Capillary liquid chromatography (cLC) and capillary electrophoresis (CE) have been critically compared for the separation of metalloproteins when using collision-cell inductively coupled plasma mass spectrometry (ICP-CC-MS) as detection system. For cLC separation, the selected column was a C ₈ (0.3 mm I.D.) and the separation conditions involved a gradient up to 80% methanol in 10 mM ammonium acetate buffer (pH 7.4). The low flow rate used (3 μL min ^-1) permitted the utilization of a high methanol content maintaining the sensitivity along the whole chromatographic run. For this purpose, a new low-flow interface has been developed based on a total consumption nebulizer. Similarly, CE has been studied as separation technique using a 75 μm I.D. fused silica capillary and a running buffer of 20 mM Tris-HNO ₃ (pH 7.4) and working at 30 kV. Metallothionein (mixture of MT-I and -II) and superoxide dismutase (SOD) have been used as protein models in order to evaluate the separation/detection capabilities using the same injection volumes in both systems (20 nL). For both hybrid systems, separation parameters such as retention factor, numbers of theoretical plates, tailing factor and resolution have been critically compared. Also, the analytical performance characteristics of both hybrid systems have been evaluated and tested by analyzing the Cu-, Zn-species present in red blood cell extracts in order to explore more adequate separation methodology for the analysis of metalloproteins in complex matrices.