Peptide content vs purity: not the same number

Purity and content answer two different questions. Purity asks: of the peptide-like material in this sample, how much is the target peptide? Content, also called assay or net peptide content, asks: of the powder's total weight, how much is the peptide itself? Because a synthetic peptide powder also holds a counter-ion and some water, the two figures differ, and a powder's content can be well below its purity.

The 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.

Two numbers, two questions

Purity comes from a chromatogram: the area of the main peak against the area of all the peaks. It is covered on our page peptide purity and HPLC. A purity figure only compares substances that show up as peaks. Water and most salts do not show up in that comparison, so purity cannot tell you what share of the weight they take.

Content is the share of the weight. The EMA guideline lists content and water as separate items on the specification of a medicine's active substance:

"assay/content;"

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

"water content;"

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

They are listed separately because they are measured separately and mean different things.

The counter-ion: the salt partner in the powder

A synthetic peptide powder carries a counter-ion: a salt partner that is part of the powder but not part of the peptide chain. The guideline names the usual ones:

"For synthetic peptides, usually acetate is used as counter ion"

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

"other counter-ions are also possible (e.g. trifluoroacetate or chloride)."

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

Because the counter-ion adds weight that is not peptide, it is one reason content is lower than purity. For more on acetate and trifluoroacetate, read TFA and acetate salts.

Water: peptides take it up from the air

The second reason is water. The guideline is direct about it:

"Peptides are often very hygroscopic powders"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.5, retrieved 12 October 2026.

Hygroscopic means the powder draws moisture from the air. The guideline asks for that tendency to be measured:

"Hygroscopicity needs to be indicated, e.g. with moisture sorption isotherms"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.1.3, retrieved 12 October 2026.

So the water in a powder is not fixed. It depends on how the material was dried, packed and kept. Our handling page on storing lyophilized peptides covers moisture in storage.

How an assay figure is expressed

When the guideline describes the assay for a medicine, it first asks for the calculation to be spelled out:

"The assay and how it is calculated should be clearly defined."

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.4.5, retrieved 12 October 2026.

It then says what basis the limits use:

"Limits of assays determined by LC are expressed in terms of the counter-ion free, anhydrous substance"

European Medicines Agency, Guideline on the Development and Manufacture of Synthetic Peptides, section 4.4.5, retrieved 12 October 2026.

"Counter-ion free, anhydrous" means the figure is worked out as if the salt partner and the water had been taken away. That is a choice of basis, and it matters. Two documents can both say "assay" and mean figures on different bases. The figure is only comparable when you know which basis was used.

Reading the two numbers together

On a certificate of analysis, look for four lines and read them as a set:

1. Purity, with its method (for example HPLC), limit and result.
2. Content or assay, with its basis stated: as is, or counter-ion free and anhydrous.
3. Counter-ion, named (acetate, trifluoroacetate or chloride) and, if given, measured.
4. Water, measured, usually as a percentage.

If purity is high but content is not stated, you know how clean the peptide is but not how much of the weight it is. If content is stated with no basis, you cannot compare it with another figure. Our guide to reading a certificate of analysis takes the whole document line by line.

Why a clear number matters under Canadian law

In Canada, how a drug is described is regulated. The Food and Drugs Act says:

"9 (1) No person shall label, package, treat, process, sell or advertise any drug in a manner that is false, misleading or deceptive or is likely to create an erroneous impression regarding its character, value, quantity, composition, merit or safety."

Food and Drugs Act, s. 9(1), retrieved 4 October 2026.

"Quantity" and "composition" are both in that list. A purity figure placed where a reader expects the amount of peptide can create the kind of erroneous impression the section names. Stating both numbers, each with what it measures, avoids that. For how Canadian rules apply to peptides in general, read are peptides legal in Canada?.

More in the quality series: TFA and acetate salts and mass spectrometry and peptide identity. Get the free library updates by email.