Research
What an HPLC purity number proves
A purity percentage is a ratio of what one detector saw in one sample. Four of the measurements that decide whether an injectable is safe are invisible to it, and a regulator writing rules for the same molecules asks for all four.
What the number is a ratio of
High performance liquid chromatography pushes a dissolved sample through a column. Different molecules come off the column at different times, a detector registers each one as a peak, and software measures the area under each peak.
A purity figure is one peak's area divided by the total area of all the peaks. Ninety-nine percent means the target peak accounted for ninety-nine percent of the signal.
Three kinds of material are missing from that denominator. Anything that comes off the column at the same moment as the target and is counted as part of it. Anything the detector does not respond to. Anything that never comes off the column at all.
None of that is a flaw in the technique. It is what the technique is for. The error is reading a separation result as an inventory of the container.
The thresholds a regulator actually applies
FDA published revised draft guidance on semaglutide and on tirzepatide in July 2026, and both documents set out what it wants done about impurities. Reading them turns a vague percentage into a specific standard.
Report every active-ingredient-related impurity present above one tenth of a percent. Identify every one present above half a percent. For any impurity found in both the proposed product and the reference product, keep it at or below the reference product's level, or one percent, whichever is higher. For a new impurity that the reference product does not have, work to get it below one percent.
Set a bare purity claim against that. A product reported as ninety-nine percent pure has one percent of something else in it, and one percent is the number at which the agency stops asking for a total and starts asking for names.
Two limits on that comparison need stating plainly. Those recommendations govern generic applications that reference an approved product, and they are drafts. They do not apply to compounded preparations, and they do not apply to material sold with a research label. They are useful here as a reference point for what a serious impurity conversation looks like, not as a rule anyone in this market has broken.
The four things chromatography cannot see
The same FDA drafts list what else has to be looked at, and the list is the answer to what a purity number leaves out.
Higher order structure, meaning the shape the molecule folds into, and aggregates, meaning molecules stuck to each other. FDA asks for these to be compared across batches at release and at the end of shelf life. Clumped peptide is chemically the same peptide, so a purity assay can pass while aggregation is the problem.
Biological activity, assessed through enzymatic, binding or cell-based assays where appropriate. Whether the molecule still does anything is a separate measurement from whether it is present.
Non-active-ingredient impurities. FDA names particulate matter, microbial contaminants, residual organic solvents, elemental impurities and leachables, and says these should meet compendial acceptance criteria and toxicological limits. Solvent left over from synthesis and metal leached from equipment are not related to the peptide and do not appear in a peptide purity ratio.
The agency then joins those threads. An evaluation of innate immune activity can be accomplished by analyzing aggregates and non-active-ingredient impurities, because those are what may alter a product's immunogenicity. If the impurities meet the limits and the aggregation profile matches the reference product, further immune testing may not be scientifically necessary. The immune question is answered through aggregates and contaminants, not through purity.
Purity and quantity are different questions
A purity percentage describes the composition of the material that was tested. It does not describe how much active molecule a milligram of powder represents.
Many peptides exist as a free base and as an acetate salt. Those forms have different molecular weights, so an identical mass of each contains a different amount of the active molecule. A certificate can be entirely accurate about purity and still be about the wrong form.
FDA hit this repeatedly when it reviewed peptide nominations. In its BPC-157 review it noted that most of the studies it assessed do not clearly identify which form was used, and that the clinical articles do not either. The agency evaluated both forms separately because the packages did not settle the question.
Checking it is one comparison. The registry number and the molecular weight on a certificate either match the form named on the label, or they describe something else.
A result without a method is not a result
Two laboratories can run the same sample and report different purity figures without either of them being wrong. The gradient, the column, the detector and the wavelength all change what is resolved and what is counted.
That is why a certificate is expected to carry a methods column beside every result. A number with no method attached cannot be compared to anything, including the same product's previous batch.
The compendial reference point for this class of material exists. The United States Pharmacopeia publishes a general chapter on the quality attributes of synthetic peptide drug substances, which is the standards document written for exactly this question. A certificate that names the standard it worked to is making a checkable statement. One that reports a bare percentage is not.
Sameness is shown over time, not on one lot
The structure of FDA's July 2026 recommendations is worth noticing on its own, because it shows how much work a comparison claim takes.
For a generic peptide, the agency recommends comparing no fewer than three batches of the proposed product against no fewer than three batches of the reference product. The proposed batches are tested at or near release and again at the end of the proposed shelf life. The reference batches are aged before expiry, under conditions matching the worst case on the label.
