Proposal for a M2 internship: Optimisation of the phosphoproteomics worklow for processing large sample cohorts
- Location: PAPPSO, UMR Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette (France)
- Date: 1st semester 2025
Context: Phosphorylation is one of the most important post-translational modifications (PTMs) of proteins, affecting about one third of all proteins, and plays a key role in regulating many important biological processes. However, like any other PTM, phosphorylation cannot be predicted from the genome or transcriptome, and its study requires specific techniques. Phosphoproteomics is currently the main approach to characterize phosphoproteins, but, as compared to proteomics, it requires special considerations in sample handling, data acquisition, and post-acquisition processing. The PAPPSO platform routinely performs phosphoproteomic analyses using a workflow based on i) protein extraction and digestion, ii) stable isotope labeling of peptides to allow sample multiplexing and improved quantitative comparisons, iii) sample fractionation for a deeper analysis where necessary, iv) phosphopeptide enrichment. While this workflow provides broad phosphoproteome coverage, it remains complex and time consuming, limiting its use in large scale studies. To address this issue, we are exploring two avenues for improving the workflow to make it faster and more efficient: