers some advantages allowing the development of an assay suitable for use in clinical practice. Moreover, the assessment of metabolic derangements characteristics of RCC might provide a complete health a...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

MetaboNexus: an interactive platform for integrated metabolomics analysis
Abstract MetaboNexus is an interactive metabolomics data analysis platform that integrates pre-processing of raw peak data with in-depth statistical analysis and metabolite identity search. It is designed to work as a desktop application hence uploading large files to web servers is not required. This could speed up the data analysis process because server queries or queues are avoided, while ensuring security of confidential clinical data on a local computer. With MetaboNexus, users can progressively start from data pre-processing, multi- and univariate analysis to metabolite identity search of significant mole...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

The year in review: highlights of the Metabolomics Society in 2014
(Source: Metabolomics)
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Application of support vector machines to metabolomics experiments with limited replicates
Abstract Identifying biomarkers that are indicative of a phenotypic state is difficult because of the amount of natural variability which exists in any population. While there are many different algorithms to select biomarkers, previous investigation shows the sensitivity and flexibility of support vector machines (SVM) make them an attractive candidate. Here we evaluate the ability of support vector machine recursive feature elimination (SVM-RFE) to identify potential metabolic biomarkers in liquid chromatography mass spectrometry untargeted metabolite datasets. Two separate experiments are considered, a low var...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

De novo synthesize of bile acids in pulmonary arterial hypertension lung
Abstract Although multiple, complex molecular studies have been done for understanding the development and progression of pulmonary hypertension (PAH), little is known about the metabolic heterogeneity of PAH. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we found bile acid metabolites, which are normally product derivatives of the liver and gallbladder, were highly increased in the PAH lung. Microarray showed that the gene encoding cytochrome P450 7B1 (CYP7B1), an isozyme for bile acid synthesis, was highly expressed in the PAH lung compared with the control. CYP7B...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Metabolic profiling by ultra-performance liquid chromatography-mass spectrometry and parallel factor analysis for the determination of disease biomarkers in Eucalyptus
Abstract In this article, we present and discuss an alternative for data analysis of the metabolic profiles of both healthy Eucalyptus globulus and those infected with the Mycosphaerella leaf disease. The crude extracts were analyzed by reversed-phase ultra performance liquid chromatography-mass spectrometry. In order to glean the most useful information from these complex measurements, parallel factor analysis (PARAFAC) was employed for pattern recognition. After PARAFAC modeling, inspection of the scores and loadings graph allowed distinction of the healthy from the infected E. globulus samples and determin...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

High-throughput, multi-platform metabolomics on very small volumes: 1 H NMR metabolite identification in an unadulterated tube-in-tube system
Abstract As small animal models of disease become more widely used, there is increasing importance and potential for characterizing their metabolomes. However, as the animal becomes smaller, the amounts of biofluids such as urine and cerebral spinal fluid available for metabolomic studies are more limited. Further, in multi-platform systems biology when the same small sample must be used for several analyses, it is a frequent requirement that no additions are made to the sample (even as simple as D2O or an NMR chemical shift reference) to maintain sample integrity. Herein we describe a method for high-throughput ...
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Proposed quantitative and alphanumeric metabolite identification metrics
(Source: Metabolomics)
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research

Metabolomics Society Board election 2014: introduction of the new officers and directors
(Source: Metabolomics)
Source: Metabolomics - November 16, 2014 Category: Biology Source Type: research