Protonex™ Red-latex bead conjugate demonstrated pH-dependent fluorescence. Unlike most of the existing fluorescent dyes that are more fluorescent at higher pH, acidic conditions enhance the fluorescence of Protonex™ Red-latex bead conjugate. The fluorescence of Protonex™ Red-latex bead conjugate dramatically increases as pH decreases from neutral to the acidic, making it a robust tool to study phagocytosis and its regulation by drugs and/or environmental factors. The lack of fluorescence outside the cell eliminates the wash steps. Protonex™ Red-latex bead conjugate provides a powerful tool to study phagocytosis. Protonex™ Red-latex bead conjugate is low fluorescent outside the cells, but fluoresce brightly red in acidic compartments (such as phagosomes, lysosomes and endosomes). This Protonex™ Red-latex bead conjugate can be also used for multiplexing cell functional analysis with green dyes such as GFP, Fluo-8®, calcein, or FITC-labeled antibodies. Protonex™ Red has the spectral properties similar to those of Texas Red, making the common filter set of Texas Red readily available to the assays of Protonex™ Red.