Guidlines to Identify Proteins

identify protein

Fistly, there is a common question for this topic:

Q: How can you identify a protein?

A: to find its sequence of amino acids.

The answer is obviously right. However, the process is not a pice of cake. If you are professional, you should know the fact that using several restriction enzymes, running gels and finding masses and so on. After these complicated work, the result may be still confused, right?

Following is some simple but accurate performing process we’d like to share with you. That is how to identify proteins without sequencing. As we all know, proteins are unique in variable length chains and consisting of a variety of amino acids. So as a result, the mass technique, which may be affected by length and composition, should be the most easiest way to distinguish proteins.

However, many different proteins share the same mass. The mass spectrometry can only identify proteins with exact masses. What’s more, when multiple proteins come within a fraction of a dalton of each other, the accuracy of mass spectrometry technique is not useful anymore.

So how can we identify proteins uniquely? There are some suggestions from VMSL: “We know that each protein has a unique sequence, but we don’t want to go through the process of sequencing a protein, especially if the protein has already been identified and characterized by someone else. We know that we can measure protein masses with great accuracy using mass spectrometry, but that multiple proteins may weigh nearly the same. What we can do is take a few hints from how detectives can tell people apart: their fingerprints. If we were to take several different proteins and digest them with a restruction enzyme (for instance, trypsin), each protein would return a unique set of peptide fragments. These fragments can then be analyzed using mass spectrometry. By comparing these experimental fragments with the fragments of know proteins, the identity of a protein can either be proven or refuted.”

Source: http://svmsl.chem.cmu.edu/vmsl/protein/pt_bg2.htm