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Statistical methods for 3D imaging mass spectrometry in proteomics and metabolomics

Objective

Since biology is by and large a 3-dimensional phenomenon, 3D imaging has a significant impact on many challenges in life sciences. 3D matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is an emerging label-free 3D imaging technology with high potential in proteomics and metabolomics. 3D MALDI-IMS is based on 2D MALDI-IMS, which in the last years has proven its value in metabolomics, glycomics, lipidomics, peptidomics, and proteomics. However, 3D MALDI-IMS cannot tap its full potential due to the lack of computational methods for processing large and complex 3D IMS data. Our main goal is to realise 3D label-free proteomics and metabolomics by providing new statistical methods for the reproducible collection of 3D MALDI-IMS data, and for un- and supervised statistical analysis and interpretation of this data. We will validate our methods in diabetes research, surgical metabolomics, and natural products research. To reach our global goal, we will develop methodologies for reproducible collection of 3D MALDI-IMS data, develop a statistical simulator of MALDI-IMS data and evaluation strategies for statistical methods, develop preprocessing, unsupervised, and supervised methods of statistical analysis of 3D MALDI-IMS data, evaluate the developed methods on simulated and real-life proteomics and metabolomics data, and implement them using efficient graphic processing unit (GPU) architecture. This project is of high importance for research-intensive SME partners, Denator and SagivTech, since it would create a new market segment for them. Expertise of partners in biomedicine and their strong connections to clinical partners ensure adoption of the new methods into clinical practice. The developed methods and protocols can be potentially used in any biomedical application where 3D MALDI-IMS is advantageous such as cancer and diabetes diagnostics, disease pathway elucidation, histopathology, and discovery of biomarkers or antibiotics.

Call for proposal

FP7-HEALTH-2012-INNOVATION-1
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Coordinator

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Address
Meyerhofstrasse 1
69117 Heidelberg
Germany

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Activity type
Research Organisations
Administrative Contact
Jill Rowe (Ms.)
EU contribution
€ 217 827

Participants (8)

DENATOR AB
Sweden
EU contribution
€ 194 925
Address
Dag Hammarskjolds Vag 10a
751 83 Uppsala

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Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Charlotte Emlind Vahul (Mrs.)
IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE
United Kingdom
EU contribution
€ 322 714
Address
South Kensington Campus Exhibition Road
SW7 2AZ London

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Activity type
Higher or Secondary Education Establishments
Administrative Contact
Tatjana Palalic (Ms.)
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
United States
EU contribution
€ 284 600
Address
Franklin Street 1111 12 Floor
94607 Oakland Ca

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Activity type
Higher or Secondary Education Establishments
Administrative Contact
Nadine Wilson (Ms.)
UNIVERSITE DE RENNES I
France
EU contribution
€ 366 215
Address
Rue Du Thabor 2
35065 Rennes Cedex

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Activity type
Higher or Secondary Education Establishments
Administrative Contact
Yolaine Bompays (Mrs.)
STEINBEIS INNOVATION GGMBH
Germany
EU contribution
€ 312 308
Address
Adornostrasse 8
70599 Stuttgart

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Activity type
Research Organisations
Administrative Contact
Uwe Haug (Mr.)
SAGIV TECH LTD
Israel
EU contribution
€ 449 000
Address
Hatidhar 16
4365104 Ra Anana

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Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Chen Sagiv (Dr.)
EUROPEAN RESEARCH SERVICES GMBH
Germany
EU contribution
€ 93 660
Address
Roentgenstrasse 19
48149 Muenster

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Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Oliver Panzer (Mr.)
UNIVERSITAET BREMEN
Germany
EU contribution
€ 555 629
Address
Bibliothekstrasse 1
28359 Bremen

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Activity type
Higher or Secondary Education Establishments
Administrative Contact
Thomas Flink