The arithmetic of chains

Look up glycine and you find 75.03203 Da. Look up a glycine inside a peptide chain and you find 57.02146 Da. Both are right. The second number is what sequences are built from, and the difference between them is exactly one water molecule.

A residue is an amino acid minus water

When two amino acids join, the carboxyl group of one and the amino group of the other form a peptide bond and release H₂O. Each amino acid in the chain has therefore lost a water’s worth of atoms, and what is left of it is called a residue. For glycine, C2H5NO2 becomes C2H3NO.

glycine            C2H5NO2   75.03203 Da
− water            H2O       18.01056 Da
= glycine residue  C2H3NO    57.02146 Da

Adding up a chain

A linear peptide with ordinary free ends is the sum of its residues plus one water: the chain still carries a hydrogen at the N-terminus and a hydroxyl at the C-terminus that no bond consumed. For Gly-Ala-Gly:

Gly  57.02146
Ala  71.03711
Gly  57.02146
H2O  18.01056
───────────────
     203.09061 Da   (C7H13N3O4)

A mass spectrometer does not report the neutral molecule. It reports an ion, most often the molecule plus a proton, [M+H]⁺, which adds 1.00728 Da; for Gly-Ala-Gly that is 204.0979. Modifications change the sum too: a disulfide bridge removes two hydrogens, an amidated C-terminus swaps OH for NH₂. The sequence mass calculator does the unmodified arithmetic for any sequence.

The twenty residues