Every peptide listing carries the same number. Ninety-eight percent. Ninety-nine percent. Sometimes 99.5, as though the extra decimal settled something.
The number is real and it is measuring something. It is measuring considerably less than the way it is used implies — and the gap between what it measures and what buyers assume it measures is the single largest information problem in this market.
What HPLC purity actually is
High-performance liquid chromatography separates a mixture by pushing it through a column; different components travel at different speeds and emerge at different times. A detector, usually reading ultraviolet absorbance at a set wavelength, records what comes off. The output is a chromatogram: a series of peaks.
Purity is then calculated as relative peak area. If the main peak accounts for 99% of the total absorbance area the detector recorded, the material is reported as 99% pure.
Read that definition again, because the qualifications are all inside it. The figure describes the proportion of what the detector saw, at that wavelength, that came off the column. It is a relative measurement, not an absolute one.
Four things it does not tell you
1. Identity
HPLC separates by physical behavior, not by structure. A peak at the expected retention time is consistent with your peptide. It does not confirm it. A closely related impurity — a deletion sequence missing one residue, or an epimer — can co-elute or sit very close, and the chromatogram alone will not distinguish them.
Identity confirmation requires mass spectrometry, which measures molecular weight directly. A certificate with HPLC purity but no mass-spec identity has told you something is 99% consistent, without establishing what that something is. That is precisely the gap FDA reviewers repeatedly flagged as inadequate characterization.
2. Anything the detector can't see
UV detection at a typical peptide wavelength responds to specific structural features, particularly aromatic residues and the peptide bond itself. Substances that absorb poorly at that wavelength register weakly or not at all. Substances that do not elute from the column never reach the detector.
So residual solvents, certain salts and various process residues can be present without appearing in the purity calculation. They are not counted as impurities because they were never counted at all.
3. How much peptide is in the vial
This is the big one, and it is almost never published.
Lyophilized peptide is not pure peptide. It typically includes counterions from synthesis — trifluoroacetate is common — plus absorbed water. Both add mass. Net peptide content is the measurement that tells you what fraction of the powder is actually peptide, and it is routinely in the seventies or eighties by weight even for material reporting 99% HPLC purity.
Those two figures answer different questions. HPLC purity asks: of the peptide-like material present, how much is the right one? Net peptide content asks: of the powder in this vial, how much is peptide at all?
The practical consequence
Two vials, both labeled 5 mg at 99% purity, can contain materially different quantities of peptide if their counterion and water content differ. A supplier publishing net peptide content is giving you information almost no one else does — and its absence is not an oversight, it is the industry norm.
4. Sterility and endotoxin
HPLC is a chemistry measurement. It says nothing about microbial contamination, and nothing about endotoxin — bacterial cell wall fragments that survive sterilization and provoke inflammatory responses. Endotoxin testing is a separate assay entirely, and a chemically immaculate preparation can carry a significant endotoxin load.
Reading a certificate of analysis
| Element | Answers | Commonly published? |
|---|---|---|
| HPLC purity | Proportion of detected material that is the main peak | Almost always |
| Mass spectrometry | Is this the right molecule? | Often |
| Net peptide content | How much of the powder is peptide? | Rarely |
| Water content | How much mass is absorbed moisture? | Rarely |
| Counterion content | How much mass is salt? | Rarely |
| Endotoxin | Bacterial contamination load | Rarely |
| Batch/lot number | Does this document match this vial? | Varies |
The last row deserves attention. A certificate that does not carry a lot number matching the vial in hand is a document about some material, not necessarily about yours. Generic certificates reused across batches are common, and they are close to informationally worthless.
Why this sat at the center of the FDA review
Agency scientists opposed all seven July nominations, and characterization ran through their reasoning. That framework's first factor is physical and chemical characterization — can this substance be reliably identified and quantified?
Several committee members who voted in favor attached conditions anyway, including requirements around authorized active pharmaceutical ingredient sourcing. Even supporters were signaling that the current supply landscape does not answer the identity question well.
Five questions for a certificate
What to check
- Is there a lot number, and does it match the vial?
- Is there mass-spec identity confirmation, not just HPLC purity?
- Is net peptide content published, or only HPLC purity?
- Is the chromatogram shown, or only a number transcribed onto a page?
- Who performed the analysis — a named independent laboratory, or the seller?
Common questions
No. HPLC purity is a relative measure of detected material, and lyophilized peptide also contains counterions and absorbed water. Net peptide content — the fraction of the powder that is actually peptide — is frequently in the seventies or eighties by weight even at 99% HPLC purity.
HPLC separates by physical behavior, not structure. A closely related impurity such as a deletion sequence can co-elute or sit very close. Mass spec measures molecular weight and confirms identity, which HPLC alone cannot.
The proportion of the material in the vial that is peptide, as opposed to counterion salt and absorbed water. It answers a different question from HPLC purity and is rarely published.
No. HPLC is a chemistry measurement and says nothing about microbial contamination or endotoxin. Those require separate assays.
Very little. Without a lot number matching the vial, the document describes some material rather than necessarily yours. Generic reused certificates are common in this market.
Sources
- US Food and Drug Administration. PCAC meeting, July 23–24, 2026. Meeting docket FDA-2026-N-2979; bulk substances docket FDA-2025-N-6895. fda.gov
- McDermott Will & Schulte. “Bulk-list bound? PCAC backs majority of peptides in two-day public meeting.” July 27, 2026.
- Orrick. “FDA Peptide Compounding Vote: What to Watch at the July PCAC Meeting.” July 2026.
- Sheppard Mullin. “Compounded Peptides on the Loose: What the Recent PCAC Meeting Means for Industry.” August 2026.