139 results found
Rocca-Serra P, Salek RM, Arita M, et al., 2015, Data standards can boost metabolomics research, and if there is a will, there is a way, Metabolomics, Vol: 12, ISSN: 1573-3890
Thousands of articles using metabolomics approaches are published every year. With the increasing amounts of data being produced, mere description of investigations as text in manuscripts is not sufficient to enable re-use anymore: the underlying data needs to be published together with the findings in the literature to maximise the benefit from public and private expenditure and to take advantage of an enormous opportunity to improve scientific reproducibility in metabolomics and cognate disciplines. Reporting recommendations in metabolomics started to emerge about a decade ago and were mostly concerned with inventories of the information that had to be reported in the literature for consistency. In recent years, metabolomics data standards have developed extensively, to include the primary research data, derived results and the experimental description and importantly the metadata in a machine-readable way. This includes vendor independent data standards such as mzML for mass spectrometry and nmrML for NMR raw data that have both enabled the development of advanced data processing algorithms by the scientific community. Standards such as ISA-Tab cover essential metadata, including the experimental design, the applied protocols, association between samples, data files and the experimental factors for further statistical analysis. Altogether, they pave the way for both reproducible research and data reuse, including meta-analyses. Further incentives to prepare standards compliant data sets include new opportunities to publish data sets, but also require a little “arm twisting” in the author guidelines of scientific journals to submit the data sets to public repositories such as the NIH Metabolomics Workbench or MetaboLights at EMBL-EBI. In the present article, we look at standards for data sharing, investigate their impact in metabolomics and give suggestions to improve their adoption.
Roessner U, Ebbels T, 2015, One minute with the Metabolomics Society's Honorary Fellows 2015, METABOLOMICS, Vol: 11, Pages: 779-781, ISSN: 1573-3882
Salek RM, Arita M, Dayalan S, et al., 2015, Embedding standards in metabolomics: the Metabolomics Society data standards task group, METABOLOMICS, Vol: 11, Pages: 782-783, ISSN: 1573-3882
Salek RM, Neumann S, Schober D, et al., 2015, Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access, Metabolomics, Vol: 11, Pages: 1587-1597, ISSN: 1573-3882
Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.
Hendrickx DM, Aerts HJWL, Caiment F, et al., 2015, diXa: a data infrastructure for chemical safety assessment, BIOINFORMATICS, Vol: 31, Pages: 1505-1507, ISSN: 1367-4803
Roessner U, Bearden DW, Ebbels T, 2015, The international Metabolomics Society in 2015: the path forward to success, METABOLOMICS, Vol: 11, Pages: 1-2, ISSN: 1573-3882
Pomyen Y, Segura M, Ebbels TMD, et al., 2015, Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets, BIOINFORMATICS, Vol: 31, Pages: 102-108, ISSN: 1367-4803
Liebeke M, Bruford MW, Donnelly RK, et al., 2014, Identifying biochemical phenotypic differences between cryptic species., Biology Letters, Vol: 10, ISSN: 1744-9561
Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.
