What does a peptide purity percentage mean?

It is usually a relative figure

For peptides, a quoted purity percentage almost always means chromatographic area percent: the proportion of total detected peak area attributable to the main peak.

That is a statement about the balance of detected components, not about the fraction of the vial's mass that is peptide.

What the figure does not include

None of these produce a UV peak, so none of them reduce a chromatographic purity figure. This is why a high area-percent figure and a substantially lower peptide-content-by-mass figure can both be accurate descriptions of the same material.

• Water — lyophilised peptides are hygroscopic and typically retain moisture.
• Counter-ions from purification, commonly acetate or trifluoroacetate salts.
• Residual solvents and non-absorbing excipients.
• Any impurity that co-elutes with the main peak under the method used.

When two figures cannot be compared

Purity figures are only comparable when the method and the reporting basis match. A figure produced under a shallow gradient with a long run time may resolve impurities that a fast method hides inside the main peak.

Comparing a chromatographic area percent from one certificate with a peptide content figure from another is comparing two different quantities that happen to share a percent sign.

Reading a figure sensibly

• Check the reporting basis — area percent, peptide content, or something else.
• Check the method conditions and run time.
• Check that the figure is tied to the batch you hold.
• Look at the chromatogram, not only the summary number.

Precision is not accuracy

A figure quoted to two decimal places is not more trustworthy than one quoted to a whole number. The decimals come from integration software; the accuracy comes from the method, the sampling and the analyst.