In contrast to proteomics significantly less efficient analytical tools are presently available for high throughput glycomics using mass spectrometry. In this article, a strategy to use the 0,2 A n ring cleavage ion at the reducing end of free glycans as a diagnostic ion for assignment of free glycans, in presence of glycopeptides containing similar glycosylation patterns, is presented for rapid distinction in complex mixtures by mass spectrometry. The MS to MS/MS automatic switching, already previously introduced for the on-line LC-MS and CE-MS analysis, is shown in this contribution to be highly functional to obtain diagnostic fragmentation patterns of free glycan precursors in rapid screening of highly complex glycoconjugate mixtures obtained from clinical samples, namely from the urine of patients suffering from congenital disorders of glycosylation. Congenital disorders of glycosylation (CDG) are inherited metabolic diseases based on defects in the glycosylation pathways of glycoconjugates. The urine of CDG patients was reported to contain O-glycans and glycosylated amino acids at concentrations two to three orders of magnitude higher in comparison with the healthy control, characterized by a high degree of heterogeneity concerning the type, number, and values of molecular ions. Using the 0,2 A n ring cleavage ion approach by tandem MS, it was possible to sort out free glycans and get them assigned. , but an assignment of a carbohydrate structure from a single experiment still represents a major task. A number of techniques has been applied for structural elucidation of components in carbohydrate mixtures, basically attempting to find diagnostic fragment ions responsible for single structures [2][3][4][5][6][7][8][9][10][11][12][13]. The possibility to obtain distinct fragmentation patterns under controlled collision energy and gas conditions along with the ability of automatic switching between MS and MS/MS mode by electrospray quadrupole time-of-flight Q-TOF instrument, represents a powerful option for high-throughput analysis of complex carbohydrate mixtures. This technique can be another option for such rapid investigation in combination with fully automated chip-ESI-QTOF-MS for high-performance glycoscreening and sequencing, developed by our group [14].The electrospray ionization followed by formation of fragment ions by collision-induced dissociation allows sensitive mapping and sequencing of oligosaccharides for identification. In general, carbohydrates undergo two different types of fragmentation: those of glycosidic cleavages and those of cross-ring fragmentation. For sequencing, glycosidic cleavages along the chain B, C, Y, Z and those from the internal oligosaccharide chain B/Y, C/Y, are major tools for structural elucidation (nomenclature by Domon and Costelo [15]). According to the cross-ring fragmentation linkage and branching patterns can be established.In this context, the formation of a D fragment ion was previously found to be diagnostic for the differentiation of isomeric triantennary N-g...