An automated protein analyzer comprising: a homogenizer for reducing protein samples to small particles; a reaction vessel in material transfer communication with said homogenizer; a reservoir for binding dye composition in fluid communication with said reaction vessel; a metering pump in fluid communication with said reservoir and said reaction vessel for distributing discrete predetermined amounts of a binding dye composition to said reaction vessel; a filter in fluid communication with said reaction vessel for separating solids from filtrate after a dye binding reaction has taken place in said reaction vessel; a colorimeter in fluid communication with said filter and said reaction vessel for measuring the absorbance of the filtrate from said reaction vessel and said filter; and a pump, upstream of said colorimeter with respect to said reaction vessel, for transferring filtrate from said reaction vessel to said colorimeter, wherein the automated protein analyzer further comprises: a valve between said reservoir and said reaction vessel; and a fluid line between said valve and said colorimeter; so that binding dye solution from said reservoir can be directed to said reaction vessel or to said colorimeter based upon the position of said valve to automatically make reference measurements; and a processor in signal communication with said colorimeter; and memory in signal communication with said processor for storing the absorbance results from reference tests made of dyes directed directly from the reservoir to the colorimeter and from sample tests made of the dye filtrate remaining after a reaction with a protein sample, for comparing the absorbance of reference and sample tests, and for calculating the protein content of a sample based on the comparisons. a homogenizer for reducing protein samples to small particles; a reaction vessel in material transfer communication with said homogenizer; a reservoir for binding dye composition in fluid communication with said reaction vessel; a metering pump in fluid communication with said reservoir and said reaction vessel for distributing discrete predetermined amounts of a binding dye composition to said reaction vessel; a filter in fluid communication with said reaction vessel for separating solids from filtrate after a dye binding reaction has taken place in said reaction vessel; a colorimeter in fluid communication with said filter and said reaction vessel for measuring the absorbance of the filtrate from said reaction vessel and said filter; and a pump, upstream of said colorimeter with respect to said reaction vessel, for transferring filtrate from said reaction vessel to said colorimeter, a valve between said reservoir and said reaction vessel; and a fluid line between said valve and said colorimeter; so that binding dye solution from said reservoir can be directed to said reaction vessel or to said colorimeter based upon the position of said valve to automatically make reference measurements; and a processor in signal communication with said colorimeter; and memory in signal communication with said processor for storing the absorbance results from reference tests made of dyes directed directly from the reservoir to the colorimeter and from sample tests made of the dye filtrate remaining after a reaction with a protein sample, for comparing the absorbance of reference and sample tests, and for calculating the protein content of a sample based on the comparisons.