The deregulation of FGF signalling is closely linked to many human diseases, including cancer. Through phosphorylation and dephosphorylation processes, FGF signalling is finely controlled. The thesis presented focuses on applying mass spectrometry tools to investigate FGF signalling using the breast carcinoma SUM52 cell line. High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAlMS) is a technique that separates and focuses ions at atmospheric pressure. It has been demonstrated the application of LC-FAIMS-MS/MS results in increased signal-to-noise ratios and improved dynamic range in analysis of complex proteomics samples. The LC-FAIMS-MS /MS method for large-scale quantitative analysis was optimized and the performance of LC-MS/MS and LC-FAIMS-MS/MS was compared. Results showed the two techniques shared good complementarity. The incorporation of FAIMS resulted in an increase of novel phosphosites and multiply-phosphorylated peptides. Next, a modified FAlMS interface was evaluated for proteomic analyses. This novel FA IMS device exhibited potential in enhancing proteomic analysis showing an increase in peak capacity and proteome coverage and a lower level of redundancy. Next, SRM was applied for accurate quantitation of75 phosphopeptides in a time-resolved way. The data revealed that these phosphorylation sites showed different associations with FGFJ stimulation. Expression patterns were clustered into early, mid- and late stage response.