Purity on a peptide certificate is almost always chromatographic purity: the main peak's area divided by the total integrated area on a reverse-phase HPLC run, expressed as a percentage. A stated ≥98% means at least 98% of the UV signal detected at 214 nm eluted as a single peak under that method.
What the remaining percent is
The balance is typically synthesis-related: deletion sequences missing one residue, incompletely deprotected chains, oxidised methionine, deamidated asparagine, or dimers. These are structurally close to the target, which is why they elute near it and why a well-resolved method matters more than the headline figure.
Purity is not content
The distinction that trips people up: purity is relative to what the detector sees. Residual water, the acetate or TFA counter-ion, and non-absorbing excipients carry no chromophore and are excluded from the calculation. A 99% pure peptide can still be 15–25% salt and water by weight. Net peptide content is a separate determination, usually by amino acid analysis.
Why it matters
For most comparative research the practical floor is ≥98%, and the gap between 98% and 99% matters less than whether identity was confirmed by mass spectrometry on the same lot.