Post-translational modifications of proteins (PTMs) act as key regulators of protein activity and of protein-protein interactions (PPIs). To date however, it has been difficult to comprehensively explore functional links between PTMs and PPIs. To address this, we developed PTMOracle: a Cytoscape app for co-analysing PTMs within PPI networks. For proteins of interest, or a whole proteome, PTMOracle can generate network visualisations to reveal complex PTM-associated relationships. PTMOracle also allows extensive data to be integrated and co-analysed with PPI networks, such as protein sequences, motifs and structural annotations such as domains and disordered regions. PTMOracle contains the OraclePainter for colouring proteins by modifications, OracleTools for network analytics, and OracleResults for exploring tabulated findings. To illustrate the use of PTMOracle, we investigated PTM-associated relationships and their role in PPIs in yeast. We explored a histone-associated network, showed how integrative approaches can be used to predict kinases involved in phosphodegrons. We also demonstrated how these approaches can be used to identify simple “decision-making modules”, which consists of a decision-making protein, two modifying enzymes and two protein interaction partners. Such modules are likely to be important for understanding how cellular signals are integrated, and how different biological outcomes are managed by multiple types of PTMs. The PTMOracle is open-source and available on the Cytoscape app store: http://apps.cytoscape.org/apps/ptmoracle.