This work combines theoretical and experimental approaches to explore the fragmentation mechanisms occurring during the collision-induced dissociation (CID) of Galactose-6-Sulfate (Gal-6S). This compound is a building block of sulfated sugars and its study can shed light on fragmentation mechanisms occurring for other related systems. In particular, to understand in detail the fragmentation mechanisms at the molecular level, we have coupled mixed quantum/classical (QM + MM) direct chemical dynamics simulations with tandem mass spectrometry (MS/MS) experiments. Our results, on one hand, are in a good agreement with the “charge-remote” picture, which is usually proposed in the literature as fragmentation mechanism to account for the formation of many fragment ions. On the other hand, to reproduce some of the fragments ions obtained during our experiments, alternate dissociation pathways are proposed.