New Computational Tools for Proteomic Analyses

Most eukaryotic proteins are modified by at least one post-translational modification (PTM). These modifications serve to diversify the function of proteins by acting as key regulators of protein activity, including the regulation of protein-protein interactions (PPIs). However, determining the function of proteins and understanding how their activity is regulated by PTMs remains challenging. This is due, at least in part, to the lack of appropriate software tools for analysing proteins and their PTMs, and for investigating the regulatory role of PTMs in PPIs. To fill this gap, three software tools for improving the identification of proteins and their PTMs, and for improving our understanding of the regulatory role of PTMs in PPIs are presented. First is MS2-Deisotoper for deisotoping high resolution MS/MS spectra. Identifying monoisotopic peaks and removing isotopic peaks from MS/MS spectra with MS2-Deisotoper led to an increase in the number of proteins identified, highlighting the importance of deisotoping for increasing coverage of the proteome. Second is MethylQuant for validating methylpeptide identifications with heavy methyl SILAC. Analysing heavy methyl SILAC data with MethylQuant led to the identification of true positive methylpeptides at both high specificity and sensitivity, thereby assisting in the identification of protein methylation sites. Third and finally is the PTMOracle Cytoscape app for co-visualising and co-analysing PTMs in the context of PPI networks. Integrating PTM and sequence-based data (i.e., domains and motifs) into PPI networks with PTMOracle, provided insights into how interactions take place. Developing queries to explore network visualisations with PTMOracle could also help raise new questions and hypotheses regarding the functional role of PTMs in PPIs. The software tools presented in this thesis therefore represent significant advances towards in the proteomic analysis of peptides and proteins, and in understanding the predominance and role of PTMs