Data dependent acquisition (DDA) of higher collision energy dissociation (HCD)-MS2 followed by electron transfer dissociation (ETD)-MS2 upon detection of glycan-specific oxonium is one of the better approaches in current LC-MS2 analysis of intact glycopeptides. Taking advantage of a new tri-hybrid Orbitrap configuration, we have experimented with adding in a parallel ion trap collision induced dissociation (CID)-MS2 data acquisition to the original HCD-product dependent (pd)-ETD function. We demonstrated the feasibility and advantage of identifying the peptide core ion directly from edited HCD-MS2 data as an easy way to reduce false positives without compromising much sensitivity in intact glycopeptide positive spectrum matches. Importantly, the additional CID-MS2 data allows validating the glycan assignment and provides insight into possible glycan modifications. Moreover, it is a viable alternative to deduce the glycopeptide backbone particularly in cases when the peptide backbone cannot be identified by ETD/HCD.