Mass spectrometry (MS) in biochemical and biophysical research of complex carbohydrates has to meet a number of challenges if compared to other biomacromolecules, like proteins and nucleic acids. MS, as an universal and indispensible tool for analysis of biological samples after introduction of soft ionization techniques, like Fast Atom Bombardment (FAB), electrospray (ESI) and matrix-assisted laser desorption ionization (MALDI), allows a high degree of flexibility to develop protocols for investigations to be conducted in a systems biology way. Glycomics arises as a discipline encompassing evaluation and discovery of carbohydrate structure and function. Intact oligomers, analyzed in the gas phase as complex mixtures, render mass over charge (m/z) values reflecting molecular ion patterns which can be assigned to defined molecular compositions. Essential requirements for such MSbased protocols are high sensitivity, high resolution and high mass accuracy. Besides, the protocols to be performed on instruments fitted with fragmentation facilities add sets of data crucial for interpretation by sequencing. Ability for sequencing are given by distinct procedures for fragmentation, which deliver compatible data sets for identification and assignment of single components from complex mixtures. Fourier Transform Ion Cyclotron Resonance (FT-ICR) MS is rendering the highest quality of data with respect to its high mass accuracy and resolving power. By hyphenation of FT-ICR MS with chips and robots development of high throughput mass spectrometry for biomedical applications became available. Generation of computer-assisted calculations opens in combination with monosaccharide building block analysis a tool for rapid de-novo assignment. Validation of glycomics procedures is carried out within the HUPO HGPI initiative to ensure the quality of analytical data in glycomics life science projects.