Conclusions:

• The Hypercarb porous graphite column demonstrated excellent separation for glycopeptide analysis, especially for short, hydrophilic peptides containing bi- or triantennary glycan chains. It allowed for their sensitive detection without any prior enrichment.

• Formation of metal adducts promoted evolution of higher-charge species, aiding ETD fragmentation of glycopeptides.

• ETD preserved labile glycans, facilitating the identification of both the peptide of interest and the site  of modification.

• Combining peptide structural information obtained by ETD and the glycan composition information obtained by CID enabled confident identification and characterization of glycopeptides within a single LC-MS analysis using an LTQ Orbitrap XL ETD mass spectrometer.

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