Abstract Commercially available Coomassie Brilliant Blue R-250 (C.I. 42660) is a popular and useful dye that strains most proteins blue on polyacrylamide gels. Some proteins from brain (rubrophilin), collagens, histones and parotid gland proteins are distinctly red when stained with coomassie Blue. Commonly used Coomassie Brilliant Blue R-250 preparations may contain more than 30 distinct colored and fluorescent components that can be separated on silica gel chromatographic columns. A specific component has been isolated on silical gel columns that stains rubrophilin and other proline-rich proteins a reddish colr. Fast atom bombardment mass spectrometry of the isolated rubrophilin straining principle indicates a molecular weight of 634 as compared to 826 for the major dye in the original Coomassie Brilliant Blue R-250. Infrared spectrometry is consistent with a different between the rubrophilin straining principle and Coomassie Brilliant Blue R-250 of a toluene sulfonic acid residue.