That is six batches, two time points and a set of measurements far wider than purity, all to support a claim that two products are the same thing.
A single certificate from a single lot is a much smaller piece of evidence than that. It is still worth having. It is not a demonstration that two vials from two orders contain the same material.
What FDA found when it read this market's certificates
When the agency reviewed peptide nominations for compounding in July 2026, it read the certificates that circulate for these substances and described what they contain.
For BPC-157 it found that most certificates report only purity results, with no information on impurity limits and no testing to demonstrate control of the impurity profile.
The consequence the agency drew was about the immune question rather than the purity question. Without impurity and aggregation data it could not rule out the risk of an immune response to an injected product.
The pattern is not that the numbers on those certificates are false. It is that the one number being reported is not the number the safety question turns on.
Reading a purity figure in about a minute
Find the method. A percentage with no stated analytical method cannot be assessed or compared.
Read the number as a remainder. Ninety-nine percent means one percent unaccounted for, and the useful question is whether anything on the page says what that one percent is.
Look for the four blind spots. Aggregates, biological activity, microbial and endotoxin results, and non-peptide contaminants such as residual solvents and elemental impurities are separate tests, and a purity assay does not cover any of them.
Check the form. Free base or acetate, with the registry number and molecular weight agreeing with the name on the label.
Check the scope. A certificate covers bulk powder. Whatever a pharmacy does after that, including sterility and endotoxin release testing on a finished preparation, is a different set of records.
Key takeaways
- A purity percentage is one peak's share of a detector's total signal, not an inventory of what is in the container.
- FDA's July 2026 peptide drafts ask for impurities to be reported above a tenth of a percent and identified above half a percent, so a bare 99 percent claim sits where the naming should start.
- Aggregates, biological activity, microbial and endotoxin results, and non-peptide contaminants are all invisible to a purity assay.
- The agency assesses innate immune risk through aggregates and non-active-ingredient impurities rather than through purity.
- Free base and acetate salt have different molecular weights, so the same percentage on the two forms describes different amounts of active molecule.
- FDA found that most certificates circulating for BPC-157 report purity alone, with no impurity limits and no profile control.
Frequently asked questions
What does an HPLC purity percentage actually measure?
It measures one peak's share of the total signal the detector produced. The sample is separated on a column, each component registers as a peak, and the target's peak area is divided by the total. Anything that comes off the column at the same time as the target, anything the detector does not respond to, and anything that never comes off the column is not in that calculation. It is a separation result rather than a list of the container's contents.
Is 99 percent purity good for an injectable peptide?
It is a reasonable-looking number that answers a narrow question. For comparison, look at FDA's July 2026 draft guidance on semaglutide and tirzepatide. It asks a generic applicant to report every active-ingredient-related impurity above one tenth of a percent, identify every one above half a percent, and control each one to one percent or the reference product's level. Those rules apply to generic applications rather than to compounded or research-labeled material, but they show that one percent is where the naming starts, not where the questions end.
Can a purity test detect peptide aggregates?
Not as a rule. Aggregated peptide is chemically the same molecule, so a purity assay can return a high figure while aggregation is the actual problem. FDA treats higher order structure and aggregates as separate comparisons in its peptide guidance, and links them directly to immune risk. In its 2026 compounding reviews the agency said that without impurity and aggregation data it could not rule out the risk of an immune response to an injected product.
Why do two labs report different purity numbers for the same material?
Because the column, the gradient, the detector and the wavelength all change which components are resolved and which are counted. Two accurate laboratories using different methods can legitimately publish different figures for one sample. That is why a certificate is expected to carry a methods column, and why a bare percentage with no method attached cannot be compared with anything, including the same product's earlier batches.
Does a high purity number mean two vials contain the same thing?
No. FDA's own approach to establishing that two peptide products are the same involves at least three batches of each, tested at release and at the end of shelf life, across measurements far wider than purity. A single certificate describes a single lot. It is worth having, and it does not establish that a later order contains the same material.
Sources
Each document below is named as it names itself, with the date printed on that document rather than the day it was read.
- Draft Guidance on Semaglutide (product-specific guidance, revised) — U.S. Food and Drug Administration, July 2026
- Draft Guidance on Tirzepatide (product-specific guidance, revised) — U.S. Food and Drug Administration, July 2026
- FDA Publishes Revised Draft Product-Specific Guidances for Certain Generic Peptide Products — U.S. Food and Drug Administration, July 2026
- FDA Briefing Document for BPC-157-Related Bulk Drug Substances, Pharmacy Compounding Advisory Committee — U.S. Food and Drug Administration, May 2026