Ipsen A, Ebbels TMD, 2014, Orders of Magnitude Extension of the Effective Dynamic Range of TDC-Based TOFMS Data Through Maximum Likelihood Estimation, Journal of the American Society for Mass Spectrometry, Vol: 25, Pages: 1824-1827, ISSN: 1044-0305
In a recent article, we derived a probability distribution that was shown toclosely approximate that of the data produced by liquid chromatography time-of-flightmass spectrometry (LC/TOFMS) instruments employing time-to-digital converters(TDCs) as part of their detection system. The approach of formulating detailed andhighly accurate mathematical models of LC/MS data via probability distributions thatare parameterized by quantities of analytical interest does not appear to have beenfully explored before. However, we believe it could lead to a statistically rigorousframework for addressing many of the data analytical problems that arise in LC/MSstudies. In this article, we present new procedures for correcting for TDC saturationusing such an approach and demonstrate that there is potential for significantimprovements in the effective dynamic range of TDC-based mass spectrometers, which could make them muchmore competitive with the alternative analog-to-digital converters (ADCs). The degree of improvement dependson our ability to generate mass and chromatographic peaks that conform to known mathematical functions andour ability to accurately describe the state of the detector dead time—tasks that may be best addressed throughengineering efforts
Tzoulaki I, Ebbels TMD, Valdes A, et al., 2014, Design and Analysis of Metabolomics Studies in Epidemiologic Research: A Primer on -Omic Technologies, AMERICAN JOURNAL OF EPIDEMIOLOGY, Vol: 180, Pages: 129-139, ISSN: 0002-9262
Hao J, Liebeke M, Astle W, et al., 2014, Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN, NATURE PROTOCOLS, Vol: 9, Pages: 1416-1427, ISSN: 1754-2189
Milner JJ, Wang J, Sheridan PA, et al., 2014, H-1 NMR-Based Profiling Reveals Differential Immune-Metabolic Networks during Influenza Virus Infection in Obese Mice, PLOS ONE, Vol: 9, ISSN: 1932-6203
Valcarcel B, Ebbels TMD, Kangas AJ, et al., 2014, Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity, Journal of the Royal Society Interface, Vol: 11, ISSN: 1742-5689
Current studies of phenotype diversity by genome-wide association studies(GWAS) are mainly focused on identifying genetic variants that influencelevel changes of individual traits without considering additional alterations atthe system-level. However, in addition to level alterations of single phenotypes,differences in association between phenotype levels are observed across differentphysiological states. Such differences in molecular correlations betweenstates can potentially reveal information about the system state beyond thatreported by changes in mean levels alone. In this study, we describe a novelmethodological approach, which we refer to as genome metabolome integratednetwork analysis (GEMINi) consisting of a combination of correlation networkanalysis and genome-wide correlation study. The proposed methodologyexploits differences in molecular associations to uncover genetic variantsinvolved in phenotype variation. We test the performance of the GEMINiapproach in a simulation study and illustrate its use in the context of obesity anddetailed quantitative metabolomics data on systemic metabolism. Applicationof GEMINi revealed a set of metabolic associations which differ betweennormal and obese individuals. While no significant associations were foundbetween genetic variants and body mass index using a standard GWASapproach, further investigation of the identified differences in metabolic associationrevealed a number of loci, several of which have been previouslyimplicated with obesity-related processes. This study highlights the advantageof using molecular associations as an alternative phenotype when studying thegenetic basis of complex traits and diseases
Salamanca BV, Ebbels TMD, De Iorio M, 2014, Variance and covariance heterogeneity analysis for detection of metabolites associated with cadmium exposure, STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, Vol: 13, Pages: 191-201, ISSN: 2194-6302
Stamler J, Brown IJ, Yap IKS, et al., 2013, Dietary and Urinary Metabonomic Factors Possibly Accounting for Higher Blood Pressure of Black Compared With White Americans Results of International Collaborative Study on Macro-/Micronutrients and Blood Pressure, HYPERTENSION, Vol: 62, Pages: 1074-1080, ISSN: 0194-911X
