Specifying synthetic peptides: why the impurity profile, not the purity figure, is the specification

A single HPLC percentage can’t tell two peptide lots apart. A specification that names impurity classes, sets individual limits and demands mass balance can

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Ask most laboratories how they specify a synthetic peptide and the answer is a single number: purity ≥98% by HPLC.

Specifying synthetic peptides: why the impurity profile, not the purity figure, is the specification

The figure is familiar, easy to compare across suppliers and simple to print on a certificate of analysis.

It is also, on its own, a poor specification. Two lots can both report 98.2% and still differ in ways that matter to an experiment or a development programme.

One may carry 1.8% spread across a dozen minor, well-characterised species.

The other may contain a single 1.5% deletion sequence that coelutes with a neighbouring peak and differs from the target by one amino acid. The purity number is identical; the material is not.

In this article, Sohail Khan argues that, for peptides made by solid-phase peptide synthesis (SPPS), the impurity profile is the specification.

The purity figure is only a summary of it. The discussion is framed around research-grade and early-development material and makes no claims about clinical or human use. 

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