Apparatus and methods for automatic amino acid sequencing of a glycopeptide by mass spectrometry. The glycopeptide is fragmented by higher energy collision dissociation fragmentation, and sequentially fragmented by collision induced dissociation fragmentation. The glycopeptide Y1 ion is isolated, and the mass spectra of fragmented glycopeptide Y1 ions provide mass spectral peaks corresponding to the amino acid sequence of the glycopeptide.