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Research Themes

We are interested in the development of technologies which enable the measurement of the dynamic proteome in space and time in a high throughput manner. More specifically, we are interested in looking at the changes in the location, interacting partners and post translational modification of proteins during dynamic cellular processes such as signalling and differentiation.

To enable the above, we have developed approaches over the past few years with the following aims:

(A) to ensure optimal experimental design and appropriate data analysis based on knowledge of data structure. We have applied our research to many quantitative proteomics platforms and created supporting software and analysis pipelines.

(B) to enable the assignment of proteins to subcellular niches and multi protein complexes using quantitative proteomics (both targeted and non-targeted workflows) coupled with machine learning methods for data mining. 


Spatial Proteomics and Protein-Protein Interactions

Mapping the Drosophila organelle proteome with the pRoloc software.
Mapping the Drosophila organelle proteome with the pRoloc software.

Localisation of Organelle Proteins using Isotope Tagging (LOPIT) (Christoforou et al, Nature Communications, 2016), which allows the assignment of proteins and protein complexes to sub-cellular locations, has been applied successfully to several biological systems (Nikolovski et al, Plant Physiol. 2012Tan et al, Proteome Res. 2009, Hall et al. Mol Cell Proteomics. 2009). The ability to assign individual proteins accurately to specific sub-cellular structures and monitor their movement within cells is of paramount importance to our understanding of cellular mechanisms.  

Interactomes using Parallel Affinity Capture (iPAC) is a method developed in collaboration with the St Johnston (Gurdon Institute) and Russell (Genetics Dept.) groups to determine genuine residents of multi protein complexes (Rees et al, Mol Cell Proteomics. 2011).





New Horizons for CCP

  1. The Lilley group has been awarded a sLoLa (BBSRC) in collaboration with the Russell and Martinez Arias groups (UCAM, Genetics), the Orengo and Jones groups (UCL) and Hubbard group (University of Manchester) to create a spatio-temporal map of the developmental fly interactomes.
  2. Kathryn Lilley and Anne Willis (MRC Toxicology Leicester) have been awarded a joint Wellcome Trust Investigator Award to study the spatial implications of translation.
  3. We are members of the Detox - IB catalyst project funded by the BBSRC with the Universities of York, Nottingham and Sheffield and several UK based industrial partners.



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