amaZon speed ETD: Optimization of CID Parameters for Improved Glycopeptide Fragmentation

CID fragmentation of glycopeptides leads to the generation of Y- and B-ions by cleavage of the attached glycan moiety whereas the peptide backbone remains intact. A good quality fragment spectrum is mandatory for successful structure identification, for instance with ProteinScape and GlycoQuest. This technical note shows the optimization of fragmentation cut-off, amplitude and time for successful glycopeptide fragmentation.