In “Calculating Protein Mass”, we briefly mentioned an analytic chemical method called mass spectrometry,
which aims to measure the mass-to-charge ratio of a particle or a molecule.
In a mass spectrometer, a sample is vaporized (turned into gas), and then particles
from the sample are ionized.
The resulting ions are placed into an electromagnetic field, which separates them based on their charge and mass. The output of
the mass spectrometer is a mass spectrum, or a plot of ions' possible mass-to-charge ratio values with
the intensity (actual observed frequency) of ions having these mass-to-charge values.
For the moment, we will ignore charge and consider a list of the ions' monoisotopic masses as a simplified spectrum.
Researchers do not possess cheap technology to go in and examine a protein one amino acid at a time
(molecules are too submicroscopic). Instead, to determine a protein's structure,
we will split several copies of the protein into smaller pieces, then weigh the resulting fragments.
To do this, we assume that each cut (breakage point) occurs between two amino acids
and that we can measure the mass of the resulting pieces for all possible cuts.
For example, the (unknown) protein "PRTEIN" can be cut in five possible ways: "P" and "RTEIN";
"PR" and "TEIN"; "PRT" and "EIN"; "PRTE" and "IN"; "PRTEI" and "N".
We then can measure the masses of all fragments, including the entire string. The "left" end of a protein
is called its N-terminus, and the ions corresponding to the protein string's prefixes
(P, PR, PRT, PRTE, PRTEI) are called b-ions.
The "right" end of the protein is called its C-terminus, and the ions corresponding
to the string's suffixes (N, IN, EIN, TEIN, RTEIN) are called y-ions.
The difference in the masses of two adjacent b-ions (or y-ions)
gives the mass of one amino acid residue; for example, the difference between the
masses of "PRT" and "PR" must be the mass of "T." By extension, knowing the masses of
every b-ion of a protein allows us to deduce the protein's identity.
