How to read a peptide sequence

A product sheet shows a line such as Gly-Ala-Lys or GAK. That is the sequence: the order of the amino acids. If you can read that line, you can also check whether a certificate of analysis adds up.

The reading direction

A peptide has a beginning and an end. The beginning is called the N-terminus, because it carries a free amino group. The end is the C-terminus, with a carboxyl group. A sequence is always written from N to C, from left to right.

Sometimes the ends are shown as well: H-Gly-Ala-Lys-OH. The H and the OH indicate that the beginning and the end have not been modified.

Two kinds of abbreviation

Each of the twenty standard amino acids has a three-letter code and a one-letter code. Short peptides are usually written in three-letter code, long ones in one-letter code.

Amino acid	3-letter	1-letter	Amino acid	3-letter	1-letter
Alanine	Ala	A	Leucine	Leu	L
Arginine	Arg	R	Lysine	Lys	K
Asparagine	Asn	N	Methionine	Met	M
Aspartic acid	Asp	D	Phenylalanine	Phe	F
Cysteine	Cys	C	Proline	Pro	P
Glutamic acid	Glu	E	Serine	Ser	S
Glutamine	Gln	Q	Threonine	Thr	T
Glycine	Gly	G	Tryptophan	Trp	W
Histidine	His	H	Tyrosine	Tyr	Y
Isoleucine	Ile	I	Valine	Val	V

Symbols for modifications

Many synthetic peptides differ from a plain chain. The most common symbols:

• Ac- at the start: the N-terminus is acetylated.
• -NH2 at the end: the C-terminus is an amide instead of an acid.
• D- before an amino acid: the mirror-image form. In one-letter code, it is often written as a lowercase letter.
• Nonstandard names such as Aib or Nle: amino acids outside the standard set of twenty.
• Cyclo, or a line between two positions: the chain forms a ring, for example through a disulfide bridge between two cysteines.

These modifications are more than a detail. They change the mass, the charge, and often how quickly a peptide is broken down.

An example to practice on

The chain below is a teaching example, not a product. The N-terminus is acetylated, the C-terminus is an amide, and positions 3 through 5 are marked as a motif. Point to an amino acid to see its full name, or switch to the schematic structure.

Example: ten amino acids

10 amino acids · 1,249.4 g/mol

SequenceStructure

1. AcN Gly 1
2. Ala 2
3. Lys 3 Binding motif 3–5
4. Leu 4
5. Ser 5
6. Glu 6
7. Phe 7
8. Trp 8
9. Arg 9
10. Asp 10 NH₂C

Point to an amino acid or use the arrow keys to see its name.

Hydrophobic

Uncharged side chain that avoids water.

Polar

Uncharged side chain that binds water.

Positively charged

Basic side chain, positive at neutral pH.

Negatively charged

Acidic side chain, negative at neutral pH.

Special (Gly, Pro, Cys)

Help determine the shape of the chain; cysteine can form a bridge.

Binding motif

Marked positions: 3–5.

The chain has 10 amino acids, shown here from the N-terminus to the C-terminus. The N-terminus is acetylated and the C-terminus is an amide. Calculated average molecular mass: 1,249.4 g/mol. Compare this figure with the mass on the certificate of analysis.

From sequence to mass

Each amino acid contributes a fixed mass to the chain. Add up the masses of all the building blocks, add one water molecule for the two ends, and you have the theoretical molecular mass. Modifications count too: an acetyl group adds about 42, and an amide at the C-terminus subtracts about 1.

Compare that calculated mass with the mass stated on the certificate of analysis. If the measured value differs by more than a fraction, it is worth asking the supplier for an explanation.

How that comparison works in a spectrum, with charge states and adducts, is explained in How to read a mass spectrum.

Why this matters

Peptide names are not always unambiguous. The same name is sometimes used for a full peptide and for a fragment of it. The sequence and the CAS number make clear which compound you are working with.

This article is background information on laboratory research. It is not medical advice or instructions for use. All products are for research use only.