Working Group 3

Advancing Methodology for Farm Animal Proteomics

Leader:  Dr Gabriel MAZZUCCHELLI
Vice-Leader:  Dr Frederique LISACEK

The focus of Working Group 3 is on the technical aspects of animal proteomics, from sample collection/preparation to protein separation, identification, and quantification in production animal body fluids, tissues and post harvest derived products. We compile knowledge from the COST members to develop generally applicable protocols for different types of specimens, offer technical support to the other WGs and highlight technological advances within the field of farm animal proteomics (FAP).  Regular interaction with WG1 and WG2 ensures close coordination of the focus of the Action and effective dissemination of knowledge.


Task 1 - Sample Handling

This task establishes standard protocols for handling samples used in FAP experiments (e.g. blood, muscle, milk). Sample collection, storage and extraction are known as critical steps for protein analysis and we aim at achieving a consistent quality of samples and produce valid and reproducible data sets. Common preparation and extraction procedures need to be developed for a given sample type.


Task 2 - Separation and Identification Technology for Farm Animal Proteomics

To reduce the complexity and allow study of proteins of lower abundance, different depletion strategies or prefractionation methods need to be compared and best practice recommended for different sample types. Emphasis will be put on evaluation and implementation of new techniques.A variety of instrument platforms (e.g. MALDI-TOF-MS, LC-MS/MS, ion mobility MS, imaging MS) are presently used for mass spectrometric protein identification by the Action members, ranging from analysis of intact proteins, use of peptide mass fingerprinting (PMF) to de novo sequencing strategies. Action members need to share methodology.


Task 3 - Protein Quantification and Bioinformatics

For comparative proteomic studies it is imperative that the concentration of individual proteins can be defined on a global scale. Recent advances and most appropriate options in mass spectrometric-based approaches to develop labeled or label-free strategies for the absolute quantification of proteins are to be reviewed and disseminated to the members of the Action. Application of bioinformatics will focus on experimental schemes both of species whose genomes are sequenced or very well described (chicken, pig or cattle) or other less-studied species (farmed fish).


Task 4 - Advanced Proteomics: Post-Translational Modifications (PTM) and Protein Complexes

The analytical methodologies used to characterize post-translational modifications (PTMs) of relevance to FAP need to be reviewed and optimal protocols developed. Protein complexes are studied by affinity methods or non-denaturing/non-reducing separation systems. These methods may require modification for species-specific applications.  

Specific Objectives of WG3

  • To collaborate and coordinate with the other two WGs providing them with essential methodology and aiming to contribute to the standardisation and general use of proteomic tools in the widest context of animal sciences,
  • To develop efficient and reliable protocols for extraction, separation and detection of proteins from a wide variety of tissues, organs, fluids and post-harvest products of farm animal origin,
  • To refine strategies for protein identification in species whose genomes were not extensively sequenced or studied,
  • To develop the technology to rapidly characterise PTMs and isoforms in samples relevant to farm animal science,
  • To establish optimal methods for investigation of protein-protein interaction and of protein complexes in relevant samples,
  • To evaluate prefractionation methods for the use in FAP for easier analysis of proteins of lower abundance,
  • To establish databases: collect and distribute useful information on a) commercial antibodies, b) consumables (e.g. for sample prefractionation), c) animal protein/proteomics literature,
  • To establish a forum/platform for troubleshooting and rapid exchange of technical know-how among different members. 





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