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Opendata, web and dolomites

METASPACE

Bioinformatics for spatial metabolomics

Total Cost €

EC-Contrib. €

Partnership

Views

Outcomes and
results

METASPACE project word cloud

Explore the words cloud of the METASPACE project. It provides you a very rough idea of what is the project "METASPACE" about.

profiling throughput emergence stimulate industry community trust databases considerable tumor putative phenotyping validation innovation domain molecular annotation metabolomics tools metaspace big clinically workflows engaging engine demonstration bioinformatics opened scientific mass validated spatial educating source hampered fibrosis resolution clinical imaging biologically create doors hundreds platform oriented linked online physiology alongside sustainable spectrometry turn data bottleneck drive downstream lack ms untargeted interpretation effort infections leads benefits outreach metabolic discoveries maximize centred polymicrobial hr metabolites academics interaction envisaged constant chemotherapy cystic ecosystem sections medicine algorithms metabolomic incorporating biology tissue

Project "METASPACE" data sheet

The following table provides information about the project.

Coordinator	EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Germany [DE]
Project website	http://metaspace2020.eu
Total cost	2˙998˙944 €
EC max contribution	2˙998˙944 € (100%)
Programme	1. H2020-EU.3.1.6. (Health care provision and integrated care)
Code Call	H2020-PHC-2014-two-stage
Funding Scheme	RIA
Starting year	2015
Duration (year-month-day)	from 2015-07-01 to 2018-06-30

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	EUROPEAN MOLECULAR BIOLOGY LABORATORY EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (HEIDELBERG)	coordinator	1˙187˙289.00
2	IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE Organization address address: SOUTH KENSINGTON CAMPUS EXHIBITION ROAD city: LONDON postcode: SW7 2AZ website: http://www.imperial.ac.uk/ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (LONDON)	participant	601˙678.00
3	VIB VZW VIB VZW Organization address address: RIJVISSCHESTRAAT 120 city: ZWIJNAARDE - GENT postcode: 9052 website: www.vib.be contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	BE (ZWIJNAARDE - GENT)	participant	381˙500.00
4	BRUKER DALTONIK GMBH BRUKER DALTONIK GMBH Organization address address: FAHRENHEITSTRASSE 4 city: BREMEN postcode: 28359 website: www.bruker-daltonik.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (BREMEN)	participant	302˙663.00
5	THE REGENTS OF THE UNIVERSITY OF CALIFORNIA THE REGENTS OF THE UNIVERSITY OF CALIFORNIA Organization address address: FRANKLIN STREET 1111, 12 FLOOR city: OAKLAND CA postcode: 94607 website: http://www.universityofcalifornia.edu/ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	US (OAKLAND CA)	participant	297˙750.00
6	UNIVERSITE DE RENNES I UNIVERSITE DE RENNES I Organization address address: RUE DU THABOR 2 city: RENNES CEDEX postcode: 35065 website: www.univ-rennes1.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (RENNES CEDEX)	participant	149˙440.00
7	EUROPEAN RESEARCH SERVICES GMBH EUROPEAN RESEARCH SERVICES GMBH Organization address address: ROENTGENSTRASSE 19 city: MUENSTER postcode: 48149 website: www.european-research-services.eu contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (MUENSTER)	participant	78˙622.00
8	SCILS GMBH SCILS GMBH Organization address address: FAHRENHEITSTRASSE 1 city: BREMEN postcode: 28359 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (BREMEN)	participant	0.00

Map

Project objective

Metabolomics is recognized as a crucial scientific domain, promising to advance our understanding of biology, physiology, and medicine. The emergence of high-resolution imaging mass spectrometry (HR imaging MS) opened doors to spatial profiling of hundreds of metabolites directly from tissue sections. However, clinical use of HR imaging MS is hampered by a lack of clinically-oriented bioinformatics tools for molecular interpretation of the complex and information-rich data produced. Our goal is to address this bottleneck. We will develop algorithms for high-throughput putative annotation of hundreds of metabolites, knowledge-based downstream analysis, and validation of biologically-relevant leads. We will create the METASPACE engine, an open online platform providing these tools integrated into validated workflows for clinical use. This engine will be evaluated in clinical case studies on metabolic phenotyping of tumor response to chemotherapy and polymicrobial infections in cystic fibrosis. This demonstration will raise awareness and build trust among potential end-users. METASPACE will create a research ecosystem for exploitation of spatial metabolomic data that benefits both academics and industry. An open-source approach will stimulate developments in this field and provide a sustainable platform capable of incorporating future bioinformatics. Our user-centred tools, linked to existing molecular databases, will enable researchers without mass spectrometry or bioinformatics experience to turn big and complex HR imaging MS data into molecular knowledge. A considerable outreach effort, alongside constant interaction with the clinical metabolomics community, will maximize impact and dissemination. By engaging and educating envisaged end-users, METASPACE will facilitate future clinical discoveries in studies that require untargeted metabolic profiling and imaging. Our project will drive innovation and create a novel bioinformatics research field centred in Europe.

