In a recent paper (Setz, P. D.; Knochenmuss, R. Phys. Chem. A 2005, 109, 4030 -4037) energy-transfer from excited matrix molecules to fluorescent traps was used to study the role of pooling reactions for the ionization processes in matrix-assisted laser desorption ionization (MALDI) using 2,5-dihydroxybenzoic acid as matrix. Exciton trapping was shown to interfere with matrix ionization. These investigations were extended to analyze the influence of fluorescent traps on both matrix and analyte ions for ␣-cyano-4-hydroxycinnamic acid and further matrices. A strong influence of the fluorescent traps on both matrix and analyte ionization was revealed, depending on the matrix:trap ratio, and manifested itself differently for low and high mass analytes. (MALDI) has become an enabling technology for the fields of protein mass spectrometry (MS) and proteomics. Despite its widespread use, e.g., for protein identification via peptide mass fingerprinting [4], a comprehensive model for the generation of free gasphase ions has not yet been developed [5,6]. All matrices in use today have been found empirically and stem from the early days of MALDI, such as ␣-cyano-4-hydroxycinnamic acid (CHCA) [7]. With regard to analyte ionization, the essential role of protonated matrix species was already discussed in the early MALDI papers proposing that the central reaction of analyte ionization in the positive ion mode is a proton transfer from protonated matrix species to analyte molecules. A so-called "photochemical" ionization model was proposed by Ehring et al. [8]; energy pooling processes and resonant two-step absorption were assumed to occur and to facilitate the generation of the primary radical cation matrix species for which more than one UV photon is needed. Karbach et al. experimentally determined the ionization potential of 2,5-DHB to be higher than the energy content of two 337 nm UV photons [9]. Resonant two-step absorption is only possible taking into consideration that the missing energy is contributed by the thermal energy of the matrix system. This photo/ thermal ionization model was analyzed more in detail by Allwood et al. [10]. Different authors proposed the possibility of energy pooling processes of two neighboring (localized) excited molecules (multicenter ionization model) [8,11,12] with higher ionization efficiency than resonant two-step absorption processes. This model was further extended by Setz et al. proposing mobile matrix excitations [13].Laser excitation also induces the MALDI ablation and evaporation process above a distinct threshold fluence. Theoretical investigations of the MALDI process on the basis of the breathing sphere model predict two desorption mechanisms: thermal vaporization of single molecules up to small clusters (four molecules or less) and ablation of large clusters at higher laser fluences [14 -16]. The mechanistic discussions and considerations have been carefully reviewed by Dreisewerd [17]. Moreover, it is included in the considerations that the diverging initial velocities as m...