Methods are provided for detecting, separating, isolating and quantifying contaminants in starting materials by separating the contaminant from the starting material using a bead coupled to an affinity moiety and quantum dot-labeling the contaminant. The contaminant is detected by the characteristic emission spectrum of the quantum dot. Also, competitive binding methods are provided wherein the starting material and a control material are contacted with a quantum dot coupled to an affinity moiety capable of binding the contaminant and a competitor complex. A decrease in the intensity of the characteristic emission spectrum of the quantum dot associated with the competitor complex from the starting material as compared to that of the control material is indicative of the presence of the contaminant in the starting material.