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.