How peptide purity testing actually works
Almost every research peptide supplier advertises a purity figure, and almost none explain what the number is measuring. Since purity is the single largest driver of price in this market, it is worth understanding what a certificate of analysis does and does not tell you.
What HPLC measures
High-performance liquid chromatography separates the contents of a sample by how strongly each component interacts with a stationary phase as a solvent gradient pushes it through a column. A detector at the far end records what emerges and when, producing a trace of peaks. Purity is reported as the area of the main peak as a percentage of the total peak area.
The consequence of that definition matters: HPLC purity is a relative figure. It tells you the proportion of ultraviolet-absorbing material that is your target peptide. It says nothing about non-absorbing content such as residual water, counter-ions or salts — which is exactly why the mass on a label is described as nominal peptide content rather than gross vial weight.
What mass spectrometry adds
HPLC confirms that a sample is largely one thing. It does not confirm that the one thing is the sequence you ordered. Mass spectrometry closes that gap by measuring the molecular mass of the eluted material and comparing it against the theoretical mass of the intended sequence. A purity result without an identity check is half an answer, which is why both appear on our certificates.
Reading a certificate of analysis
- Lot number — it must match the number printed on the vial in your hand, not just the product name.
- Test date — a certificate issued long before your batch was synthesised is describing a different material.
- The chromatogram itself, not only the summary figure: a clean single peak reads very differently from a main peak flanked by shoulders.
- The observed mass against the theoretical mass for the sequence.
- Appearance and solubility notes, which often explain handling behaviour at the bench.
Why 99% is the sensible threshold
The gap between 95% and 99% sounds narrow and is not. At 95%, one part in twenty of the ultraviolet-absorbing material is something other than your target — commonly truncated sequences from incomplete coupling during synthesis, which are chemically similar enough to co-elute and structurally different enough to behave differently in an assay. For comparative work across a series, that is an uncontrolled variable sitting inside your reagent.
How we apply this
Every lot we release is assayed by HPLC and by mass spectrometry, and is held back unless purity is 99% or above. Vials are labelled with their lot number, and the certificate for your specific lot is available on request at any point after ordering. All material is supplied for in-vitro laboratory research only.