Initiative for Model Organism Proteomics (iMOP)

The initiative is active within HUPO and EUPA.

The initiative re-named back from the recently used “Initiative on multi-organism proteomics” to its original name, “Initiative for model organism proteomics”, as the fields of action have been re-oriented.

1.      Definition model organism

iMOP considers organisms as models when they are appropriate to address its fields of action, especially those relevant i) to the study of biological mechanisms of importance to human health and disease, ii) to better understand pathogenicity, pathogen reservoirs, and the emergence of resistance, and iii) those that can be used as sentinels of our environment or relevant for the One-Health concept.

• Evolutionary Biology and Medicine
• Comparative proteomics to identify and characterize new molecular fundamental mechanisms, especially those difficult to study directly in humans, and take advantage of different evolutionary trajectories to find new therapeutic/preventive levers for human health
• Proteogenomics on model organisms to identify novel coding sequences, delineate their structure and regulatory elements, characterize the function of the encoded proteins, and understand their phylogenetic occurrence, and derive information for the human proteome annotation
• Proteomics to identify and characterize new biologics and drugs and their potential therapeutic performances
• Environmental proteomics and toxicology
• Proteomics to understand the fate of pathogens in the environment, their reservoirs, their spread, and the development of antibiotic resistances
• Toxicoproteomics to analyse the effects of environmental factors and pollutants on model organisms and derive knowledge for human health
• Ecotoxicoproteomics with sentinel organisms to monitor the quality of the environment

• Promote the development of databases and tools to improve inter-organism comparison and better link proteins from models with human diseases (homology-search, orthology-search, function definition, post-translational modifications and maturation, relative protein abundances and regulations)
• Benchmark proteogenomics tools and promote ideas to improve the annotation of the genomes of representative branches of the tree of life and understand the code of life (relationships between genome/transcriptome/proteome/metabolome)
• Instigate the use of single-cell proteomics for valuable models to understand the heterogeneities in term of cell structure, functioning, and response to changes in their environment
• Contribute to establish some models as sentinels for monitoring the environment and models that could be representative for toxicology measurements
• Promote the relevance of some models to the study of either the mechanisms that underlie human pathophysiology or the mechanisms that could help fight human diseases
• Federate efforts for new methodologies to identify and characterize new biologics and drugs and evaluate their potential therapeutic performances

4.      Links with other EuPA initiatives

Synergies will be explored with EuBIC (databases and bioinformatics pipelines), Metaproteomics Initiative (holobiont models, microorganisms as source of new biologics), Food and Nutrition Proteomics (models to understand diseases), Standardization (proteogenomics, toxicoproteomics, ecotoxicoproteomics).

• September 2021: online meeting to further discuss and develop the agenda; estimated number of participants. 10-15
• Development of (a) common project(s) to be worked on
• Session at EuPA conference in 2022 (Leipzig)

• New chairs will be elected in Sept. 2021 (online meeting)

Chair: Andreas Tholey, Kiel, Germany

Co-chairs: Jean Armengaud, Univ. Paris-Saclay, France

Fabrice Bertile, Univ. de Strasbourg, France

Dörte Becher, Univ. Greifswald, Germany 

Key documents and links:

• 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.