A protein analysis instrument and method are disclosed. The method includes mixing a binding dye composition and a protein sample using a homogenizer, measuring a parameter selected from the group consisting of the speed of the homogenizer and the resistance of the mixture to the homogenizer, adjusting the speed of the homogenizer based upon the measured parameter, pumping unreacted dye composition from the mixture and to a calorimeter, and measuring the absorbance of the dye composition in the calorimeter. Aspects of the invention also include inserting a spout into a sample cup at a position where the spout opening is positioned to avoid foam and precipitate generated by the mixing step and above the bottom of the sample cup and thereafter pumping the dye composition from the mixture in the sample cup through the spout and to a colorimeter.