What 99% HPLC purity really means

Every vial that leaves our warehouse carries a number: a purity percentage on the certificate of analysis. For lab-grade peptides that figure is almost always 98% or higher, and on our catalog most items sit at 99%. But what does that percentage actually measure, and why does the remaining 1–2% get so little attention?

The measurement

The purity figure comes from reversed-phase high-performance liquid chromatography — HPLC. The sample is dissolved, pushed through a hydrophobic column at high pressure, and the detector registers each distinct compound as it elutes. The area under the target peak, divided by the total area of all peaks, gives you purity.

That definition matters: purity is a ratio among peptide-related components, not among everything in the vial. Water, salts and counter-ions are not counted in the denominator. This is why purity figures and net-peptide content are two separate numbers on a COA — and why they sometimes surprise researchers who conflate them.

What the other 1–2% is

• Deletion sequences — the synthesizer skipped an amino acid in a coupling step.
• Truncation sequences — chain growth stopped early on a small fraction of resin sites.
• Incompletely deprotected intermediates — side-chain protecting groups that survived cleavage.
• Oxidation or cyclization artefacts — small rearrangements during synthesis or storage.
• Residual TFA or acetic acid — counter-ions from the final purification step.

None of these should block a typical research workflow, but they matter for dose planning (use net-peptide weight, not gross), for protocols sensitive to counter-ion identity, and for structure-activity studies where homologue background can confound readouts.

If your experiment needs a tighter spec, talk to us. We can route your order to a batch with a higher nominal purity or commission a custom synthesis at >99.5% — both come with the same HPLC evidence attached to the shipment.