How can you identify a protein? The obvious answer is to find its sequence of amino acids; however, that is a long and painful process. It involves using several restriction enzymes and running gels and finding masses... a lot of work. And then there is the question whether the protein in question has been identified already. If it is, then all you would want to do is confirm its identity without performing very much work.

So how can you identify a protein without actually sequencing it? A good starting place would be to find out what makes the protein in question unique. Proteins are unique chains of variable length, made up of varying amino acids. One of the easiest ways to distinguish between proteins should be mass. After all, mass will be affected by length and composition.

Unfortunately, it is possible for many different proteins to have nearly the same mass. Mass spectrometry can help by giving almost exact masses. However, the accuracy of mass spectrometry is not particularly useful when multiple proteins come within a fraction of a dalton of each other.

The problem we are left with is how to uniquely identify proteins. 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.