The utility of post-source decay (PSD) matrix-assisted laser desorption/ionization time-offlight mass spectrometry (MALDI-TOF-MS) was investigated for the structural analysis of phosphatidylcholine (PC). PC did not produce detectable negative molecular ion from MALDI, but positive ions were observed as both [PCϩH] ϩ and [PCϩNa] ϩ . The PSD spectra of the protonated PC species contained only one fragment corresponding to the head group (m/z 184), while the sodiated precursors produced many fragment ions, including those derived from the loss of fatty acids. The loss of fatty acid from the C-1 position (sn-1) of the glycerol backbone was favored over the loss of fatty acid from the C-2 position (sn-2). Ions emanating from the fragmentation of the head group (phosphocholine) included ϩ , ϩ and ϩ , which corresponded to the loss of trimethylamine (TMA), non-sodiated choline phosphate and sodiated choline phosphate, respectively. Other fragments reflecting the structure of the head group were observed at m/z 183, 146 and 86. The difference in the fragmentation patterns for the PSD of [PCϩNa] ϩ compared to [PCϩH] ϩ is attributed to difference in the binding of Na ϩ and H ϩ . While the proton binds to a negatively charged oxygen of the phosphate group, the sodium ion can be associated with several regions of the PC molecule. Hence, in the sodiated PC, intermolecular interaction of the negatively charged oxygen of the phosphate group, along with sodium association at multiple sites, can lead to a complex and characteristic ion fragmentation pattern. The preferential loss of sn-1 fatty acid group could be explained by the formation of an energetically favorable six-member A s major constituents of cell membranes, phospholipids (PL) have an essential role in regulating biophysical properties, protein sorting and cell signaling pathways. Structurally, PLs are diacyl(alkyl)glycerols esterified to a phosphate-containing polar head group. The nature of the head group dictates the particular PL class. PL molecular species are defined by the nature of the acyl (alkyl) residues attached to the C-1 (also called sn-1, using stereospecific numbering) and C-2 positions (sn-2) of the glycerol backbone. The molecular species are uniquely and differentially distributed among different tissues [1,2], and because of their importance in regulating development, function and adaptation [3][4][5], analysis of PL molecular species and their alterations is of considerable interest in many areas of biological research.Thin layer chromatography (TLC) [6 -8] and normal-phase high performance liquid chromatography (HPLC) [9,10] are well suited for the separation of PL classes, whereas the separation of molecular species within each class may be accomplished using gas chromatography (GC) [11,12] or reversed-phase HPLC [13][14][15] (see [5] for a review on lipid molecular species analysis). Conversion of PL species to GCsuitable derivatives is laborious and time consuming, and often results in analyte loss. Moreover, HPLC can