Geschmack ist vorhersagbar: Mit FlavorMiner. FlavorMiner heißt das Tool, das IPB-Chemiker und Partner aus Kolumbien jüngst entwickelt haben. Das Programm kann, basierend auf maschinellem Lernen (KI), anhand der…
Seit Februar 2021 bietet Wolfgang Brandt, ehemaliger Leiter der Arbeitsgruppe Computerchemie am IPB, sein Citizen Science-Projekt zur Pilzbestimmung an. Dafür hat er in regelmäßigen Abständen öffentliche Vorträge zur Vielfalt…
Deutsch, E. W.; Perez-Riverol, Y.; Chalkley, R. J.; Wilhelm, M.; Tate, S.; Sachsenberg, T.; Walzer, M.; Käll, L.; Delanghe, B.; Böcker, S.; Schymanski, E. L.; Wilmes, P.; Dorfer, V.; Kuster, B.; Volders, P.-J.; Jehmlich, N.; Vissers, J. P. C.; Wolan, D. W.; Wang, A. Y.; Mendoza, L.; Shofstahl, J.; Dowsey, A. W.; Griss, J.; Salek, R. M.; Neumann, S.; Binz, P.-A.; Lam, H.; Vizcaíno, J. A.; Bandeira, N.; Röst, H.;Expanding the Use of Spectral Libraries in ProteomicsJ. Proteome Res.174051-4060(2018)DOI: 10.1021/acs.jproteome.8b00485
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
Publikation
van Rijswijk, M.; Beirnaert, C.; Caron, C.; Cascante, M.; Dominguez, V.; Dunn, W. B.; Ebbels, T. M. D.; Giacomoni, F.; Gonzalez-Beltran, A.; Hankemeier, T.; Haug, K.; Izquierdo-Garcia, J. L.; Jimenez, R. C.; Jourdan, F.; Kale, N.; Klapa, M. I.; Kohlbacher, O.; Koort, K.; Kultima, K.; Le Corguillé, G.; Moreno, P.; Moschonas, N. K.; Neumann, S.; O’Donovan, C.; Reczko, M.; Rocca-Serra, P.; Rosato, A.; Salek, R. M.; Sansone, S.-A.; Satagopam, V.; Schober, D.; Shimmo, R.; Spicer, R. A.; Spjuth, O.; Thévenot, E. A.; Viant, M. R.; Weber, R. J. M.; Willighagen, E. L.; Zanetti, G.; Steinbeck, C.;The future of metabolomics in ELIXIRF1000Research61649(2017)DOI: 10.12688/f1000research.12342.2
Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.
Publikation
Schober, D.; Salek, R. M.; Neumann, S.;Towards standardized evidence descriptors for metabolite annotationsCEUR Workshop Proc.1692E 1-5(2016)
Motivation: Data on measured abundances of small molecules from biomaterial is currently accumulating in the literature and in online repositories. Unless formal machine-readable evidence as-sertions for such metabolite identifications are provided, quality assessment based re-use will be sparse. Existing annotation schemes are not universally adopted, nor granular enough to be of practical use in evidence-based quality assessment.Results: We review existing evidence schemes for metabolite identifications of variant semantic expressivity and derive require-ments for a ‘compliance-optimized’ yet traceable annotation model. We present a pattern-based, yet simple taxonomy of intu-itive and self-explaining descriptors that allow to annotate metab-olomics assay results both in literature and data bases with evi-dence information on small molecule analytics gained via technol-ogies such as mass spectrometry or NMR. We present example annotations for typical mass spectrometry molecule assignments and outline next steps for integration with existing ontologies and metabolomics data exchange formats.
Publikation
Rocca-Serra, P.; Salek, R. M.; Arita, M.; Correa, E.; Dayalan, S.; Gonzalez-Beltran, A.; Ebbels, T.; Goodacre, R.; Hastings, J.; Haug, K.; Koulman, A.; Nikolski, M.; Oresic, M.; Sansone, S.-A.; Schober, D.; Smith, J.; Steinbeck, C.; Viant, M. R.; Neumann, S.;Data standards can boost metabolomics research, and if there is a will, there is a wayMetabolomics1214(2016)DOI: 10.1007/s11306-015-0879-3
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.