Initiative on MultiOrganism Proteomes (iMOP)

Overview of project:

The model organism community is growing steadily and the number of comprehensive model organism proteome data being generated is continuously increasing. To standardize efforts and to make optimum use of the proteomics data acquired in model organisms, a new HUPO initiative in model organism proteomes (iMOP) was proposed and was approved by the HUPO Initiatives Committee at the HUPO 9th Annual World Congress in Sydney on 21 September, 2010. iMOP will stimulate the scientific exchange within this community, and HUPO best practices and standards can be brought to the model organism researchers. Their needs towards the central databases will be better represented, catalyzing the integration of proteomics and organism-specific databases.

Vision and mission:

a. Model organism proteomes

Model organisms have been used for decades to study embryogenesis, development and other fundamental biological processes. They are easy to grow in the laboratory and have rather short generation times. The conservation of disease pathways between model organisms and human allows model organisms to be used to study disease pathogenesis and to develop drugs. Many model organisms are important commensals or pathogens and thus very closely interacting with the human proteome. The conservation between model organisms and crop plants is leading to improved crop performance.    Historically, research on model organisms depended largely on genetic approaches. More recently, however, large-scale approaches such as genomics and proteomics have become an essential part of model organism research. Unfortunately, the community of model organism researchers is highly fragmented, first because they work on many different model organism species, and second because of their wide distribution around the world. Often, groups that start proteomic projects in model organisms have a previous expertise in genomics but are new in the field of proteomics. Moreover, many of these groups face similar technical challenges in their efforts to characterize the proteome of their favorite model organism: small size, difficulties in obtaining pure cell populations, integration of proteomics data into already well-established organism-centered databases.

In order to better address these challenges, we propose to establish a new HUPO initiative on model organism proteomes (iMOP) to create a global network of experimental and bioinformatics groups interested in model organism proteomes. The initiative will ensure that the same principles, protocols, and standards used in all current HUPO initiatives are also applied in the future to all model organisms. The iMOP initiative will not focus on a 2 single species but rather will bring together model organism proteomicists to reach the critical mass necessary to get influence and impact within the scientific community.

b. Scientific objectives

iMOP will pursue the following objectives:

– Integrate different model organism research groups into a model organism proteomics community and promote interaction between them

The vision of iMOP is to join groups covering a broad spectrum of model organisms and methods into a common model organism proteomics community. iMOP will facilitate the combination of resources and efforts of different labs. Scientific interactions within iMOP will be encouraged through the exchange of visiting researchers between the labs, as well as workshops during the regular HUPO meetings and specific iMOP meetings.

– Adopt HUPO standards and best practices.

In analogy to already running HUPO initiatives, the use of best practices will be established within the model organism community Data storage and exchange using established platforms will be facilitated by following the PSI guidelines for standardized data acquisition and analysis.

– Integrate and link proteome and organism-specific databases

Several proteomics data repositories exist encompassing different species. Proteomics data are also being integrated into model organism-specific databases. To facilitate access to all proteome data, iMOP will help to efficiently link proteome-centric and organism-based databases. Such linked model organism datasets will be a valuable resource of information also for human proteome projects.

– Develop software tools to navigate databases

Since most biologists are interested in using rather than generating proteomics data, it is important that proteomics data will be easily accessible, easily manipulated and analyzed, and that different datasets will be easily compared. iMOP will help develop software tools to navigate the databases and to extract and compare sub-datasets. Such tools should for example allow for the global comparison of proteomes of different model organisms. Moreover, because many of these proteins have counterparts in human cells, these tools will allow for a comparative analysis of pathways and mechanisms conserved between model organisms and humans.

Leadership:

Emøke Bendixen, Chair
Andreas Tholey, Co-Chair
Dörte Becher, Co-Chair
Kathrin Riedel, Co-Chair
Joshua Heazlewood, Co-Chair

Key documents and links:

  • iMOP website – www.imop.uzh.ch
  • iMOP full Description document – Sep 2010
  • Journal of Proteomics – Volume 73, Issue 11, Pages 2051-2290 (10 October 2010):Model organism proteomics Edited by Christian H. Ahrens, Sabine P. Schrimpf, Erich Brunner and Ruedi Aebersold
  • Heazlewood JL, Schrimpf SP, Becher D, Riedel K, Tholey A,  Bendixen E (2015). Multi-organism proteomes (iMOP): advancing our understanding of human biology. Proteomics, 15: 2885-2894.

  • Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, van Wijk K, von Mering C, Weiss M, Zheng X (2012). The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics, 12: 340-345.

  • Tholey A, Treitz C, Kussmann M, Bendixen E, Schrimpf SP, Hengartner MO. (2013). Model organism proteomics - from holobionts to human nutrition. Proteomics, 13: 2537 - 2541.

For more information or participation opportunities please contact office(at)hupo.org.



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