Purity and peptide content are not the same number

Purity is a proportion of the peptide-related material: of everything the chromatography column separated, how much was the target peptide rather than a related impurity.

Peptide content is a proportion of the whole vial: of the total mass you are holding, how much is peptide at all.

A lyophilised peptide can be reported at 99% purity and around 80% peptide content on the same certificate, and neither figure contradicts the other.

Not contamination, and not filler added by anybody. Two things, both a consequence of how the material is made:

• Counter-ions. Peptides are purified as salts. Acetate or trifluoroacetate stays bound to the basic residues, and it has mass. On a peptide with several lysines or arginines this alone can be a tenth of the vial.
• Residual water. Freeze-drying removes most of the water, not all of it. Karl Fischer titration measures what is left; a few per cent is ordinary and it is reported on the certificate as its own line.

Neither is a defect. Both are why the two numbers differ, and why a peptide content in the seventies or eighties is normal rather than alarming.

From the method. Solid-phase synthesis and reversed-phase purification both rely on trifluoroacetic acid: once as the agent that cleaves the peptide from the resin, and again as the ion-pairing reagent in the chromatography. Freeze-drying the resulting solution therefore leaves the peptide as a trifluoroacetate salt. The review Pharmaceuticals 2025, on TFA as a counterion in synthetic peptides sets this out.

Exchanging it for acetate is a separate, deliberate step rather than something that happens on its own. How much counter-ion a molecule carries depends on how many basic sites it has: lysine, arginine and histidine residues, and the free amine at the N-terminus.

This part is arithmetic anyone can check. Acetate weighs 60.05 g/mol and trifluoroacetate 114.02 g/mol. Those numbers are fixed, so their share of the salt depends entirely on how heavy the peptide is.

• A short peptide. Epitalon has a theoretical mass of 390.35 g/mol. One acetate is roughly 13% of the mass of the salt; one trifluoroacetate is roughly 23%. Close to a quarter of what was weighed out need not be peptide at all.
• A longer one. BPC-157 is 1419.53 g/mol. The same single acetate is now about 4% of the mass, and trifluoroacetate about 7%.

So the shorter the peptide, the larger the share of the weighed mass that is counter-ion, and the more the peptide content is the figure that settles the question. For a compound of a few hundred g/mol, a certificate quoting purity alone has left out the number that matters most.

Because the two figures answer different questions and only one of them is about the mass in front of you. If a vial states 5 mg and the peptide content is in the low eighties, the mass of peptide is not 5 mg. Anyone working from the label figure alone is working from a different number than the certificate supports.

The peptide calculator works in volumes and concentrations from whatever mass you enter. Which mass to enter is a decision for the person at the bench, and the certificate is what informs it.

Purity is the flattering number. It is the larger of the two, it is the one that reaches 99%, and it is the one that appears on listings. Peptide content is smaller, harder to explain, and rarely quoted by sellers who are not asked.

That is the whole of the reason to ask for it. A seller quoting 99% and nothing else has answered the easier question, and may not have the harder answer at all - peptide content requires a separate determination, and a certificate that omits it is a certificate that did not pay for one.

A complete certificate states both, along with the water content, because the three only mean anything together. Peptorium publishes no certificates and states no purity figure as a measurement; what it publishes is what a certificate contains, so the omission can be spotted on anyone's.