Underivatized neutral oligosaccharides from human milk were analyzed by nano-electrospray ionization (ESI) using a quadrupole ion trap mass spectrometer (QIT-MS) in the negative-ion mode. Under these conditions neutral oligosaccharides are observed as deprotonated molecules [M ÏȘ H] ÏȘ with high intensity. CID-experiments of these species with the charge localized at the reducing end lead to C-type fragment ions forming a "new" reducing end. Fragmentations are accompanied by cross-ring cleavages that yield information about linkages of internal monosaccharides. Several isomeric compounds with distinct structural features, such as different glycosidic linkages, fucosylation and branching sites were investigated. The rules governing the fragmentation behavior of this class of oligosaccharides were elucidated and tested for a representative number of certain isomeric glycoforms using the MS/MS and MS n capabilities of the QIT. On the basis of the specific fragmentation behavior of deprotonated molecules, the position of fucoses and the linkage type (Gal â€133 GlcNAc or Gal â€134 GlcNAc) could be determined and linear and branched could be differentiated. Rules could be established which can be applied in further investigations of these types of oligosaccharides even from heterogenous mixtures. . It creates new demands for analytical tools for structure elucidation of complex oligosaccharides comprising composition, sequence, branching, and linkage analysis, including anomericity and finally also ring sizes and absolute configuration, i.e., identity of the subunits. Mass spectrometry (MS) offers the possibility of structural investigations of oligosaccharides; this has been demonstrated using fast atom bombardment (FAB-MS) [2,3]. Electrospray (ESI) MS and matrix-assisted laser desorption ionization (MALDI) MS have been applied to the investigation of carbohydrates of biological origin [4,5]. Their ability to deliver structural information on different levels depends on the mass analyzer coupled to the ion source. In general, mass spectrometry provides the possibility of structural elucidation based on characteristic fragmentations of the molecules under investigation. A nomenclature for the possible fragment ions of oligosaccharides has been proposed by Domon and Costello [6], i.e., B and C for fragment ions containing the nonreducing side, Y and Z for those containing the reducing sugar unit, as well as A and X type fragment ions for those arising from cross-ring cleavages.In MALDI-MS neutral oligosaccharides are usually observed as singly-cationized (typically sodiated) species [7], which offers a simple means for screening complex mixtures. As MALDI is mostly coupled to a time-of-flight (TOF) mass analyzer, options for structural analysis are restricted to metastable fragment-ion analysis post-source decay (PSD) [8]. Some successful attempts for structure elucidation have been made for underivatized and derivatized oligosaccharides by MALDI/PSD analysis [9 -15]. However, fragmentation is poorly controllable, but some...