After protein separation, proteins need to be distinguished somehow. That is why scientists perform a process called protein staining – a color-producing reaction where a dye binds with a protein and makes it visible. There are several different dyes that researchers can stain proteins with.

Coomassie Blue Dyes

This is the most common dye used to detect proteins. The reason is because Coomassie blue dyes can effectively make proteins visible in a short period of time. It is also inexpensive and easy to use. The biggest advantage of this stain is that it doesn't permanently change proteins. They can be efficiently recovered because the dye can be removed easily. However, the limitation of this method is it takes more time and reagents to stain and then un-stain the target protein. 

Coomassie blue dye connects to parts of proteins that are basic and hydrophobic. When the proteins are placed in an acidic buffer solution, they change from a light-brown color to a dark-blue color. 

Silver Stains

This stain is a little bit more sensitive than Coomassie blue dye and more expensive. The silver stain is used both in basic and acidic solutions, making it easy to use. However, due to its sensitivity, it might be difficult to separate the silver stain and the target protein. If scientists want to use this method of protein staining, they need to decide whether or not it is necessary to recover as much protein as possible. 

Zinc Stains

While Coomassie blue dyes and silver stains directly stain the target protein, zinc stains work quite the opposite; they stain not the protein itself but the area around it. The whole process takes approximately 15 minutes. Just like blue dyes, zinc stains can be simply removed from proteins, making them easily recoverable. 

Fluorescent Dyes and Stains

These stains are usually the most expensive due to their fluorescence. Some of them are as sensitive as silver stains, while some are sensitive like Coomassie blue dye. Just like blue, zinc, and silver stains, fluorescent dyes target the protein, sometimes modifying it. However, even if the protein was modified, it is not permanent. Protein staining is usually fast with fluorescent dyes – the process takes place within an hour. Some of them are also environmentally friendly, meaning scientists can safely dispose of them.