Computational analysis of large-scale proteomics datasets and protein-protein interaction networks

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Proteins are molecules that govern the behaviour of the cell. To accomplish their function, proteins typically interact with each other to form larger macromolecules called protein complexes. Mass spectrometry allows the identification and quantification of proteins and of their interactions. However, currently used software packages struggle to identify and quantify proteins and interactions that have a low abundance. This makes it difficult to obtain a good understanding of the protein interactions that contribute to the assembly and regulation of protein complexes. In our research program, we will design algorithms that will integrate genomics and interactomics data to facilitate the identification of proteins using mass spectrometry. We will also develop software packages that will identify and quantify proteins while they are being analyzed by mass spectrometry instruments. This will allow us to automatically direct the instrument towards the analysis of lower abundance proteins. Finally, protein interactions that are detected with mass spectrometry can be grouped into networks of interactions. We will analyze such networks of interactions to identify protein complexes and understand which interactions are vital for their assembly, their transport to the proper location in the cell, and their regulation.