METASPACE
Bioinformatics for spatial metabolomics
Total Cost €
0EC-Contrib. €
0Partnership
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Explore the words cloud of the METASPACE project. It provides you a very rough idea of what is the project "METASPACE" about.
Project "METASPACE" data sheet
The following table provides information about the project.
| Coordinator |
EUROPEAN MOLECULAR BIOLOGY LABORATORY
Organization address contact info |
| 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.
| # | ||||
|---|---|---|---|---|
| 1 | EUROPEAN MOLECULAR BIOLOGY LABORATORY | DE (HEIDELBERG) | coordinator | 1˙187˙289.00 |
| 2 | IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE | UK (LONDON) | participant | 601˙678.00 |
| 3 | VIB VZW | BE (ZWIJNAARDE - GENT) | participant | 381˙500.00 |
| 4 | BRUKER DALTONIK GMBH | DE (BREMEN) | participant | 302˙663.00 |
| 5 | THE REGENTS OF THE UNIVERSITY OF CALIFORNIA | US (OAKLAND CA) | participant | 297˙750.00 |
| 6 | UNIVERSITE DE RENNES I | FR (RENNES CEDEX) | participant | 149˙440.00 |
| 7 | EUROPEAN RESEARCH SERVICES GMBH | DE (MUENSTER) | participant | 78˙622.00 |
| 8 | SCILS GMBH | 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
| 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
| 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 Vázquez-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, Günther 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: E7645–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 planet—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-Félix; Searles, Stephen; Mills, Robert H.; Satterfield, Kendall; Protsyuk, Ivan; Hoffner, Nicole; Purdy, Trevor; Castro-Falcón, Gabriel; Zhang, Chao Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats published pages: 10775–10784, ISSN: 0003-2700, DOI: 10.1021/acs.analchem.6b03456 |
Analytical Chemistry 2 | 2019-06-03 |
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