Cy3-Tris NTA compound is used as a sensitive fluorescent probe for detecting polyhistidine-labeled proteins in cells, solution and solid surfaces. In combination with other color tris-NTA compounds (such as #12615 and #12617), it can be used for multicolor analysis of polyhistidine-tagged proteins. Fluorescent tris-NTA compounds provide an efficient method for site-specific and stable noncovalent fluorescence labeling of polyhistidine-tagged proteins. In contrast to the transient binding of conventional mono-NTA, the multivalent interaction of tris-NTA conjugated fluorophores form a much more stable complex with polyhistidine-tagged proteins. The high selectivity of tris-NTA compounds toward cumulated histidines enable the selective labeling of proteins in cell lysates and on the surface of live cells. Fluorescent tris-NTA conjugates can be applied for the analysis of a ternary protein complex in solution and on surfaces. The transition metal ions (e.g., Ni ion)-mediated complexation of polyhistidine-labeled proteins with fluorescent tris-NTA conjugates provides a sensitive reporter for detecting and monitoring protein-protein interactions in real time.