Mass Spectrometry of Amino Acids and Proteins

Likemostmatter (with the exception of, say, neutron stars), proteins and peptides are mostly made of nothing – an ephemeral cloud of electrons with very little mass surrounding tiny and very dense atomic nuclei that contain nearly all of themass (i.e., peptides and proteins aremade of atoms). Atoms havemass and the unit ofmass that is most convenient to use is called the atomic mass unit (abbreviated amu or u) or in biological circles a Dalton (Da). Over the years, physicists and chemists have argued about what standard to use to define an atomicmass unit, but the issue seems to have been settled in 1959 when the General Assembly of the International Union of Pure andApplied Chemistry defined an atomicmass unit as being exactly 1/12 of themass of the most abundant carbon isotope (C) in its unbound lowest energy state. Therefore, one atom of C has a mass of 12.0000 u. Using this as the standard, one proton has a measured mass of 1.00728 u and one neutron is slightly heavier at 1.00866 u. One C atom contains six protons and six neutrons, the sum of which is clearly more than the mass of 12.0000 u. A carbon atom is less than the sum of its parts, and the reason is that the protons and neutrons in a carbon nucleus are in a lower energy state than free protons and neutrons. Energy and mass are interchangeable via Einstein’s famous equation (E1⁄4mc), and so this “mass defect” is a result of the nuclear forces that hold neutrons and protons together within an atom. This mass defect also serves as a reminder of why people like A. Q. Khan are so dangerous [1]. Each element is defined by the number of protons per nucleus (e.g., carbon atoms always have six protons), but each element can have variable numbers of neutrons. Elements with differing numbers of neutrons are called isotopes and each isotope possesses a different mass. In some cases, the additional neutrons result in stable isotopes, which are particularly useful inmass spectrometry (MS) in amethod called