Purity figures are the headline number on every peptide certificate, and the one most often compared between suppliers without checking whether the comparison means anything.
What the number is
Reverse-phase HPLC separates the sample by hydrophobicity and a detector reports absorbance over time. Purity is the area of the main peak divided by the total area of all peaks, at a stated wavelength. It is area percent, not mass percent — different molecules absorb differently, so peak area is a proxy for quantity rather than a direct measure of it.
Why 98 and 99 are often the same material
Between two lots of the same sequence, one point of area percent is frequently within the run-to-run variation of the method itself. Integration choices — where the analyst places the baseline, whether a shoulder is counted as part of the main peak or separately — move the figure by a comparable amount. Treating 99% as meaningfully better than 98% on that basis is reading noise.
What actually differs: the shape of the remainder
Two percent spread across a dozen small peaks is a different material from two percent concentrated in one closely eluting peak. The single-peak case usually means a specific related impurity the gradient did not resolve — commonly a deletion sequence missing one residue, or an oxidised form. The scattered case suggests general degradation.
Which matters more depends on your work, but you cannot tell them apart from the headline figure. You need the chromatogram. A purity number with no trace behind it is an assertion, not a measurement.
The three checks that make a comparison valid
- Same method. Reverse-phase HPLC in both cases, not one HPLC and one unstated.
- Same wavelength. 214 nm detects the peptide bond and sees essentially everything peptidic. 280 nm detects aromatic residues and is blind to sequences without them — which flatters purity on those sequences.
- Chromatogram present. Both of them, so the remainder can be compared rather than assumed.
The figure that usually matters more
Peptide content. A material can be 99% pure and 78% peptide content at the same time, with no contradiction — purity describes the peptide present, content describes how much of the powder is peptide at all. A 99% pure vial at 76% content delivers less peptide than a 98% pure vial at 88%, and the purity comparison points the wrong way entirely.
If you are choosing between two lots on documentation, compare peptide content first, then look at the chromatograms, and treat the last point of purity as a tiebreaker rather than a criterion.