Peptide Molecular Weight Guide

The molecular weight of a peptide is the total mass of its atoms, found by adding up the masses of its amino acids. This guide explains the arithmetic behind the molecular weight calculator. It is not medical advice.

What the calculation means

Each amino acid in a chain loses a water molecule when it joins the next one. So the mass of each amino acid inside the chain is its residue mass, and the finished peptide has one extra water at the ends.

The formula

Peptide mass = sum of residue masses + one water (H₂O)
Water is 18.0153 Da (average) or 18.0106 Da (monoisotopic).

Average vs monoisotopic

Average mass uses the average atomic weights found in nature. It is the value used for weighing and for molar calculations.
Monoisotopic mass uses the most abundant isotope of each element. Mass spectrometers usually report values close to this.

Worked example (mathematical example only)

Gly-His-Lys (GHK). Average residue masses: Gly 57.0519, His 137.1411, Lys 128.1741. Sum = 322.3671. Add water 18.0153. Total = 340.38 Da (average).

Terminal modifications

N-terminal acetylation adds about 42.01 Da (monoisotopic). C-terminal amidation lowers the mass by about 0.98 Da (monoisotopic), because OH becomes NH₂.

What the calculator assumes

A linear peptide with a free N-terminus and a free C-terminus.
Only the 20 standard amino acids. Other residues, disulfide bonds, salts and other changes are not included.

Common mistakes

Forgetting to add the water.
Mixing average and monoisotopic values.
Using a mass that already includes a counter-ion or modification.

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Mathematical calculation only. Not medical advice.