How to Read a Peptide Sequence: Codes, Termini and Modifications

Reference sheets and certificates of analysis describe a peptide with a string of letters. This guide explains how to read that notation, what the two ends of a peptide are, and what the common modification marks mean. It is general background for laboratory researchers.

What a sequence describes

A peptide is a chain of amino acids joined end to end. Its sequence lists the amino acids in order. Two peptides with the same amino acids in a different order are different molecules with different properties.

Three-letter and one-letter codes

Each of the 20 standard amino acids has a three-letter code and a one-letter code. The three-letter form is easier for a person to read, and the one-letter form is compact and common for longer sequences.

Amino acid	3-letter	1-letter
Glycine	Gly	G
Lysine	Lys	K
Proline	Pro	P
Valine	Val	V
Histidine	His	H

The tripeptide Lys-Pro-Val, for example, is written KPV. Our KPV reference sheet uses both forms.

Direction: N-terminus to C-terminus

A peptide has two ends. The N-terminus has a free amino group, and the C-terminus has a free carboxyl group. Sequences are always written from the N-terminus on the left to the C-terminus on the right. Reversing the order gives a different peptide.

Common marks on the ends

• Free acid. If nothing is written at the C-terminus, the end is usually a free carboxylic acid. Some sources write “-OH” to make this explicit.
• Amide. A C-terminal amide is written “-NH2”. It removes the negative charge of the acid and changes the mass by about one dalton.
• Acetyl. An N-terminal acetyl group is written “Ac-” before the sequence. It blocks the positive charge of the free amine.

A peptide’s mass depends on these details, which is one reason a mass-spectrometry result can distinguish forms that share a sequence. See how to read a mass spectrometry report.

Other notations you may see

• D-amino acids. Natural amino acids are the L form. A D form is often written with a lowercase letter or with a “D-” prefix, for example D-Ala.
• Disulfide bonds. Two cysteine residues can form a bridge. It is often shown with a line between the cysteines or with a note such as “Cys2-Cys7”.
• Cyclic peptides. A ring is shown with “cyclo” before the sequence, or with a line joining the two ends.
• Lipidation or other attachments. A fatty acid, a sugar or a polyethylene glycol chain can be attached to a side chain. These are usually described in words or by a chemical name, and they change both the mass and the behaviour of the molecule.
• Unusual residues. Non-standard amino acids may be given by a name, an abbreviation or an “Aib”-style code, defined in a note.

Sequence length versus mass

Longer peptides are heavier. As a rough guide, the average amino acid residue adds about 110 daltons. KPV is three residues plus the ends, and its mass is about 342 daltons. The mass listed on a reference sheet or a COA is the value to compare with a mass-spectrometry result.

What to check on a document

1. Is the full sequence given, with both ends stated? A name alone is not a specification.
2. Does the mass match the stated sequence and ends? The expected mass should follow from them.
3. Are modifications written out? Anything not in the standard 20 should be described.
4. Is the same notation used in every document for that product? Mismatches suggest a transcription problem.

What a sequence does not tell you

• Purity or content. A sequence names the target molecule. How much of it is in a vial is measured separately. See how to read a peptide COA.
• Structure in three dimensions. Folding, if any, depends on the conditions.

Where to go next

Terms used here appear in the peptide research glossary. Methods that check the identity of a peptide are described in how peptide purity is tested.

This page is general background for laboratory researchers. It does not describe uses, doses or effects of any compound in humans or animals. For laboratory research use only.