How peptides are synthesised
Last updated: 11 September 2026
Purity figures make more sense once you know where impurities come from. Most research peptides are made by solid-phase synthesis, and the characteristic impurities of that process are a direct consequence of how it works.
Solid-phase synthesis, briefly
The chain is built one amino acid at a time on a solid resin support. Each cycle couples the next amino acid, then removes a protecting group so the following one can attach. The finished chain is cleaved from the resin and purified.
Building on a support is what makes the process practical: excess reagents and by-products are washed away at every step rather than separated at the end.
Where impurities come from
Coupling is not perfect at every cycle. A step that fails leaves a chain missing one residue — a deletion sequence — which is chemically very similar to the target and therefore hard to separate. Incomplete deprotection, side reactions on reactive residues, and truncated chains contribute the rest.
Longer sequences accumulate more of these, which is why purity is harder to achieve at length (see what a purity percentage proves). It is also why a deletion sequence is the impurity most likely to survive purification: it is nearly the right molecule.
What this means for a certificate
Chromatographic purity separates the target from these related substances, which is exactly what makes the method appropriate (HPLC and mass spectrometry answer different questions) — the impurities of concern are peptide-like and do appear as peaks. What it does not capture is residual solvent, counter-ion content or water, which come from the cleavage and purification steps and are not chromatographic peaks.
That is the concrete reason a purity percentage and a full certificate are different things, and it is covered further at what a purity percentage proves.
Frequently asked questions
What is solid-phase peptide synthesis?
Building a peptide chain one amino acid at a time on a solid resin support, washing away excess reagents at each step, then cleaving and purifying the finished chain.
What is a deletion sequence?
A chain missing one residue because a coupling step failed. It is chemically close to the target, which makes it the impurity most likely to survive purification.
Why is purity harder for longer peptides?
Because every coupling cycle has a small failure rate, and a longer sequence has more cycles for those failures to accumulate across.
This page is educational and intended for research and informational use only. It is not medical advice, a treatment recommendation, or dosing guidance, and it makes no claims about outcomes. Body Pharm EU supplies research-grade materials for laboratory use. These statements have not been evaluated by the EMA.