International Journal of Mass Spectrometry 219 (2002) 515–523 Irradiation effects in MALDI and surface modifications Part I: Sinapinic acid monocrystals I. Fournier, J.C. Tabet, G. Bolbach ∗ Laboratoire de Chimie Structurale Organique et Biologique, Université P&M CURIE, CNRS–UMR 7613, Boˆ ıte 45, 4 Place Jussieu 75252, Paris Cedex 05, France Received 25 January 2002; accepted 19 April 2002 Dedicated to Dr. Yannik Hoppilliard on the occasion of her 60th birthday. Abstract The origin of the irradiation effect on the ion production in MALDI processes, using large sinapinic acid crystal, was studied in conjunction with the surface modifications. Characterization of the crystal irradiated surfaces by a commercial N 2 laser, from which ion production was quenched at the normal laser threshold energy, with scanning electron microscopy and light microscopy show very dramatic modifications of the surface structure. Three main regions with different morphologies were observed. A region with small craters in the center of the spot, a strong perturbed contiguous area with hill–valley patterns and a bead periodical structure extending up to the rim of the spot. Periodical bead structure mainly is responsible for the disappearance of ion production. Theses structures are eliminated after one or two shots at high energy. The analysis of the uppermost layers of the irradiated and non-irradiated surfaces, performed by chemical ionization with quadrupole mass analyzer, indicates that the matrix, at surface, yields mainly to decarboxylated sinapinic acid. The physical properties of the modified matrix can be responsible for the structural changes on the irradiated target and the vanishing of ion production. (Int J Mass Spectrom 219 (2002) 515–523) © 2002 Elsevier Science B.V. All rights reserved. Keywords: MALDI; Irradiation effects; Ablation process; Ionization processes; Mechanisms 1. Introduction Although matrix-assisted laser desorption/ionization (MALDI) [1,2] is now a powerful tool in analysis and is extensively used especially in bioanalysis, ablation/ionizations processes are still not well un- derstood. Great instrumental developments have been realized the last 10 years but are still lacking a better understanding of the chemico-physical phenomena involved in MALDI. However, several studies have been dedicated to fundamental processes and differ- ∗ Corresponding author. E-mail: bolbach@ccr.jussieu.fr ent desorption and/or ionization models have been proposed. Nevertheless, some striking features remain difficult to interpret even in the frame of the models. For example, decreasing of signal intensity during a MALDI experiment is currently observed. In a previous paper, we described laser irradiation effects on sinapinic acid large crystals [1]. At the laser energy of the ion production threshold (matrix and peptide), the ion peak intensity decays with the number of laser shots and drops to zero after typically 120 laser shots. On the same spot, the ion signal can- not be recovered at the energy threshold at any time thereafter. However, one or two laser shots at high 1387-3806/02/$ – see front matter © 2002 Elsevier Science B.V. All rights reserved. PII S1387-3806(02)00704-2