A powerful method for detailed structural analysis based on electrospray ionization high-capacity ion-trap multiple-stage mass spectrometry (MS) is for the first time introduced in glycolipidomics. The method was optimized for accurate structural elucidation of human brain gangliosides and specifically applied to normal adult human hippocampus-associated structures. The multiple-stage MS experiments reported here allowed for a complete structural characterization of the oligosaccharide moiety of a GM1 ganglioside species. This was achieved by elucidating the sequence and identification of the GM1a structural isomer from the sialic acid attachment site at the neutral oligosaccharide chain. Moreover, the determination of the d18:1/18:0 sphingoid base/fatty acid composition of the ceramide moiety could be confirmed by this method. The novel protocol developed here proves high potential for rapid, reliable, and reproducible investigation of complex lipid-linked carbohydrates such as polysialylated gangliosides or species carrying some other groups that easily cleave off.