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Reading a peptide sequence

Posted by Alpha Aminos · Jul 21st 2026

Peptide names are written in a shorthand that assumes you already know it. Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-NH2 is a complete and precise description of a molecule, and it is unreadable until someone explains the notation. Here is the whole convention in one page.

One letter, three letters

Every amino acid has a three-letter abbreviation and a one-letter code. Sequences are written left to right, N-terminus first.

G E P P P G K P A D D A G L V

That is BPC-157, and in three-letter form it is Gly-Glu-Pro-Pro-Pro-Gly-Lys-Pro-Ala-Asp-Asp-Ala-Gly-Leu-Val. The one-letter codes are terser and the three-letter codes are harder to misread, which is why a good reference gives both.

Two traps. Leucine (L) and isoleucine (I) have identical masses and are indistinguishable by mass spectrometry alone. Lysine (K, 128.09) and glutamine (Q, 128.06) differ by 0.036 daltons, which a low-resolution instrument will not separate.

The ends, and what caps them

A peptide has a free amine at one end and a free acid at the other unless something has been done to them.

  • Ac- at the front means the N-terminal amine has been acetylated. It adds 42 daltons and removes a positive charge. TB-500 is Ac-LKKTETQ; the acetyl group is the entire difference between it and the plain heptapeptide.
  • -NH2 at the end means the C-terminus is an amide rather than an acid. It removes 1 dalton and one negative charge. SS-31, retatrutide, tesamorelin and Melanotan II are all amidated.

Both modifications appear constantly, both are load-bearing, and neither is decoration.

Residues that are not standard

Twenty amino acids are encoded genetically. Synthesis is not restricted to them, and the interesting molecules usually are not.

  • D-Phe — the mirror image of ordinary phenylalanine. Same mass, same formula, different three-dimensional arrangement. Mass spectrometry cannot tell the two apart; HPLC can, because they come off the column at different times.
  • Nle (norleucine) — a straight-chain leucine isomer, often substituted for methionine specifically to remove an oxidation site.
  • Aib (2-aminoisobutyric acid) — an α,α-disubstituted residue that constrains the backbone. No ribosome makes it. Retatrutide has two.
  • Dmt (2′,6′-dimethyltyrosine) — tyrosine with two extra methyls on the ring. The second residue of SS-31.
  • αMeL — α-methylleucine, another backbone-constraining substitution.

Brackets mean a ring

cyclo[…] means the residues inside are joined into a ring. In Melanotan II the bond runs between the aspartate side chain and the lysine side chain — a lactam bridge, side chain to side chain, not end to end.

Forming that bond expels a molecule of water, so a cyclic peptide weighs 18 daltons less than the same chain left open. On a certificate, that is precisely how you tell a closed ring from a failed one.

Parentheses on a residue mean something is attached

K(C20 diacid-γGlu-AEEA) in retatrutide reads: a lysine whose side chain carries a twenty-carbon diacid fatty chain, connected through a γ-linked glutamate and an AEEA spacer. That is lipidation, and it is why the molecule behaves like a surfactant.

Ranges mean a fragment

ACTH(4–7) means residues four through seven of adrenocorticotropic hormone. Semax is that fragment with Pro-Gly-Pro added on the end. α-MSH(11–13) is KPV. TB-500 is the acetylated 17–23 stretch of thymosin β4.

A fragment is not the parent. TB-500 weighs 889 daltons; thymosin β4 weighs roughly 4,900. Anyone selling “TB-500” at the larger mass is selling a different molecule under the same name, and the mass spectrum on the certificate is where you would find that out.

Putting it back together

Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-NH2 reads: an acetylated N-terminus; a norleucine; a six-residue ring closed between the aspartate and lysine side chains, containing a D-phenylalanine; an amidated C-terminus. That is Melanotan II, and every character of it was doing work.

Full sequences, formulas, masses, CAS numbers and origins for everything in the catalog are in the compound reference.

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