Quantitative proteome analyses suggest that the well-established stain colloidal 
Coomassie Blue, when used as an infrared dye, may provide sensitive, 
post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. 
Considering the central role of two-dimensional gel electrophoresis in top-down 
proteomic analyses, a more cost effective alternative such as Coomassie Blue 
could prove an important tool in ongoing refinements of this important 
analytical technique. To date, no systematic characterization of Coomassie Blue 
infrared fluorescence detection relative to detection with SR has been reported. 
Here, seven commercial Coomassie stain reagents and seven stain formulations 
described in the literature were systematically compared. The selectivity, 
threshold sensitivity, inter-protein variability, and linear-dynamic range of 
Coomassie Blue infrared fluorescence detection were assessed in parallel with 
Sypro Ruby. Notably, several of the Coomassie stain formulations provided 
infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly 
exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie 
Blue infrared fluorescence detection was found to significantly exceed that of 
Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted 
fluorescence response, Sypro Ruby was able to detect a few additional protein 
spots, amounting to 0.6% of the detected proteome. Thus, although both detection 
methods have their advantages and disadvantages, differences between the two 
appear to be small. Coomassie Blue infrared fluorescence detection is thus a 
viable alternative for gel-based proteomics, offering detection comparable to 
Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the 
cost.