Amorphous molybdenum sulfide (MoS x ) is a potent catalyst for the hydrogen evolution reaction (HER). Since mechanistic investigations on amorphous solids are particularly difficult, we use a bottom-up approach and study the [Mo3S13]2- nanocluster and its protonated forms. The mass selected pure [Mo3S13]2- as well as singly and triply protonated [HMo3S13]- and [H3Mo3S13]+ ions, respectively, were investigated by a combination of collision induced dissociation (CID) experiments and quantum chemical calculations. A rich variety of H x S y elimination channels was observed, giving insight into the structural flexibility of the clusters. In particular, it was calculated that the observed clusters tend to keep the Mo3 ring structure found in the bulk and that protons adsorb primarily on terminal disulfide units of the cluster. Mo-H bonds are formed only for quasi-linear species with Mo centers featuring empty coordination sites. Protonation leads to increased cluster stability against CID. The rich variety of CID dissociation products for the triply protonated [H3Mo3S13]+ ion, however, suggests that it has a large degree of structural flexibility, with roaming H/SH moieties, which could be a key feature of MoS x to facilitate HER catalysis via a Volmer-Heyrovsky mechanism.