What is in a synthetic peptide besides the peptide

A synthetic peptide sample can hold more than the target chain. Alongside it can sit close relatives made during synthesis and storage: chains with one amino acid missing, chains with one too many, short chains that stopped growing, forms with an amino acid flipped into its mirror image, and chains changed by reactions such as oxidation. These are the peptide-related impurities that a purity test measures.

The names and quotations below come from the European Medicines Agency's guideline for synthetic peptides in medicines, a European standard. We use it to explain the terms. It does not describe any product.

Why impurities look so much like the peptide

A synthetic peptide is built one amino acid at a time; see how synthetic peptides are made. If one step does not go to completion, some chains miss a link and carry on growing. If a step goes wrong in another way, some chains gain an extra link. The result is a set of molecules that differ from the target by one small piece, which makes them hard to separate and hard to tell apart.

Deletion sequences: one link missing

The guideline defines the most familiar kind:

"Deletion sequences are peptides with one or several amino acids missing"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.3.2, retrieved 12 October 2026.

A deletion sequence is almost the same chain, with a gap. Its mass is lower than the target's by the mass of the missing amino acid, which is one way mass spectrometry can spot it; see mass spectrometry and peptide identity.

Insertion sequences: one link too many

The opposite also happens. The guideline describes the case where an extra amino acid gets into the chain, and says that in that case:

"an insertion sequence is generated."

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.3.2, retrieved 12 October 2026.

An insertion sequence carries one extra amino acid, and so a higher mass.

Truncated sequences: chains that stopped short

During synthesis, chains that failed to take the next amino acid may be blocked on purpose so they stop growing. The guideline calls this blocking step acetylation, and names what it leaves behind:

"The acetylation procedure results in acetylated peptide fragments (truncated sequences)."

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.3.2, retrieved 12 October 2026.

Truncated sequences are shorter than the target, and carry the cap at their end.

Diastereomers: a link flipped into its mirror image

Most amino acids come in two mirror-image forms. A chain built from the right forms, with one link in the wrong form, has the same mass and the same sequence but a different shape. The guideline warns how many of these can arise:

"a multitude of different diastereoisomers of the target peptide can be formed"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.3.2, retrieved 12 October 2026.

And where they can come from:

"the manufacturing process can be a source of stereoisomers formation, for example by epimerisation"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.3.2, retrieved 12 October 2026.

Because a diastereomer has the same mass as the target, mass spectrometry alone does not catch it. That is one reason a purity method has to be able to separate it.

Changes after the chain is made

Some impurities form later, while the material is kept. In its section on stability, the guideline lists typical reactions:

"oxidation of Cys and Met residues, deamidation, hydrolysis"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.7.1, retrieved 12 October 2026.

In plain words: cysteine and methionine can react with oxygen; some side chains can lose an amide group (deamidation); and the chain itself can be split by water (hydrolysis). These are reasons storage conditions matter; see storing lyophilized peptides and how long peptides last.

How impurities are counted

For medicines, the guideline sets the points at which these by-products must be reported, identified and qualified:

"peptide-related impurities should be reported above 0.1%, identified above 0.5% and qualified above 1.0%"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.4.1, retrieved 12 October 2026.

A purity figure of 98% means the related impurities above add up to about 2% of what the method sees. A fuller certificate of analysis lists the largest single impurities, not only the total. How the number is made is on peptide purity and HPLC.

Why this matters under Canadian law

The Food and Drugs Act has a section on the condition of drugs sold in Canada:

"8 No person shall sell any drug that (a) was manufactured, prepared, preserved, packaged or stored under unsanitary conditions; or (b) is adulterated."

Food and Drugs Act, s. 8, retrieved 4 October 2026.

That section is about the law, not about chemistry: it shows that how a drug is made and stored is a legal question in Canada as well as a technical one. Whether a peptide may be sold at all is a separate question, covered on are peptides legal in Canada?.

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