Polyanionic oligosaccharides such as dermatan sulfate (DS) and chondroitin sulfate (CS) exhibit poor ionization efficiencies and tend to undergo thermal fragmentation through the loss of SO 3 under conventional ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) conditions. A new ionic liquid matrix (ILM), a guanidinium salt of α-cyano-4-hydroxycinnamic acid, facilitates direct UV-MALDI mass spectrometric (MS) analysis of underivatized DS and CS oligosaccharides up to a decasaccharide in their common form as sodium salts. The resulting mass spectra show very low extent of fragmentation through an SO 3 loss. The new ILM is suitable for MALDI-MS analysis of mixtures containing oligosaccharides with different numbers of sulfo groups.The use of room-temperature ionic liquids as matrices is a fast growing area of matrixassisted laser desorption/ionization mass spectrometry (MALDI-MS) method development. Ionic liquid matrices (ILMs) have a number of advantages over conventional crystalline matrices including the homogeneity of the analyte-matrix mixture and high vacuum stability of the matrix. 1,2 ILMs have been shown effective in MALDI-MS analysis of several classes of biological molecules including peptides and proteins, 3 phospholipids, 4 oligonucleotides, 5 and neutral oligosaccharides. 6 The goal of this work was to develop a facile MALDI-timeof-flight (TOF)-MS method for the characterization of glycosaminoglycan (GAG)-derived oligosaccharides using an ILM.When analyzed by mass spectrometry, GAG-derived oligosaccharides have a tendency to fragment through the loss of SO 3 (Δ −102 m/z). In electrospray ionization (ESI) mass spectrometry, these polysulfated, polycarboxylated oligosaccharides often result in several peaks, corresponding to intact oligosaccharide and fragments due to the SO 3 loss, 7 each of which can be sodiumcationized, protonated, or both and have various charge states. 8 The advantage of MALDI is that multiply charged species are not observed in the reflector mass spectra, 9 simplifying data interpretation as compared to the ESI mass spectra. However, due to their thermal lability, poor ionization efficiency, and a tendency to undergo extensive Na/H exchange, polyanions such as GAG-derived oligosaccharides are rarely analyzed by MALDI-MS, and methods for such analysis are scarce.To date, a very few methods have been reported for MALDI-MS analysis of underivatized GAG-derived oligosaccharides. 10-12 A peptide complexation method described by Juhasz and Biemann 13,14 allows the detection of polysulfated oligosaccharides by MALDI-MS in a form of noncovalent complexes with basic peptides, (Gly-Arg) n , where n exceeds the number of sulfo groups in the oligosaccharide by one. While this method is sensitive and affords MALDI mass spectra in which SO 3 loss is suppressed, 15 it is limited by the availability of synthetic peptides. Recently, we reported a successful MALDI-MS analysis of sodium salts of an octasulfated disaccharide and an octasulfated pentasaccharide in their uncomp...