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"≥99% pure" is the most repeated claim in this industry and the least explained. This page sets out what the number is derived from, how the two standard analytical methods differ, how to read the chromatogram behind the figure, and — just as importantly — what a purity percentage cannot tell you.
Reverse-phase high-performance liquid chromatography pushes the dissolved sample through a non-polar stationary phase under a solvent gradient. Components separate by hydrophobicity and leave the column at different times, passing a UV detector. Peptide bonds absorb strongly near 214nm, so that wavelength is the conventional read. Purity is reported as area percent: the area under the main peak divided by the total area of all integrated peaks.
Electrospray ionisation mass spectrometry ionises the sample and measures mass-to-charge ratios, giving an observed molecular mass. That figure is compared with the theoretical mass calculated from the amino acid sequence. A chromatographically clean sample with the wrong mass is a clean sample of the wrong molecule, which is exactly why purity alone is an incomplete answer.
The two methods answer different questions and neither substitutes for the other. Running them per lot rather than once per compound matters because purity is a property of a specific synthesis and purification run, not of a product name.
A Certificate of Analysis worth reading includes the trace, not only the summary line. Four things to look at:
The x-axis position of a peak, in minutes. The main product should elute as a single, sharp, symmetrical peak. Consistent retention time across lots of the same compound under the same method is a good sign of a consistent process.
The headline purity figure. 99.1% means the main peak accounts for 99.1% of the total integrated peak area under that method — not that the vial is 99.1% peptide by mass.
Small peaks close to the main peak are commonly synthesis-related: deletion sequences, truncations or oxidised variants. Their size, not merely their presence, is what matters.
Where the analyst draws the baseline changes the number. A chromatogram image lets you see whether the integration looks reasonable; a bare percentage on a page does not.
Any supplier who presents a single percentage as the whole answer is overselling the technique. These constraints are inherent to the analysis:
Change the gradient, the column or the detection wavelength and the same sample can report a different area percent. A purity figure is only meaningful alongside the method used to produce it, which is why the method belongs on the certificate.
UV area percent describes the chromatographic profile of what was injected. It does not tell you peptide content by weight, which is affected by residual water, counter-ions such as acetate or trifluoroacetate, and residual solvent. Peptide content is a separate assay.
Salts and some excipients do not absorb meaningfully at that wavelength, so they do not appear as peaks. This is a known and normal limit of the technique, not a defect in the report.
A PDF with no lot number, no test date and no named method cannot be tied to the vial in front of you. Traceability is the property that makes the document worth anything.
That is the standard we hold ourselves to. Our lot records are searchable — enter a lot number and you get the record for that batch, or a clear "not found". We do not generate a result for a lot we cannot match.
