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Metabolomics

Nowadays, gene discovery has been made very efficient with the combination of deep sequencing and the exploitation of natural variation. Just in Arabidopsis, hundreds of genetic loci have been identified as influencing a wide variety of processes, and we aim to go from gene-of-interest to characterized protein product using approaches to “take a picture” of the comprehensive metabolome of the plant.

The IPB is currently operating a wide range of NMR and mass spectrometry instruments for metabolomics across all four departments, which are integrated into our Metabolomics Platform.

The experimental work is complemented by extensive Cheminformatics and Bioinformatics research to process and interpret the huge amounts of data. The IPB is operating the first European MassBank server, and hosts several online tools for metabolite identification.

Contact partner for all interests concerning the metabolomics platform is Dr. Steffen Neumann.

Publications by Tag: Metabolomics

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Displaying results 1 to 10 of 25.

Publications

Moreno, P., Beisken, S., Harsha, B., Muthukrishnan, V., Tudose, I., Dekker, A., Dornfeldt, S., Taruttis, F., Grosse, I., Hastings, J., Neumann, S. & Steinbeck, C. BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology BMC Bioinformatics 16, 56, (2015) DOI: 10.1186/s12859-015-0486-3

Background: Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets

annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Results: We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.Conclusions: BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Publications

Brack, W., Altenburger, R., Schüürmann, G., Krauss, M., López Herráez, D., van Gils, J., Slobodnik, J., Munthe, J., Gawlik, B. M., van Wezel, A., Schriks, M., Hollender, J., Tollefsen, K. E., Mekenyan, O., Dimitrov, S., Bunke, D., Cousins, I., Posthuma, L., van den Brink, P. J., López de Alda, M., Barceló, D., Faust, M., Kortenkamp, A., Scrimshaw, M., Ignatova, S., Engelen, G., Massmann, G., Lemkine, G., Teodorovic, I., Walz, K.-H., Dulio, V., Jonker, M. T.O., Jäger, F., Chipman, K., Falciani, F., Liska, I., Rooke, D., Zhang, X., Hollert, H., Vrana, B., Hilscherova, K., Kramer, K., Neumann, S., Hammerbacher, R., Backhaus, T., Mack, J., Segner, H., Escher, B. & de Aragão Umbuzeiro, G. The SOLUTIONS project: Challenges and responses for present and future emerging pollutants in land and water resources management Science total Environ 503-504, 22-31, (2015) DOI: 10.1016/j.scitotenv.2014.05.143

SOLUTIONS (2013 to 2018) is a European Union Seventh Framework Programme Project (EU-FP7). The project aims to deliver a conceptual framework to support the evidence-based development of environmental policies with regard to water quality. SOLUTIONS will develop the tools for the identification, prioritisation and assessment of those water contaminants that may pose a risk to ecosystems and human health. To this end, a new generation of chemical and effect-based monitoring tools is developed and integrated with a full set of exposure, effect and risk assessment models. SOLUTIONS attempts to address legacy, present and future contamination by integrating monitoring and modelling based approaches with scenarios on future developments in society, economy and technology and thus in contamination. The project follows a solutions-oriented approach by addressing major problems of water and chemicals management and by assessing abatement options. SOLUTIONS takes advantage of the access to the infrastructure necessary to investigate the large basins of the Danube and Rhine as well as relevant Mediterranean basins as case studies, and puts major efforts on stakeholder dialogue and support. Particularly, the EU Water Framework Directive (WFD) Common Implementation Strategy (CIS) working groups, International River Commissions, and water works associations are directly supported with consistent guidance for the early detection, identification, prioritisation, and abatement of chemicals in the water cycle. SOLUTIONS will give a specific emphasis on concepts and tools for the impact and risk assessment of complex mixtures of emerging pollutants, their metabolites and transformation products. Analytical and effect-based screening tools will be applied together with ecological assessment tools for the identification of toxicants and their impacts. The SOLUTIONS approach is expected to provide transparent and evidence-based candidates or River Basin Specific Pollutants in the case study basins and to assist future review of priority pollutants under the WFD as well as potential abatement options.

Publications

Libiseller, G., Dvorzak, M., Kleb, U., Gander, E., Eisenberg, T., Madeo, F., Neumann, S., Trausinger, G., Sinner, F., Pieber, T. & Magnes, C. IPO: a tool for automated optimization of XCMS parameters BMC Bioinformatics 16, 118, (2015) DOI: 10.1186/s12859-015-0562-8

Background: Untargeted metabolomics generates a huge amount of data. Software packages for automated data processing are crucial to successfully process these data. A variety of such software packages exist, but the outcome of data processing strongly depends on algorithm parameter settings. If they are not carefully chosen, suboptimal parameter settings can easily lead to biased results. Therefore, parameter settings also require optimization. Several

parameter optimization approaches have already been proposed, but a software package for parameter optimization which is free of intricate experimental labeling steps, fast and widely applicable is still missing.

