Mass spectrometry (MS) has become the most popular technique in the analysis of complex biomolecules such as glycoproteins and carbohydrates. Standardized methods for the assessment of the protein primary structure using proteolytically derived peptides have been successfully implemented in high-throughput proteomics work-¢ows based on tandem MS fragmentation data (Mann et al. 2001). The preceding sequencing of the genome contributed signiˆcantly to the ability of tandem MS to identify proteins and the success of current standard proteomics work¢ows.