Proteins mainly act in association with other proteins in a dynamic way to reach a tight control of cellular processes. To address these issues modern mass spectrometry-based proteomics strategies are combined with efficient biochemical approaches, like affinity-purification methods.

We have expertise in interactomics, ie the analysis of protein complexes and protein networks, in a qualitative and quantitative manner.

Objective

Identify protein partners using one protein of interest as a bait
Determine the dynamics of protein complexes (variations in protein partners abundances in different conditions or in time)
Determine the stoichiometry of associated proteins using quantitative proteomics

Strategies

We apply affinity-purification approaches combined with quantitative mass spectrometry analysis (AP-MS) to identify proteins associated to a bait protein of interest. Depending on the sample and the bait protein several purification methods can be applied (immunopurification of endogenous proteins, affinity-purification of tagged proteins using various tags). In any case, a relevant control experiment is conducted to distinguish contaminant protein associations from true interactors. Differential quantitative proteomics analysis between the bait and the control assays then allows the identification of specific protein partners of the bait protein.

The ProFI teams have been developing strategies to maintain labile interactions in vivo using crosslinking agents, to analyze specific interactions across various samples using abundance correlation profiling, to cluster proteins with similar dynamics.

Protein complexes and interactomics investigations rely on our quantitative proteomics strategies and instrumentation used for large-scale and targeted quantification.