Deliverables

List of deliverables.
Evaluation of the online engine	Documents, reports	2019-03-22 17:40:03

Take a look to the deliverables list in detail: detailed list of METASPACE deliverables.

Publications

List of publications.
year	authors and title	journal	last update
2018	Quan Gu, Kirill Veselkov Bi-clustering of metabolic data using matrix factorization tools published pages: , ISSN: 1046-2023, DOI: 10.1016/j.ymeth.2018.02.004	Methods	2019-06-03
2018	Kirill Veselkov, Jonathan Sleeman, Emmanuelle Claude, Johannes P. C. Vissers, Dieter Galea, Anna Mroz, Ivan Laponogov, Mark Towers, Robert Tonge, Reza Mirnezami, Zoltan Takats, Jeremy K. Nicholson, James I. Langridge BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-22499-z	Scientific Reports 8/1	2019-06-03
2018	Dieter Galea, Ivan Laponogov, Kirill Veselkov Exploiting and assessing multi-source data for supervised biomedical named entity recognition published pages: 2474-2482, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty152	Bioinformatics 34/14	2019-06-03
2018	Clifford A. Kapono, James T. Morton, Amina Bouslimani, Alexey V. Melnik, Kayla Orlinsky, Tal Luzzatto Knaan, Neha Garg, Yoshiki VÃ¡zquez-Baeza, Ivan Protsyuk, Stefan Janssen, Qiyun Zhu, Theodore Alexandrov, Larry Smarr, Rob Knight, Pieter C. Dorrestein Creating a 3D microbial and chemical snapshot of a human habitat published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-21541-4	Scientific Reports 8/1	2019-06-03
2017	Dieter Galea, Paolo Inglese, Lidia Cammack, Nicole Strittmatter, Monica Rebec, Reza Mirnezami, Ivan Laponogov, James Kinross, Jeremy Nicholson, Zoltan Takats, Kirill A. Veselkov Translational utility of a hierarchical classification strategy in biomolecular data analytics published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-14092-7	Scientific Reports 7/1	2019-06-03
2017	Aaron C. Hartmann, Daniel Petras, Robert A. Quinn, Ivan Protsyuk, Frederick I. Archer, Emma Ransome, Gareth J. Williams, Barbara A. Bailey, Mark J. A. Vermeij, Theodore Alexandrov, Pieter C. Dorrestein, Forest L. Rohwer Meta-mass shift chemical profiling of metabolomes from coral reefs published pages: 11685-11690, ISSN: 0027-8424, DOI: 10.1073/pnas.1710248114	Proceedings of the National Academy of Sciences 114/44	2019-06-03
2018	Ivan Laponogov, Noureddin Sadawi, Dieter Galea, Reza Mirnezami, Kirill A Veselkov ChemDistiller: an engine for metabolite annotation in mass spectrometry published pages: 2096-2102, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty080	Bioinformatics 34/12	2019-06-03
2017	Tal Luzzatto-Knaan, Neha Garg, Mingxun Wang, Evgenia Glukhov, Yao Peng, Gail Ackermann, Amnon Amir, Brendan M Duggan, Sergey Ryazanov, Lena Gerwick, Rob Knight, Theodore Alexandrov, Nuno Bandeira, William H Gerwick, Pieter C Dorrestein Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae published pages: , ISSN: 2050-084X, DOI: 10.7554/eLife.24214	eLife 6	2019-06-03
2016	John H.R. Burns, Theodore Alexandrov, Ekaterina Ovchinnikova, Ruth D. Gates, Misaki Takabayashi Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework published pages: 51-57, ISSN: 0022-2011, DOI: 10.1016/j.jip.2016.08.007	Journal of Invertebrate Pathology Volume 140	2019-06-03
2016	Judith M. Lotz, Franziska Hoffmann, Johannes Lotz, Stefan Heldmann, Dennis Trede, Janina Oetjen, Michael Becker, GÃ¼nther Ernst, Peter Maass, Theodore Alexandrov, Orlando Guntinas-Lichius, Herbert Thiele, Ferdinand von Eggeling. Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition published pages: , ISSN: 1570-9639, DOI: 10.1016/j.bbapap.2016.08.018	Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Volume 1864, Issue 9	2019-06-03