Results: We implemented the software package IPO (‘Isotopologue Parameter Optimization’) which is fast and free of labeling steps, and applicable to data from different kinds of samples and data from different methods of liquid chromatography - high resolution mass spectrometry and data from different instruments. IPO optimizes XCMS peak picking parameters by using natural, stable 13C isotopic peaks to calculate a peak picking score. Retention time correction is optimized by minimizing relative retention time differences within peak groups. Grouping parameters are optimized by maximizing the number of peak groups that show one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiments, and the resulting scores are evaluated using response surface models. IPO was tested on three different data sets, each consisting of a training set and test set. IPO resulted in an increase of reliable groups (146% - 361%), a decrease of non-reliable groups (3% - 8%) and a decrease of the retention time deviation to one third.

Conclusions: IPO was successfully applied to data derived from liquid chromatography coupled to high resolution mass spectrometry from three studies with different sample type s and different chromatographic methods and devices. We were also able to show the potential of IPO to increase the reliability of metabolomics data. The source code is implemented in R, tested on Linux and Windows and it is freely available for download at https://github.com/glibiseller/IPO. The training sets and test sets can be downloaded from https://health.joanneum.at/IPO.

Publications

Altenburger, R., Ait-Aissa, S., Antczak, P., Backhaus, T., Barceló, D., Seiler, T.-B., Brion, F., Busch, W., Chipman, K., López de Alda, M., de Aragão Umbuzeiro, G., Escher, B. I., Falciani, F., Faust, M., Focks, A., Hilscherova, K., Hollender, J., Hollert, H., Jäger, F., Jahnke, A., Kortenkamp, A., Krauss, M., Lemkine, G. F., Munthe, J., Neumann, S., Schymanski, E. L., Scrimshaw, M., Segner, H., Slobodnik, J., Smedes, F., Kughathas, S., Teodorovic, I., Tindall, A. J., Tollefsen, K. E., Walz, K.-H., Williams, T. D., Van den Brink, P. J., van Gils, J., Vrana, B., Zhang, X. & Brack, W. Future water quality monitoring — Adapting tools to deal with mixtures of pollutants in water resource management Sci Total Environ 512–513, 540–551, (2015) DOI: org/10.1016/j.scitotenv.2014.12.057

Environmental quality monitoringofwaterresourcesis challenged with providing the basisfor safe guarding the environment against adverse biological effects of anthropogenic chemical contamination from diffuse and point sources. While current regulatory efforts focus on monitoring and assessing a few legacy chemicals, many more anthropogenic chemicals can be detected simultaneously in our aquatic resources. However, exposure to chemical mixtures does not necessarily translate into adverse biological effects nor clearly shows whether mitigation

measures are needed. Thus, the question which mixtures are present and which have associated combined effects becomes central for defining adequate monitoring and assessment strategies. Here we describe the vision of the international, EU-funded project SOLUTIONS, where three routes are explored to link the occurrence of chemical mixtures at specific sites to the assessment of adverse biological combination effects. First of all, multi-residue target and non-target screening techniques covering a broader range of anticipated chemicals

co-occurring in the environment are being developed. By improving sensitivity and detection limits for known bioactive compounds of concern, new analytical chemistry data for multiple components can be obtained and used to characterise priority mixtures. This information on chemical occurrence will be used to predict mixture toxicity and toderive combined effecte stimatessuitable for advancing environmental quality standards. Secondly, bioanalytical tools will be explored to provide aggregate bioactivity measuresintegrating all components that produce common (adverse) outcomes even for mixtures of varying compositions. The ambition is to provide comprehensive arrays of effect-based tools and trait-based field observations that link multiple chemical exposures to various environmental protection goals more directly and to provide improved in situ observations for impact assessment of mixtures. Thirdly, effect-directed analysis (EDA) will be applied to identify major drivers of mixture toxicity. Refinements of EDA include the use of statistical approaches with monitoring information for guidance of experimental EDA studies. These three approaches will be explored using case studies at the

Danube and Rhine river basins as well as rivers of the Iberian Peninsula. The synthesis offindings will be organised toprovide guidance for futuresolution-oriented environmenta lmonitoring and exploremore systematic ways to assess mixture exposures and combination effects in future water quality monitoring.

Publications

Griss, J., Jones, A. R., Sachsenberg, T., Walzer, M., Gatto, L., Hartler, J., Thallinger, G. G., Salek, R. M., Steinbeck, C., Neuhauser, N., Cox, J., Neumann, S., Fan, J., Reisinger, F., Xu, Q.-W., del Toro, N., Perez-Riverol, Y., Ghali, F., Bandeira, N., Xenarios, I., Kohlbacher, O., Vizcaino, J. A. & Hermjakob, H. The mzTab Data Exchange Format: communicating MS-based proteomics and metabolomics experimental results to a wider audience Molecular & Cellular Proteomics 13, 2765-2775, (2014) DOI: 10.1074/mcp.O113.036681

The HUPO Proteomics Standards Initiative (PSI) has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS) based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools like Microsoft Excel or R. We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplementary material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. This ranges from a simple summary of the final results up to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found at http://mztab.googlecode.com.

