Purity vs Net Peptide Content: The 99% That Is Not 99%
A vial certified 99% pure typically contains 15-25% less actual peptide than the label weight. Both figures are honest. They measure different things.
Two different numbers, routinely confused
A certificate of analysis usually carries a purity figure, commonly 98% or 99%. That number describes the proportion of the peptide that is present which is the correct sequence, as resolved by chromatography. It says nothing about how much peptide is in the vial. Net peptide content, sometimes called peptide content or assay, is the separate figure describing what proportion of the vial's total mass is peptide at all. A vial can be 99% pure and 78% peptide content simultaneously, and both figures are accurate.
Where the missing mass goes
The rest is counter-ions, residual water and residual solvent. Peptides synthesised by solid-phase methods are cleaved and purified using trifluoroacetic acid, and the peptide leaves that process as a TFA salt. TFA typically accounts for 10 to 20% of the final mass depending on how many basic residues the sequence carries. Lyophilised powder is also hygroscopic and retains bound water, commonly another 5 to 10%. Neither is a contaminant in the sense of something that should not be there; both are a normal consequence of how peptides are made.
Why this matters for anyone comparing products
Two vials both labelled 10mg, both certified 99% pure, can contain measurably different amounts of peptide if one reports 85% net content and the other reports 78%. The purity figure alone will not reveal that. This is the single most common reason two products that look identical on paper behave differently, and it is why net peptide content is the figure worth asking for.
Why most certificates omit it
Net peptide content requires a separate assay - amino acid analysis, nitrogen determination or quantitative NMR - which costs more than running a chromatography trace. Many certificates therefore report purity alone, because purity is what the purification step already generates data for. Its absence is usually cost rather than concealment, but a supplier who can produce it on request is demonstrating something a supplier who cannot is not.
What to ask for, in order
The batch-specific certificate first, because a generic certificate not tied to your batch number describes a different production run. Then the purity figure with the method that produced it. Then net peptide content, or an acknowledgement that it was not assayed. A supplier who answers all three plainly is giving you a complete picture; one who conflates purity and content is either not reading their own paperwork or is relying on you not to.
Acetate salt and why some products differ
Some manufacturers perform a salt exchange, replacing TFA with acetate. Acetate is generally preferred for peptides intended for biological work because TFA has documented effects in cell culture at low concentrations. A product specified as an acetate salt has had an extra processing step, and that will be stated on the certificate if it was done.