Communication and environment sensing are fundamental for the regulation of the majority of the cellular functions. In cells there are dedicated networks that are responsible for signalling, which gives the ability to the cell of sensing the external and internal environment allowing rapid response and adaptation to changes and stress events. A major component of these networks are post translational modifications. Their attachment to proteins in response to a change in the surrounding conditions can have very drastic consequences on modified proteins. Since post translational modification can heavily influence the cellular fate it is essential to identify these modifications and to understand their functioning, to better comprehend how cells respond to environments changes and different types of stress events to which they are continuously subjected. In this work we analyse a type of modification called S-palmitoylation, which is recently emerging as signalling/regulatory modification. S-Palmitoylation, or more generally “acylation”, is the addition of an acyl chain to the SH-group of a cysteine via a thioester bond. This type of modification has a big impact at the cellular level. In different studies about palmitoylated proteins, functional consequences are observed at the cellular level, like altered signalling capacity, activity modulation, regulation of protein stability and localization. Palmitoylation was studied using a mathematical modelling approach. Based on experimental data we developed models of the palmitoylation process of different proteins. Using a bottom up approach we first investigated the consequences of protein palmitoylation on the endoplasmic reticulum chaperone calnexin, to better understand the consequences of palmitoylation at the protein level. Following the same approach we investigated the effects of palmitoylation on DHHC6, a palmitoyltransferase that is responsible for palmitoylation of calnexin, which itself undergoes palmitoylation from the palmitoyltransferase DHHC16. In the last part of the project we focused on the study of palmitoylation at the network level. For this purpose we reconstructed the palmitoylation cascade of calnexin, including in the model all the proteins involved in the palmitoylation process of this protein. This network of palmitoylation allowed us to investigate the dynamics of palmitoylation at the network level, focusing in the characterization of those mechanisms that are responsible for regulation of palmitoylation on different substrates. This work provides an unprecedented level of understanding of palmitoylation dynamics, both at the protein and network level. Moreover all the models and the tools for model analysis used in this work have been developed keeping in mind the final goal of reconstructing the entire palmitoylation network. Thanks to the approach we chose for modelling, the calnexin network model developed during this project can be easily expanded to include other portions of the palmitoylation networks. Similarly the tools developed for model analysis can be easily adapted to work on post-translational modification assays and analysis of biological functions from the smaller to the larger scales.