What 99% HPLC purity actually tells you
Purity figures around 99% appear on almost every research peptide sold. The number is real and it is useful, but it answers a narrower question than most buyers assume, and the gap between the question it answers and the question people think it answers is large enough to matter.
It is an area percentage, not a mass percentage
In a chromatogram, each component of the sample produces a peak. The reported purity is the area of the main peak divided by the total area of all peaks, expressed as a percentage.
That is a ratio between things the detector can see. It is not the proportion of the vial's contents by weight.
The detector only sees part of the sample
Peptide HPLC typically uses ultraviolet detection at around 214 nanometres, where the peptide bond absorbs. Anything that does not absorb at that wavelength produces no peak and therefore contributes nothing to the calculation.
Water does not absorb. Nor do the counterions left over from purification, most commonly trifluoroacetate. Nor do residual salts. None of these appear in the chromatogram, so none of them reduce the reported purity — even though all of them occupy mass in the vial.
Purity and peptide content are different numbers
Net peptide content answers the question people usually mean: of the material in this vial, how much is actually peptide? It is measured separately, typically by amino acid analysis or nitrogen determination.
The two figures routinely diverge. A lyophilised peptide can be 99% pure by HPLC and still be substantially less than 99% peptide by mass, because water and counterion make up the balance. This is normal, expected, and not a sign of a bad batch — but a certificate that reports only the first number leaves the second unanswered.
What to look for instead
Ask for the chromatogram, not only the summary figure. A trace shows the shape of the main peak and the size and position of the impurities, which a single number cannot.
Check the detection wavelength and the gradient. Purity measured under one set of conditions is not directly comparable to purity measured under another.
And read the purity figure as what it is: strong evidence that the material is chromatographically clean, and no evidence at all about what else shares the vial with it.