2016	Andrew Palmer, Prasad Phapale, Ilya Chernyavsky, Regis Lavigne, Dominik Fay, Artem Tarasov, Vitaly Kovalev, Jens Fuchser, Sergey Nikolenko, Charles Pineau, Michael Becker, Theodore Alexandrov FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry published pages: 57-60, ISSN: 1548-7091, DOI: 10.1038/nmeth.4072	Nature Methods 14/1	2019-06-03
2016	Amina Bouslimani, Alexey V. Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R. da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, and Pieter C. Dorrestein Lifestyle chemistries from phones for individual profiling published pages: E7645â€“E7654, ISSN: 0027-8424, DOI: 10.1073/pnas.1610019113	PNAS vol 113 no 48	2019-06-03
2017	Daniel Petras, Alan K Jarmusch, Pieter C Dorrestein From single cells to our planetâ€”recent advances in using mass spectrometry for spatially resolved metabolomics published pages: 24-31, ISSN: 1367-5931, DOI: 10.1016/j.cbpa.2016.12.018	Current Opinion in Chemical Biology Volume 36	2019-06-03
2016	Palmer, A., Trede, D., Alexandrov, T. Where imaging mass spectrometry stands: here are the numbers published pages: 107, ISSN: 1573-3882, DOI: 10.1007/s11306-016-1047-0	Metabolomics 12: 107	2019-06-03
2016	Alexandrov, Theodore; Cichewicz, Robert H.; Sanchez, Laura M; Garg, Neha; Mohimani, Hosein; Zeng, Yi; Miao, Vivian; Edlund, Anna; Cai, Shengxin; Dorrestein, Pieter C.; Gurevich, Alexey; Luzzatto-Knaan, Tal; Lim, Yan Wei; Melnik, Alexey V; Rohwer, Forest; Pevzner, Pavel A.; Schiffler, Stefan Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen published pages: , ISSN: 2379-5077, DOI: 10.1128/mSystems.00139-16	mSystems Volume 1 Issue 6	2019-06-03
2016	Nima Abbassi-Ghadi, Ottmar Golf, Sacheen Kumar, Stefan Antonowicz, James S. McKenzie, Juzheng Huang, Nicole Strittmatter, Hiromi Kudo, Emrys A. Jones, Kirill Veselkov, Robert Goldin, Zoltan Takats, George B. Hanna Imaging of Esophageal Lymph Node Metastases by Desorption Electrospray Ionization Mass Spectrometry published pages: 5647-5656, ISSN: 0008-5472, DOI: 10.1158/0008-5472.CAN-16-0699	Cancer Research 76/19	2019-06-03
2016	Misaki Takabayashi; Burns, John H.R.; Ruth D. Gates; Theodore Alexandrov; Katya Ovchinnikova Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques published pages: , ISSN: 2352-3409, DOI: 10.1016/j.dib.2016.09.009	Data in Brief 1	2019-06-03
2016	Petras, Daniel; Wojnicz, Aneta; Morton, Jamie; McCall, Laura-Isobel; Hook, Vivian; Yang, Jin; Steffen, Dana; Quinn, Robert A.; Knight, Rob; Podvin, Sonia; Garg, Neha; Vargas, Fernando; Tuttle, Robert; Bouslimani, Amina; Dang, Tam; Kapono, Clifford A.; Ling, Tie-Jun; Sapp, Valerie; Luzzatto-Knaan, Tal; Meehan, Michael J; Shires, Sarah; Merritt, Jonathan K.; Jiang, Yike; Bandeira, Nuno; Todoric, Jelena; Shah, Sahil; Floros, Dimitrios J.; McGrath, Aaron P.; Koester, Irina; Dorrestein, Pieter C.; Alexandrov, Theodore; Chen, Liangyu; White, Margot; Leber, Christopher A.; Nothias, Louis-FÃ©lix; Searles, Stephen; Mills, Robert H.; Satterfield, Kendall; Protsyuk, Ivan; Hoffner, Nicole; Purdy, Trevor; Castro-FalcÃ³n, Gabriel; Zhang, Chao Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats published pages: 10775â€“10784, ISSN: 0003-2700, DOI: 10.1021/acs.analchem.6b03456	Analytical Chemistry 2	2019-06-03

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