Glycosyl inositol phosphoceramides (GIPC) are the main sphingolipids in plants, and optimization of their extraction and detection is still in the focus of research. Mass spectrometry provides new options for the analysis and structural elucidation of this complex class of lipids. The coupling of linear ion trap and orbitrap (LTQ Orbitrap) enabled various fragmentation experiments (MS(2), MS(3)) by collision-induced dissociation (CID) and pulsed-Q dissociation (PQD). For structural analysis, GIPC-fragment ions were detected in the positive and negative ion mode with exact masses; therefore, fragmentation patterns were observed and finally structures have been characterized regarding polar head group, fatty acid, and sphingoid base. GIPC profiling was performed for spinach, white cabbage, sunflower seeds, and soybeans. The total GIPC concentration in these plants ranged from 1.1 to 88.4 μg/100 g dry weight with t18:1/h24:0 as the main ceramide structure and hexose-hexuronic acid-inositol phosphate and N-acetylhexosamine-hexuronic acid-inositol phosphate as polar head groups.