Proteomics is transitioning from inventory mapping to the mapping of functional cellular contexts. This has been enabled by progress in technologies as well as conceptual strategies. Here, we review recent advances in this area with focus on cellular signalling pathways. We discuss genetics-based methods such as yeast two hybrid methods as well as biochemistry-based methods such as two-dimensional gel electrophoresis, quantitative proteomics, interaction proteomics, and phosphoproteomics. A central tenet is that by its ability to capture dynamic changes in protein expression, localisation and modification modern proteomics has become a powerful tool to map signal transduction pathways and deliver the functional information that will promote insights in cell biology and systems biology.