Reference
Working out a peptide’s molecular weight
A peptide’s mass is not a property you look up — it is a consequence of its sequence, and you can calculate it with a table and a calculator. Which is what makes a mass spectrometry result something you can check rather than something you take on trust.
The arithmetic
Joining two amino acids releases a molecule of water. So the mass of a chain is not the sum of the free amino acids — it is the sum of what each contributes once it is in the chain, plus a single water molecule for the two free ends.
In practice you use residue masses, which already have that water subtracted. Add up the residues, add 18.02 for the termini, and you have the molecular weight.
Residue masses
Average masses in daltons. Note that leucine and isoleucine are identical — they contain the same atoms arranged differently, which is why mass alone can never tell them apart.
| Residue | Mass (Da) | Residue | Mass (Da) |
|---|---|---|---|
| Gly | 57.0519 | Asp | 115.0886 |
| Ala | 71.0788 | Gln | 128.1307 |
| Ser | 87.0782 | Lys | 128.1741 |
| Pro | 97.1167 | Glu | 129.1155 |
| Val | 99.1326 | Met | 131.1926 |
| Thr | 101.1051 | His | 137.1411 |
| Cys | 103.1388 | Phe | 147.1766 |
| Leu | 113.1594 | Arg | 156.1875 |
| Ile | 113.1594 | Tyr | 163.1760 |
| Asn | 114.1038 | Trp | 186.2132 |
| Water (both termini) | 18.0153 | ||
Two worked examples
Both of these are compounds whose names are their sequences, which makes them unusually easy to check — see how sequences are written.
GHK
| Gly | 57.0519 |
| His | 137.1411 |
| Lys | 128.1741 |
| Water | 18.0153 |
| Total | 340.38 Da |
KPV
| Lys | 128.1741 |
| Pro | 97.1167 |
| Val | 99.1326 |
| Water | 18.0153 |
| Total | 342.44 Da |
Those totals are computed from the table above rather than typed in, so if the table is ever wrong the examples will be wrong with it — which is the point. Check them against a published molecular weight for either compound and they should agree.
Why this is worth knowing
Mass spectrometry establishes identity by comparing a measured mass against the mass the sequence predicts. Knowing where the predicted figure comes from turns that from an assertion into something you can verify with a calculator.
It also makes several degradation routes legible. An oxidised methionine adds about 16 Da; a deamidated asparagine adds about 1 Da; a missing residue subtracts exactly that residue's mass from the table above. Each has a specific, recognisable size.
Two things the number cannot settle
- Leucine and isoleucine are identical in mass. No mass measurement distinguishes them.
- Nor are mirror images distinguishable — a D-residue weighs exactly what its L counterpart weighs.
Average masses are used above. Mass spectrometry often reports monoisotopic mass instead, calculated from the single most common isotope of each element, which gives slightly different figures. Comparing a monoisotopic measurement against an average calculation is a common way to convince yourself something is wrong when it is not.
