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Material decomposition methods are used to identify and quantify multiple tissue components in spectral CT but there is no published method to quantify the misidentification of materials. This paper describes a new method for assessing misidentification and mis-quantification in spectral CT. We scanned a phantom containing gadolinium (1, 2, 4, 8 mg/mL), hydroxyapatite (54.3, 211.7, 808.5 mg/mL), water and vegetable oil using a MARS spectral scanner equipped with a poly-energetic X-ray source operated at 118 kVp and a CdTe Medipix3RX camera. Two imaging protocols were used; both with and without 0.375 mm external brass filter. A proprietary material decomposition method identified voxels as gadolinium, hydroxyapatite, lipid or water. Sensitivity and specificity information was used to evaluate material misidentification. Biological samples were also scanned. There were marked differences in identification and quantification between the two protocols even though spectral and linear correlation of gadolinium and hydroxyapatite in the reconstructed images was high and no qualitative segmentation differences in the material decomposed images were observed. At 8 mg/mL, gadolinium was correctly identified for both protocols, but concentration was underestimated by over half for the unfiltered protocol. At 1 mg/mL, gadolinium was misidentified in 38% of voxels for the filtered protocol and 58% of voxels for the unfiltered protocol. Hydroxyapatite was correctly identified at the two higher concentrations for both protocols, but mis-quantified for the unfiltered protocol. Gadolinium concentration as measured in the biological specimen showed a two-fold difference between protocols. In future, this methodology could be used to compare and optimize scanning protocols, image reconstruction methods, and methods for material differentiation in spectral CT.