Ebbels T, Dunn W, 2013, Report on the 9th Annual International Conference of the Metabolomics Society, METABOLOMICS, Vol: 9, Pages: 935-937, ISSN: 1573-3882
, 2013, The continuing growth and development of YOUR metabolomics society, Metabolomics, Vol: 9, Pages: 529-531, ISSN: 1573-3882
Liebeke M, Hao J, Ebbels TMD, et al., 2013, Combining Spectral Ordering with Peak Fitting for One-Dimensional NMR Quantitative Metabolomics, ANALYTICAL CHEMISTRY, Vol: 85, Pages: 4605-4612, ISSN: 0003-2700
Blazquez M, Carretero A, Ellis JK, et al., 2013, A Combination of Transcriptomics and Metabolomics Uncovers Enhanced Bile Acid Biosynthesis in HepG2 Cells Expressing CCAAT/Enhancer-Binding Protein β (C/EBPβ), Hepatocyte Nuclear Factor 4α (HNF4α), and Constitutive Androstane Receptor (CAR), Journal of proteome research, Pages: 130515154744008-130515154744008
Cantor GH, Beckonert O, Bollard ME, et al., 2013, Integrated Histopathological and Urinary Metabonomic Investigation of the Pathogenesis of Microcystin-LR Toxicosis, VETERINARY PATHOLOGY, Vol: 50, Pages: 159-171, ISSN: 0300-9858
Astle W, De Iorio M, Richardson S, et al., 2012, A Bayesian Model of NMR Spectra for the Deconvolution and Quantification of Metabolites in Complex Biological Mixtures, JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, Vol: 107, Pages: 1259-1271, ISSN: 0162-1459
Vinken M, Maes M, Cavill R, et al., 2012, Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures, Archives of Toxicology, Vol: 87, Pages: 883-894
Posma JM, Garcia-Perez I, De Iorio M, et al., 2012, Subset Optimization by Reference Matching (STORM): An optimized statistical approach for recovery of metabolic biomarker structural information from ¹H NMR spectra of biofluids, Analytical Chemistry, Vol: 84, Pages: 10694-10701, ISSN: 0003-2700
We describe a new multivariate statistical approach to recover metabolite structure information from multiple 1H NMR spectra in population sample sets. SubseT Optimization by Reference Matching (STORM) was developed to select subsets of 1H NMR spectra that contain specific spectroscopic signatures of biomarkers differentiating between different human populations. STORM aims to improve the visualization of structural correlations in spectroscopic data using these reduced spectral subsets containing smaller numbers of samples than the number of variables (n<<p). We have used ‘statistical shrinkage’ to limit the number of false positive associations and to simplify the overall interpretation of the auto-correlation matrix. The STORM approach has been applied to findings from an on-going human Metabolome-Wide Association study on Body Mass Index to identify a biomarker metabolite present in a subset of the population. Moreover, we have shown how STORM improves the visualization of more abundant NMR peaks compared to a previously published method (STOCSY). STORM is a useful new tool for biomarker discovery in the ‘omic’ sciences that has a widespread applicability. It can be applied to any type of data, provided that there is interpretable correlation among variables, and can also be applied to data with more than 1 dimension (e.g. 2D-NMR spectra).
Hao J, Astle W, De Iorio M, et al., 2012, BATMAN-an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model, BIOINFORMATICS, Vol: 28, Pages: 2088-2090, ISSN: 1367-4803
Hao J, Astle W, De Iorio M, et al., 2012, BATMAN - The Bayesian AuTomated Metabolite Analyser for NMR Spectra
Ipsen A, Ebbels TMD, 2012, Prospects for a Statistical Theory of LC/TOFMS Data, JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, Vol: 23, Pages: 779-791, ISSN: 1044-0305
Kamleh MA, Ebbels TMD, Spagou K, et al., 2012, Optimizing the Use of Quality Control Samples for Signal Drift Correction in Large-Scale Urine Metabolic Profiling Studies, ANALYTICAL CHEMISTRY, Vol: 84, Pages: 2670-2677, ISSN: 0003-2700
Benton HP, Want E, Keun HC, et al., 2012, Intra- and Interlaboratory Reproducibility of Ultra Performance Liquid Chromatography-Time-of-Flight Mass Spectrometry for Urinary Metabolic Profiling, ANALYTICAL CHEMISTRY, Vol: 84, Pages: 2424-2432, ISSN: 0003-2700
Cazier J-B, Kaisaki PJ, Argoud K, et al., 2012, Untargeted Metabolome Quantitative Trait Locus Mapping Associates Variation in Urine Glycerate to Mutant Glycerate Kinase, JOURNAL OF PROTEOME RESEARCH, Vol: 11, Pages: 631-642, ISSN: 1535-3893
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