Instrument tuning commonly used for peptide analysis and for proteomics causes a high degree of fragmentation for glycopeptides. This results in a strongly biased glycosylation pattern. To obtain correct results for glycopeptides, both the cone voltage and the collision energy has to be reduced significantly. A suitable standard for tuning the instrument for glycopeptide analysis is aspartic acid (which fragments under similar conditions as glycopeptides); while low mass sugar fragments (for example, at 657.3 Da) are good indicators for the presence/absence of glycopeptide fragmentation.

Keywords: N-glycosylation, glycopeptide, glycoprotein, mass spectrometry, MS/MS, energy dependence, fragmentation, proteomics, glycomics