Publications

González-Beltrán, A., Neumann, S., Maguire, E., Sansone, S.-A. & Rocca-Serra, P. The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. BMC Bioinformatics 15 (Suppl 1), S:11, (2014) DOI: 10.1186/1471-2105-15-S1-S11

Background.:

matic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment.

Results

The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data.

Conclusions

The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking.

Software availability

The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa webcite, where the issue tracker allows users to report bugs or feature requests.

Publications

Stanstrup, J., Gerlich, M., Dragsted, L.O. & Neumann, S. Metabolite profiling and beyond: approaches for the rapid processing and annotiation of human blood serum mass spectrometry data. Anal Bioanal Chem 405, 5037-5048, (2013) DOI: 10.1007/s00216-013-6954-6

In this paper, we describe data processing and metabolite identification approaches which lead to a rapid and semi-automated interpretation of metabolomics experiments. Data from metabolite fingerprinting using LC-ESI-Q-TOF/MS were processed with several open-source software packages, including XCMS and CAMERA to detect features and group features into compound spectra. Next, we describe the automatic scheduling of tandem mass spectrometry (MS) acquisitions to acquire a large number of MS/MS spectra, and the subsequent processing and computer-assisted annotation towards identification using the R packages MetShot, Rdisop, and the MetFusion application. We also implement a simple retention time prediction model using predicted lipophilicity logD, which predicts retention times within 42 s (6 min gradient) for most compounds in our setup. We putatively identified 44 common metabolites including several amino acids and phospholipids at metabolomics standards initiative (MSI) levels two and three and confirmed the majority of them by comparison with authentic standards at MSI level one. To aid both data integration within and data sharing between laboratories, we integrated data from two labs and mapped retention times between the chromatographic systems. Despite the different MS instrumentation and different chromatographic gradient programs, the mapped retention times agree within 26 s (20 min gradient) for 90 % of the mapped features.
Books and chapters

Neumann, S., Rasche, F., Wolf, S. & Böcker, S. Metabolite Identification and Computational Mass Spectrometry.. In: The Handbook of Plant Metabolomics, Metabolite Profiling and Networking. (Weckwerth, W. & Kahl, G.). Wiley-VCH 289-303, (2013) ISBN: 978-3-527-32777-5 DOI: 10.1002/9783527669882.ch16

Previous chapters have introduced protocols and examples for high-throughput metabolomics experiments. Metabolite identification is an important step in these experiments, bridging the metabolomics experiment, metabolite profiling, and the biological interpretation of the results. The elemental composition of the individual metabolites is the most basic information that can be calculated already from the mass spectrometry (MS) profiling data. For a more thorough identification, the “interesting” peaks are subjected to MS2, or even higher-order MSn measurements. Such spectra carry rich structural hints, revealing building blocks of the unknown compound, or allowing comparison with databases of reference spectra. This chapter describes a general strategy to identify metabolites, and proceeds through the steps of the identification for two example compounds, first calculating elemental compositions, performing in silico identification without reference spectra, and finally spectral library lookup.

Publications

Schymanski E.L. & Neumann, S. The Critical Assessment of Small Molecule Identification (CASMI): Challenges and Solutions. Metabilotes 3(3), 517-538, (2013) DOI: 10.3390/metabo3030517

The Critical Assessment of Small Molecule Identification, or CASMI, contest was founded in 2012 to provide scientists with a common open dataset to evaluate their identification methods. In this article, the challenges and solutions for the inaugural CASMI 2012 are presented. The contest was split into four categories corresponding with tasks to determine molecular formula and molecular structure, each from two measurement types, liquid chromatography-high resolution mass spectrometry (LC-HRMS), where preference was given to high mass accuracy data, and gas chromatography-electron impact-mass spectrometry (GC-MS), i.e., unit accuracy data. These challenges were obtained from plant material, environmental samples and reference standards. It was surprisingly difficult to obtain data suitable for a contest, especially for GC-MS data where existing databases are very large. The level of difficulty of the challenges is thus quite varied. In this article, the challenges and the answers are discussed, and recommendations for challenge selection in subsequent CASMI contests are given.
Publications

Deutsch, E.W., Chambers, M., Neumann, S., Levander, F., Binz, P.-A., Shofstahl, J., Campbell, D.S., Mendoza, L., Ovelleiro, D., Helsens, K., Martens, L., Aebersold, R., Moritz, R.L. & Brusniak, M.-Y. TraML: a standard format for exchange of selected reaction monitoring transition lists Mol Cell Proteomics 11(4), (2012) DOI: 10.1074/mcp.R111.015040

Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring.

This page was last modified on 10.03.2014.

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