Mass spectrometry has become the method of choice for glycopeptide characterization. Beside the instrumental setup an appropriate software solution is necessary to support glycopeptide identification and reduce time-consuming processing and de novo analysis time. GlycoQuest (search algorithm in ProteinScape) is Bruker’s well-established solution and provides reliable results in terms of glycopeptide identification.

This technical note describes a new optimized classification workflow for glycopeptides analysed with the Glycopeptide Instant Expertise™ acquisition method (QTof series).