5/31/17. MS processing. Overview. Overview. my spectrum + my biological question. Annotation & Databanks. An organized collection of information

Transcription

1 MS processing Annotation & banks Franck Giacomoni, Yann Guitton 01/06/2017 v CC by-nc-nd : Overview An organized collection of information Dilbert cartoon, by Scott Adams finding metabolite candidates...linking knowledge and experimental observations Overview my spectrum + my biological question 1

2 Large databank set Chemical compounds banks Home based libraries Spectral libraries Genome-wide metabolic reconstruction based databases References repositories PSM V43 D169 Alfalfa fields in the desert, 1893 More than 500 references available Commercials banks «In House» banks A local knowledge aggregation Representation of one particular question Interoperability issue or limit Reference banks Long term support New submission possibilities Curation steps Author: McCracken, Theresa Overview 2

3 Quantity vs Quality 157,000,000 entries A public repository of information on small molecules and their biological activities A Comprehensive Species- Metabolite Relationship base 50,000 entries Inventory Source: Powered: ChEBI Chemical databank Chemical Entities of Biological Interest Freely available dictionary of molecular entities focused on small chemical compounds. 41,000 entities fully annotated EMBL EBI 3

4 Star status Manually annotated by the ChEBI team Manually annotated by a third party, Marked as deleted or obsolete. ChEBI Ontologies : Molecular structure, roles and subatomic particle information. Manual search by mass / formula Web services LipidMaps Chemical family databank LIPID MAPS Structure base A relational db encompassing structures and annotations of biologically relevant lipids 40,673 unique lipid structures National Institute of General Medical Sciences Chemical structure rules Naming convention Downloadable spectra MSMS predicted data available in pos/neg mode Lipids classification Manual search by mass / formula / s Web services 4

5 MassBank.JP 41,000 MS spectra 47,000 compounds Spectral Bank base of comprehensive, high-resolution mass spectra of metabolites Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (s) Distributed database / Contributions Downloadable spectra High precision and accurate mass spectra of primary/secondary. met. Massive work on controled vocabulary/format: [PDF] Detailed MS data / metadata Spectral/structure searching utilities Search for merged spectra Web services API GMD GC-MS spectral databank Golm Metabolome base Reference mass spectra from biologically active metabolites quantified using GC-MS. 26,000 spectra and 3500 structures Max Planck Institute of Molecular Plant Physiology 5

6 Downloadable spectra Mass spectra and retention time indices of pure reference substances Quantitative data Spectral searching utilities Web services API HMDB Species/Metabolomics databank Human Metabolome base base containing detailed information about small molecule metabolites found in the human body 74,461 metabolite entries The Metabolomics Innovation Centre (TMIC) Downloadable spectra - MS, MSMS (and NMR) from various instruments (low/high res.) Predicted spectra Human metabolites with chemical properties, biochemistry data and clinical data MetaboCards and hudge cross-links work Spectral/structure searching utilities No public web service 6

7 Kyoto Encyclopedia of Genes and Genomes Metabolic pathway db KEGG COMPOUND is a collection of small molecules, biopolymers, and other chemical substances that are relevant to biological systems. 18,039 metabolites and small molecules Kanehisa Lab. - NPO Bioinformatics Japan Compounds (not available as full resource) Biological roles Not adapted for metabolomics direct uses Reference Pathway Metabolism information Strong link with metabolic pathways maps WebServices API Dbs Overlaps and Metabolome coverage Venn diagram showing the overlap between open mass spectral databases (HMDB, MassBank, GNPS, and ReSpect) This table shows how PeakForest chemical library covers genome scale reconstructions of metabolic networks. This mapping is performed using MetExplore webservice. Sources: Vinaixa et al. 2016, TrAC - DOI: /j.trac and PeakForest project 7

8 A case of Chinese whispers Source: Cl. Frainay INRA Toxalim «Take Home» message During annotation Using only one database is difficult Be aware about the quality of the selected bank A match in a bank is a clue NOT a proof Enrich your results with: banks IDs INCHI (chem. structure representation) And please - Make the effort to submit your experimental/annotated data to Repositories (MetaboLights, W4M DOI, ) References Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 The Human Metabolome base in Nucleic Acids Res Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S. LMSD: LIPID MAPS structure database Nucleic Acids Research 35: p. D PMID: [doi: /nar/gkl838] PMID: Hummel J., Strehmel N., Bölling C., Schmidt S., Walther D., Kopka J. (2013) Mass Spectral Search and Analysis Using the Golm Metabolome base. In: The Handbook of Plant Metabolomics, Wiley-VCH Verlag GmbH & Co. KGaA; ; Vinaixa, M., Schymanski, E. L., Neumann, S., Navarro, M., Salek, R. M., & Yanes, O. (2016). Mass spectral databases for LC/MS- and GC/MS-based metabolomics: state of the field and future prospects. Trends in Analytical Chemistry, 78, Kanehisa, M., S. Goto, et al. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Research 40(D1): D109-D114 Horai, Hisayuki and Arita, Masanori and Kanaya, Shigehiko and Nihei, Yoshito and Ikeda, Tasuku and Suwa, Kazuhiro and Ojima, Yuya and Tanaka, Kenichi and Tanaka, Satoshi and Aoshima, Ken and et al. (2010). MassBank: a public repository for sharing mass spectral data for life sciences. In Journal of Mass Spectrometry, 45 (7), pp [doi: /jms.1777] Sud, M. and Fahy, E. and Cotter, D. and Brown, A. and Dennis, E. A. and Glass, C. K. and Merrill, A. H. and Murphy, R. C. and Raetz, C. R. H. and Russell, D. W. and et al. (2007). LMSD: LIPID MAPS structure database. In Nucleic Acids Research, 35 (base), pp. D527 D532. [doi: /nar/gkl838] Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for Nucleic Acids Res. 24 8