Despite more than six decades of successful Golgi research, the fundamental question as to how biosynthetic material is transported through the secretory pathway remains unanswered. New technologies such as live cell imaging and correlative microscopy have highlighted the plastic nature of the Golgi, one that is sensitive to perturbation yet highly efficient in regaining both structure and function. Single molecule-microscopy and super resolution-microscopy further adds to this picture. Various models for protein transport have been put forward, each with its own merits and pitfalls but we are far from resolving whether one is more correct than the other. As such, our laboratory considers multiple mechanisms of Golgi transport until proven otherwise. This includes the two classical modes of transport, vesicular transport and cisternal progression/maturation as well as more recent models such as tubular inter- and intra-cisternal connections (long lasting or transient) and inter-Golgi stack transport. In this article, we focus on an emerging inductive technology, mass spectrometry-based proteomics that has already enabled insight into the relative composition of compartments and subcompartments of the secretory pathway including mechanistic aspects of protein transport. We note that proteomics, as with any other technology, is not a stand-alone technology but one that works best alongside complementary approaches.