Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) is applied for the investigation of C(2)-ceramide complexes with transition metal ions. Ceramide plays an important role in the regulation of various signaling pathways leading to proliferation, differentiation or apoptotic cell death. The formation and fragmentation of doubly charged cluster ions as well as singly charged cluster ions of C(2)-ceramide with transition metal ions (Mn(2+), Fe(2+), Co(2+) and Ni(2+)) are studied by ESI-MS/MS in the positive mode. Tube lens offset voltage and concentrations of C(2)-ceramide and transition metals are optimized to determine the best conditions for generating doubly charged cluster ions. The fragmentation pathways of metal ion complexes with C(2)-ceramide and the compositions of these complexes are determined by collision induced dissociation (CID). All transition metal ions (Mn(2+), Fe(2+), Co(2+) and Ni(2+) except Cu(2+)) shows similar complexation with C(2) ceramide. The unique complexation behavior of copper(II) is responsible for the different geometry of the complexes and relatively lower affinity of ceramide to copper(II) than those to other transition metals.