The dissociation mechanism of duplex DNA has been investigated in detail by collisioninduced dissociation experiments at different collision regimes. MS/MS experiments were performed either in a quadrupole collision cell (hybrid quadrupole-TOF instrument) or in a quadrupole ion trap with different activation times and energies. In addition to the noncovalent dissociation of the duplex into the single strands, other covalent bond fragmentation channels were observed. Neutral base loss from the duplex is favored by slow activation. In fast activation conditions, however, the major reaction channel is the noncovalent dissociation into single strands, which is highly entropy-favored. Fast activation regimes can favor the entropy-driven noncovalent dissociation, while in slow heating conditions the competition with enthalpy-driven covalent fragmentation can completely hinder the dissociation of the complex. We also evidence that the noncovalent dissociation of DNA duplex is a multistep process involving a progressive unzipping, preferentially at terminal positions. This is proposed to be a general feature for complexes containing a high number of contributing interactions organized at the interface of the ligands. The overall (observed) dissociation kinetics of noncovalent complexes can therefore depend on a complicated mechanism for which a single transition state description of the kinetics is too simplistic. [1][2][3][4] led to tremendous development of the study of noncovalent complexes by mass spectrometry. ESI gently transfers the complexes from the solution to the gas phase by a progressive desolvation assisted by collisions in the source [5], by heating in a capillary [6], or both. Once the intact complexes have been obtained in the gas phase, they can be studied by MS/MS collision-induced dissociation (CID) in quadrupoles [7][8][9], in ion traps [10,11], in ICR cells [12,13], blackbody radiation in ICR cells [14, 15, . . .], or in-source dissociation techniques (heated capillary dissociation [16,17], in-source CID [13, 18 -20]. All these methods give access to the relative dissociation kinetics of the complexes [21], which depends on the nature and the strength of the interactions between the constitutive units. Tandem mass spectrometry has therefore the potency to become a method of choice to probe the intrinsic interactions between biomolecules in the absence of solvent.Currently, the interpretation of the MS/MS on large complexes is still based on a simplistic view inherited from earlier studies on small molecules. The usual picture is based on the RRKM [22-26] (Rice-Rampsberger-Kassel-Marcus) statistical theory of unimolecular dissociation. The expression of the rate constant k(E) depends on an enthalpic term (the critical energy E 0 ), and on the activation entropy (through a degeneracy factor and the density of states of the reactant and the transition state). For large molecules, the link between the observed fragmentation yield and the microscopic characteristics of the complex is difficult to make ...