if the mobile phase contains solvents with a higher proton affinity than water, proton-transfer reactions take place that lead to protonated the solvent with higher proton affinity. for example, when methanol solvent is present, the cluster solvent ions would be choh(ho)(choh). fragmentation does not normally occur inside the apci source. if a fragment ion of a sample is observed, thermal degradation has taken place by the heated nebulizer interface, followed by the ionization of the decomposition products.