Peptide Nomenclature: Reading Sequences, Analog Codes and Salt Forms
Catalogue names, certificate headings and journal articles rarely describe a peptide the same way. One source uses a trade code, another a bracketed substitution string, a third a fragment range, and a purchase order that copies the wrong one can bring in the wrong molecule. Peptide nomenclature follows a small set of conventions, and once you know them, a name like Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-NH2 reads as a precise description rather than a string of symbols. This guide works through those conventions with examples from a research catalogue, then turns them into a checklist for specifying compounds on volume orders.
Peptide nomenclature in one worked example
Take the Melanotan-II string above and read it piece by piece:
- Ac- The N-terminus is acetylated, so it carries no free amine.
- Nle The first residue is norleucine, a non-coded amino acid.
- cyclo[ … ] The residues inside the brackets form a ring, here a lactam between the aspartate and lysine side chains.
- D-Phe Phenylalanine in its D-form, the mirror image of the natural residue.
- -NH2 The C-terminus is an amide rather than a free acid.
Every element changes the molecular formula, the mass and often the behaviour on an HPLC column. Drop one of them from a specification and the reorder may not be the same compound. Our comparison of cyclic and linear peptides covers what the ring itself does.
Residue codes and reading direction
Sequences are always written from the N-terminus on the left to the C-terminus on the right. The same residues in reverse order form a different molecule with the same composition, so direction is never optional. Each standard amino acid has a three-letter and a one-letter code; lysine is Lys or K, proline Pro or P, valine Val or V. Non-standard residues are usually written with multi-letter abbreviations only.
| Abbreviation | Residue | Why it appears in analogs |
|---|---|---|
| Aib | α-aminoisobutyric acid | Extra methyl group resists enzymatic cleavage and favours helices |
| Nle | Norleucine | Methionine replacement without the oxidisable sulfur |
| Orn | Ornithine | Shorter basic side chain, often used in lactam bridges |
| Nal | Naphthylalanine | Bulky aromatic side chain for receptor contacts |
| pGlu | Pyroglutamic acid | Cyclised N-terminal glutamine or glutamate |
| D-Xaa | Any D-amino acid | Resists stereospecific proteases |
Substitution notation in square brackets
When an analog differs from a named parent at specific positions, the changes are listed in square brackets before the parent’s name, each with its position number. Melanotan-1 is written [Nle4, D-Phe7]-α-MSH: the thirteen-residue α-MSH sequence, except that residue 4 is norleucine and residue 7 is D-phenylalanine. The modified growth hormone-releasing factor sold as CJC-1295 without DAC is [D-Ala2, Gln8, Ala15, Leu27]-GRF(1-29)-NH2, four substitutions on a fragment with an amidated C-terminus. Our article on the DAC and no-DAC forms explains what each of those changes is for.
The bracket convention is compact and precise, which is why certificates and papers favour it over trade names.
Fragment ranges and trade names
Two numbers in parentheses after a parent name mark a continuous stretch of that parent’s sequence. GRF(1-29) means residues 1 to 29 of growth hormone-releasing factor, which is the molecule sold as sermorelin. ACTH(4-7) is a four-residue piece of adrenocorticotropic hormone, and Semax is that fragment extended with Pro-Gly-Pro. AOD-9604 is described in the literature as a modified version of the C-terminal hGH(176-191) region.
The practical consequence is for literature searching. Much of the primary research indexes a compound under its fragment notation, not its commercial name, so a search on one term can miss most of what exists. When a trade name returns little, try the range. Some names also cover more than one molecule in the market; products sold as TB-500 are one example, where the name has been applied to different sequences related to thymosin beta-4. Checking the sequence on the certificate settles the question.
Terminal groups and other modifications
Several short prefixes and suffixes describe changes at the ends or across the chain:
- -NH2 or “amide”: amidated C-terminus, lowering mass by just under 1 Da compared with the free acid.
- -OH: free C-terminal acid, sometimes written explicitly to distinguish it from an amidated relative.
- Ac-: acetylated N-terminus, adding 42 Da.
- cyclo or a stated bridge such as “Cys2–Cys7 disulfide”: a ring and where it closes.
- DAC, lipid or PEG labels: a group attached to extend stability or change binding, which adds substantial mass.
Salt forms on the label
A name ending in “acetate” or “TFA” states the counter-ion paired with the peptide’s basic groups. Trifluoroacetate is the usual form after reversed-phase purification; acetate is chosen when TFA could interfere with cell-based work. The salt is part of the powder’s mass, which is why vial weight overstates peptide mass. The correction is explained in net peptide content. For calculations, use the molecular weight of the free peptide and treat the salt separately.
Writing names on a purchase order
For labs ordering many vials or reordering over a long study, a precise specification prevents surprises. A good line item includes:
- The common name and the full sequence in three-letter code, N- to C-terminus.
- Every modification: substitutions, D-residues, terminal groups and any ring or conjugate.
- The calculated molecular formula and mass for the free peptide.
- The salt form, if your work depends on it.
- Any alternative names you have seen, so receiving staff can match paperwork.
File the certificate against each lot, noting the vial’s cap and crimp colour, which Bulk Peptides uses to match vials to their certificates. Our products are third-party tested for HPLC purity, with certificates for some products available on the certificates of analysis page.
Names and structures here are given for identification in laboratory research. Bulk Peptides supplies these compounds for in-vitro use only; they are not approved for use in humans or animals.
