Terminal capping: N-acetylation and C-terminal amidation
Last reviewed 2026-10-10 · Sable Peptides · Research use only
Sable research method explainer. Updated 2026-10-10. Research use only.
Short answer
A plain linear peptide has a free amine at its N-terminus and a free carboxylic acid at its C-terminus. Many synthetic and natural peptides have one or both ends capped. An acetyl group (Ac-) on the N-terminal amine and an amide (-NH2) in place of the C-terminal acid are the two most common caps. Each removes a charge at that end and blocks exopeptidases that need a free terminus.
Reading the notation
Ac- at the start of a sequence means N-acetylation. SNAP-8 is written Ac-Glu-Glu-Met-Gln-Arg-Arg-Ala-Asp-NH2, so it is capped at both ends. Thymosin alpha-1 is a 28-residue N-terminally acetylated peptide.
-NH2 at the end means a C-terminal amide. Oxytocin, gonadorelin, triptorelin, kisspeptin-10, GHRP-6, ipamorelin and SS-31 all end in an amide.
-OH at the end, where shown, means a free acid. Melanotan II and PT-141 share the same lactam-bridged core, but Melanotan II ends in an amide and PT-141 in a free carboxylic acid. Comparing their formulas on the /ref pages shows the one-unit mass difference this causes.
Some N-terminal residues form their own cap. Pyroglutamate (pGlu), at the start of gonadorelin and triptorelin, is a cyclised glutamine or glutamate with no free amine.
What the caps change
Charge. At neutral pH a free N-terminus is mostly protonated (+1) and a free C-terminus mostly deprotonated (-1). Acetylation removes the positive charge and amidation removes the negative one. This shifts the isoelectric point and can change solubility and HPLC retention.
Mass. Acetylation adds C2H2O, about 42.04 g/mol. Amidation replaces -OH with -NH2, a change of about -0.98 g/mol. That is small, but it is easily resolved by mass spectrometry, and it is one reason the expected mass on a certificate must match the exact capped structure.
Protease susceptibility. Aminopeptidases and carboxypeptidases act on free termini. Capping is a common way to slow this. Li and colleagues reported that N-terminal acetylation improved the stability of an antimicrobial peptide against protease degradation in their assays (Li et al., 2021).
Where the caps come from
In solid-phase synthesis the C-terminal amide is set by the choice of resin: amide-forming resins release a peptide amide on cleavage. N-acetylation is done on the resin as a final step, with acetic anhydride, before cleavage. In nature, C-terminal amides are made enzymatically from glycine-extended precursors, a route that has also been adapted for production (Merkler, 1994).
Why it matters when checking identity
Uncapped or partly capped variants are typical related impurities. A free-acid variant of an amidated peptide differs by about 1 Da and may elute close to the main peak. Make sure the formula you compare against is the capped form given on the /ref page. Sable checks identity against the expected mass of the capped structure, and the certificate for your batch is available for every lot at /coa. Sable Peptides has been operating since 2019 and supplies every compound mentioned here as laboratory research material only. Nothing on this page is advice on use in people or animals, and no administration or medical-use information is provided.
Key terms
- N-terminus
- The end of the chain with the free alpha-amine (unless capped).
- C-terminus
- The end with the free alpha-carboxyl (unless capped).
- Acetylation
- Adding an acetyl group (CH3CO-) to an amine.
- Amidation
- Converting a carboxylic acid (-COOH) to a primary amide (-CONH2).
- Pyroglutamate (pGlu)
- A cyclised N-terminal glutamine or glutamate with no free amine.
Common questions
What does -NH2 at the end of a sequence mean?
A C-terminal amide in place of the free carboxylic acid.
How much mass does N-acetylation add?
About 42.04 g/mol (C2H2O).
What is the difference between Melanotan II and PT-141?
They share a lactam-bridged core. Melanotan II ends in an amide and PT-141 in a free acid.
Related explainers
- Cyclic vs linear peptides: what ring closure changes
- Monoisotopic vs average mass: reading peptide mass data
Related reference pages
Sources
- Li Y, et al. N-terminal acetylation of antimicrobial peptide L163 improves its stability against protease degradation. J Pept Sci. 2021;27. https://doi.org/10.1002/psc.3337
- Merkler DJ. C-terminal amidated peptides: production by the in vitro enzymatic amidation of glycine-extended peptides and the importance of the amide to bioactivity. Enzyme Microb Technol. 1994;16(6):450-456. https://doi.org/10.1016/0141-0229(94)90014-0
- Merrifield RB. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J Am Chem Soc. 1963;85:2149-2154. https://doi.org/10.1021/ja00897a025
Questions
What does -NH2 at the end of a sequence mean?
A C-terminal amide in place of the free carboxylic acid.
How much mass does N-acetylation add?
About 42.04 g/mol (C2H2O).
What is the difference between Melanotan II and PT-141?
They share a lactam-bridged core. Melanotan II ends in an amide and PT-141 in a free acid.
Sources
CoA for every lot — request yours and we email it within 2 hours.
Research use only. Not for human or veterinary use. No health claims.