In this work, atmospheric pressure photoionization was investigated for use in characterizing protein palmitoylation, which is a major post-translational modification of membrane proteins. The study focused on native and palmitoylated peptides originating from plasma membrane proteolipids, such as tetraspanins CD9 and CD151. Mass spectrometry experiments were performed using synchrotron radiation as a tunable UV source that provides optimal energy for photoionization (SR-APPI). In the positive ion mode, intense fragment ions corresponding to a. 6, candy ions were observed. Interestingly, these fragment ions conserved the palmitoyl modification, thus allowing for unambiguous structural characterization of the palmitoylated peptides. In-source fragmentation under APPI conditions offers a unique complement to conventional methods such as MS/MS, and the results demonstrate that APPI is a versatile and promising technique for the in-source characterization of post-translational modifications and top-down proteomics of membrane proteins. (C) 2012 Elsevier B.V. All rights reserved.