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METASPACE

Bioinformatics for spatial metabolomics

Total Cost €

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EC-Contrib. €

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Partnership

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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 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

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

year authors and title journal last update
List of publications.
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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