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Publications - Stress and Develop Biology

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Publications

Hoffmann, N.; Rein, J.; Sachsenberg, T.; Hartler, J.; Haug, K.; Mayer, G.; Alka, O.; Dayalan, S.; Pearce, J. T. M.; Rocca-Serra, P.; Qi, D.; Eisenacher, M.; Perez-Riverol, Y.; Vizcaíno, J. A.; Salek, R. M.; Neumann, S.; Jones, A. R. mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics Anal Chem 91, 3302-3310, (2019) DOI: 10.1021/acs.analchem.8b04310

Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.
Publications

Schober, D.; Jacob, D.; Wilson, M.; Cruz, J. A.; Marcu, A.; Grant, J. R.; Moing, A.; Deborde, C.; de Figueiredo, L. F.; Haug, K.; Rocca-Serra, P.; Easton, J.; Ebbels, T. M. D.; Hao, J.; Ludwig, C.; Günther, U. L.; Rosato, A.; Klein, M. S.; Lewis, I. A.; Luchinat, C.; Jones, A. R.; Grauslys, A.; Larralde, M.; Yokochi, M.; Kobayashi, N.; Porzel, A.; Griffin, J. L.; Viant, M. R.; Wishart, D. S.; Steinbeck, C.; Salek, R. M.; Neumann, S. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data Anal Chem 90, 649–656, (2018) DOI: 10.1021/acs.analchem.7b02795

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.
Publications

Brunner, F.; Rosahl, S.; Lee, J.; Rudd, J.J.; Geiler, C.; Kauppinen, S.; Rasmussen, G.; Scheel, D.; Nürnberger, T. Pep-13, a plant defense-inducing pathogen-associated pattern from <em>Phytophthora transglutaminases</em> EMBO J 21, 6681-6688, (2002)

Innate immunity, an ancient form of defense against microbial infection, is well described for animals and is also suggested to be important for plants. Discrimination from self is achieved through receptors that recognize pathogen-associated molecular patterns (PAMPs) not found in the host. PAMPs are evolutionarily conserved structures which are functionally important and, thus, not subject to frequent mutation. Here we report that the previously described peptide elicitor of defense responses in parsley, Pep-13, constitutes a surface-exposed fragment within a novel calcium-dependent cell wall transglutaminase (TGase) from Phytophthora sojae. TGase transcripts and TGase activity are detectable in all Phytophthora species analyzed, among which are some of the most destructive plant pathogens. Mutational analysis within Pep-13 identified the same amino acids indispensable for both TGase and defense-eliciting activity. Pep-13, conserved among Phytophthora TGases, activates defense in parsley and potato, suggesting its function as a genus-specific recognition determinant for the activation of plant defense in host and non-host plants. In summary, plants may recognize PAMPs with characteristics resembling those known to trigger innate immune responses in animals.
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