The relative signal intensities of [M + H]+ vs [M + Na]+ ions of some small peptides were found to be highly matrix‐dependent in matrix‐assisted laser desorption/ionization (MALDI) experiments when sinapinic acid, α‐cyano‐4‐hydroxycinnamic acid and 2,5‐dihydroxybenzoic acid were used as matrices. Presumably, this observation results from the competition of two different mechanisms for the ionization steps. Possible mechanisms for the formations of [M + H]+ and [M + Na]+ ions are proposed and discussed in the pursuit of defining the ionization step in MALDI. Several experiments were designed and performed for the further refinement of the mechanism. The results suggest that proton transfer from a matrix molecule to an analyte plays an important role in the ionization step. The transferring proton may be derived from photoionized or electronically excited matrix molecules. In contrast, some data are most consistent with a gas‐phase mechanism for [M + Na]+ ions.
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