"I think the biggest innovations of the 21st century will be at the intersection of biology and technology. A new era is beginning." Steve Jobs, 2010

Proteomics of Post-translational Modifications

By modifying the chemical properties of proteins, post-translational modifications (PTMs) enormously expand the functional diversity of the proteome. Thus, deciphering PTMs is essential for understanding the dynamics of signaling networks and consequently the complexity of living organisms. Mass spectrometry (MS) is an indispensable gold-standard technology for mapping PTMs on a global scale and therefore exploring cellular signaling pathways in normal and disease states. Despite the successful application of proteomics to the investigation of a range of PTMs, technical challenges have hampered the MS investigation of other biologically important PTMs, such as ADP-ribosylation. We are devising strategies for an unbiased and comprehensive proteomic analysis of this PTM that will allow the identification and quantification of sites of ADP-ribosylation on all possible amino acids.

ADP-ribosylation and the DNA damage response

ADP-ribosylation is one of the key signaling molecules that regulates DNA repair, a critical process in maintaining genome stability, which is compromised in cancer and ageing. Following activation by DNA strand breaks, PARPs catalyze poly(ADP-ribosylaton) of key chromatin components, including histones. This creates an environment that is permissive for the repair of DNA lesions, via chromatin relaxation and recruitment of DNA repair factors to sites of DNA damage through their interactions with PARylated chromatin proteins. However, the precise molecular mechanisms by which PARPs regulate chromatin dynamics during DNA repair signaling remain largely unexplored. To identify these mechanisms, we are developing and applying advanced quantitative proteomics to profile ADP-ribosylation sites during the DNA damage response in mammalian cell cultures and the model organism C. elegans. Our proteomics analysis will allow the identification of unknown players in the DNA damage response and determine at the modification site level the role of ADP-ribosylation in this essential signaling pathway.

Detection of PTMs by re-analysis of proteomics datasets

Identification of unknown/unexpected PTMs by proteomic data re-analysis is an emerging sub-field of proteomics recently boosted by the increased availability of raw data shared in public repositories. Thus, the experimental part of our research is complimented by the detection of sites of ADP-ribosylation and other understudied PTMs by computational reprocessing of phosphoproteomics datasets.

Third-party funding

  • 2016 - 2018 | Marie Curie Individual Fellowship (to Juan Jose Bonfiglio)
    Decoding the DNA damage signalling in C. elegans by proteomic analyses of ADP-ribosylation

  • 2014 - 2018 | DFG, CECAD grant

  • 2010 - 2014 | Wellcome Trust, Sir Henry Wellcome fellowship