A lab assistant is asked to pull the primary literature on sermorelin before a new study is set up. A database search on the name returns a thin list, and most hits are reviews. A senior colleague suggests searching “GRF(1-29)NH2” instead, and the results multiply. Same molecule, different name. Research peptide names follow a set of compact conventions, and once they are familiar, a string like [Nle4, D-Phe7]-alpha-MSH stops looking like noise and starts reading like a specification.
This guide decodes the notation piece by piece: sequence direction, fragment ranges, substitution brackets, terminal groups, added moieties and salt forms.
Sequence direction and amino acid codes
Each standard amino acid has a three-letter code (Gly, Lys, Pro) and a one-letter code (G, K, P). By convention, sequences are written from the N-terminus on the left to the C-terminus on the right. KPV therefore means Lys-Pro-Val, with lysine carrying the free amine end.
Order is not cosmetic. Lys-Pro-Val and Val-Pro-Lys have the same composition and the same mass but are different compounds, with different chromatographic behavior and different fragmentation in a mass spectrometer. When a source does not state direction, assume N-to-C.
Numbers in parentheses: fragments of a longer parent
A pair of numbers in parentheses after a parent name identifies a continuous stretch of that parent’s sequence, counted from its N-terminus. ACTH(4-10) means residues 4 through 10 of adrenocorticotropic hormone. GRF(1-29) means the first 29 residues of growth hormone-releasing factor, the sequence catalogued as sermorelin in its amidated form.
Catalog listings often describe a compound by the fragment it is based on, for instance Semax as an ACTH(4-7)-based peptide. When a listing does this, the fragment tells you the core, and the full sequence line tells you whether anything was added to it.
The practical lesson for literature searches: if a trade or catalog name turns up little, search again using the fragment notation, and the reverse.
Square brackets: what was changed
Brackets placed before a parent name list substitutions relative to that parent, each with its position number. [Nle4, D-Phe7]-alpha-MSH is the alpha-MSH sequence with norleucine at position 4 and D-phenylalanine at position 7, the analog catalogued as Melanotan 1.
Most bracketed changes belong to two families:
- D-amino acids. Natural residues are the L-form. A “D-” prefix marks the mirror-image form, commonly introduced because proteases are stereospecific and cleave D-containing sites much more slowly.
- Non-proteinogenic residues. These sit outside the standard twenty: norleucine (Nle), ornithine (Orn), aminoisobutyric acid (Aib) and others.
A single name can carry several of these changes at once, so read the bracket as a list and check each position against the parent sequence. If the abbreviations are unfamiliar, the research peptide glossary is a useful companion.
Terminal groups: what the ends are doing
Unless stated otherwise, a peptide’s C-terminus is a free carboxylic acid and its N-terminus is a free amine. Modifications are written at the relevant end:
- -NH2 or “amide” at the right-hand end means the C-terminus is amidated. GRF(1-29)NH2 is the amidated form.
- Ac- at the left-hand end means the N-terminal amine is acetylated.
Either modification removes a charged terminus, which changes the molecule’s overall charge and its stability. Because amidated and free-acid versions share a sequence, the suffix is the only part of the name that separates them, so it should never be dropped when recording a compound.
Name components that are not sequence
Some parts of a name describe an added chemical group rather than residues. The clearest example is DAC, short for Drug Affinity Complex. In CJC-1295 with DAC, the peptide carries an added maleimide-containing group, so the compound’s formula and mass differ from the version without it even though the peptide backbone is shared. The comparison is set out in CJC-1295 vs CJC-1295 DAC. When a name contains an abbreviation that is not an amino acid code, look up what group it denotes before assuming two products are the same.
Salt forms and why they change the numbers
Peptides with basic residues such as lysine or arginine are normally isolated as salts. Trifluoroacetate (TFA) is the usual counter-ion after reverse-phase purification, since TFA is a standard mobile phase additive. Acetate is a common alternative when TFA could interfere with an assay. The difference is explained in TFA vs acetate counter-ions.
The counter-ion has mass, and lyophilized material also holds some residual water. As a result, the weight of powder is not the same as the weight of peptide. A salt designation in a name is a reminder that any gravimetric calculation needs to account for the non-peptide fraction.
Putting it together: a worked example
Consider a hypothetical catalog entry written as Ac-[D-Ala2, Nle5]-X(1-12)-NH2 acetate. Reading it in order:
- X(1-12) says the core is the first twelve residues of a parent called X, counted from its N-terminus.
- [D-Ala2, Nle5] says two positions differ from the parent: position 2 is D-alanine and position 5 is norleucine.
- Ac- says the N-terminal amine is acetylated.
- -NH2 says the C-terminus is an amide rather than a free acid.
- acetate names the counter-ion the material was isolated with.
Five pieces of information in one line, and each one changes the molecular formula, the expected mass or the handling arithmetic. If any piece is missing from a label or a paper, the compound is not fully specified, and it is reasonable to ask for the complete notation before comparing two materials.
Quick decoding table
| Notation | Meaning | Example |
|---|---|---|
| Left to right | N-terminus to C-terminus | KPV = Lys-Pro-Val |
| (n-m) | Fragment, residues n through m of the parent | ACTH(4-10) |
| [Xn] | Residue X substituted at position n | [Nle4] |
| D- | D-enantiomer of the residue | D-Phe |
| Ac- | Acetylated N-terminus | Ac-peptide |
| -NH2 | Amidated C-terminus | GRF(1-29)NH2 |
| Nle, Orn, Aib | Non-proteinogenic residues | Aib at position 1 |
| TFA / acetate | Counter-ion (salt form) | Peptide TFA salt |
Questions
Why does the same peptide appear under different names?
Catalog and code names often differ from the systematic fragment or analog notation used in primary papers. Searching under both forms gives a fuller picture of the literature.
Does a D- prefix change the molecular mass?
No. A D-residue has the same formula and mass as its L-form, so mass spectrometry alone cannot distinguish them. Chiral methods or reference standards are needed.
Is the counter-ion part of the peptide’s name?
It is often omitted, but it is part of the material. A full description names the salt form because it affects the mass of powder per unit of peptide.
What does a number range without a parent name mean?
It is incomplete. A fragment range only has meaning relative to a named parent sequence, and sometimes a species, so ask for the full notation.
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