Protein samples submitted for routine separation and analysis by two-dimensional electrophoretic techniques are often a mixture of proteins from different species, cell types, subcellular components, or even unknown contaminants. Varying amounts of individual components can account for many of the major effects seen in an experiment and can mask other, more subtle changes. This paper presents methods for estimating the percentages of these components in a mixture and procedures for correcting for their presence. The methods are tested by using a simple data set composed of differing amounts of two pure fractions.