A certificate of analysis is the only document standing between your business and whatever is actually in the vial. Most people in this industry glance at a purity number, see something above 98%, and file it.
That number is the least informative part of the page, and a COA can be entirely truthful while telling you almost nothing. Here is how to read one properly.
First: who wrote it?
Before any result matters, establish provenance.
A COA issued by the manufacturer on its own letterhead is a manufacturer's claim. A COA from an independent accredited laboratory testing a sample it received directly is evidence. These are not the same document and should not carry the same weight in your file.
Check for:
- Laboratory name, address, and accreditation — ISO/IEC 17025 for testing labs. An unnamed "third-party lab" is not third-party.
- A batch or lot number that matches the vial in your hand. A COA for a different lot is decorative.
- Date of analysis and date of manufacture. A three-year-old COA tells you about a batch that no longer exists.
- Analyst signature and report number.
If you cannot trace the document to a named lab and a specific lot, stop. Nothing below applies. Provenance is also the first thing APA checks before listing a supplier in its vetted vendor network, so if a source can't clear this bar on your desk, it wouldn't clear it on ours either.
Identity: does the molecule match the label?
Purity without identity is meaningless — a sample can be 99% pure something else.
Mass spectrometry confirms molecular weight. You want to see the observed mass compared against the theoretical mass for the stated sequence, matching to within a small tolerance. If the report shows only a chromatogram and no MS data, identity has not been established.
For anything intended for clinical use, amino acid analysis or sequencing data is stronger still, though less commonly supplied.
Purity: read the chromatogram, not the headline
HPLC purity is typically reported as area percent — the peak of interest as a proportion of total peak area at a given wavelength.
What to actually look for:
- The chromatogram itself, not just the number. A COA that states 99.2% without showing the trace is asking you to trust an arithmetic claim you cannot check.
- Gradient and column conditions. Purity is method-dependent. A short, shallow gradient can hide closely eluting impurities. Two labs can honestly report different numbers for the same material.
- Named impurity peaks. Related substances — deletion sequences, truncated chains, oxidation and deamidation products — are the ones that matter, because they are structurally similar and biologically unpredictable.
- Detection wavelength. Commonly 214 nm for the peptide backbone. Purity reported only at 280 nm may under-represent impurities lacking aromatic residues.
Peptide content vs. net peptide content — the number nobody checks
This is where most reconstitution and dosing errors originate.
A vial labelled 10 mg is often 10 mg of lyophilized powder, not 10 mg of peptide. The powder also contains water, counterions, and residual salts.
- Peptide content (by nitrogen analysis or quantitative amino acid analysis) tells you what proportion of the powder mass is actually peptide. For a TFA-salt peptide this is frequently in the 70–85% range.
- Water content (Karl Fischer) is often 5–10% in a lyophilized product.
- Counterion content — typically trifluoroacetate from purification, sometimes acetate — accounts for much of the remainder. TFA content is worth knowing independently; acetate-exchanged material is generally preferred where it matters.
A COA reporting 99% HPLC purity and 78% net peptide content is not contradictory. It means the peptide present is very pure, and the powder is 78% peptide. If your protocol assumes otherwise, every calculation downstream is wrong by more than a fifth — the same kind of quiet, compounding error that shows up later as a documentation gap in supplier due diligence.
If net peptide content is absent from the COA, ask for it in writing. Its absence is the single most common gap.
Safety testing: what's missing is the point
For any material that could reach a person, the absence of these is disqualifying:
- Bacterial endotoxin (LAL), reported in EU/mg with a specification, not merely "passes"
- Bioburden or sterility, as appropriate to the product
- Residual solvents, against recognised limits
- Elemental impurities / heavy metals
- Appearance and solubility
Also check that every result carries a specification, not just a value. "Endotoxin: 0.12 EU/mg" without a stated limit is a measurement, not a pass.
Eleven red flags
- No lot number, or a lot number that doesn't match the product
- Manufacturer-issued COA presented as third-party
- Purity stated with no chromatogram
- No mass spectrometry or other identity confirmation
- Missing net peptide content
- No water or counterion data
- Results without specifications
- Identical COAs across multiple lots — real batches vary
- Purity above 99.9%, which is rarely achievable and rarely honest
- No analysis date, or a date preceding manufacture
- Unnamed testing laboratory, or a lab that cannot be located
Building it into your process
Reading one COA well is a skill. Making it a system is what protects the business:
- Require a lot-specific COA for every shipment, not once per supplier — the APA forms library has an intake template built around exactly these fields, so this becomes a checkbox instead of a judgment call each time
- Keep COAs for the full retention period applicable to your operation, indexed by lot
- Verify independently at intervals. Send a sample from a random lot to an accredited lab annually and compare against the supplier's document. Suppliers who know you do this behave differently.
- Record what you did with each lot, so a discrepancy can be traced forward to affected product
Sourcing documentation and identity and quality testing were recurring themes in the FDA's July 2026 advisory committee discussion of peptide compounding — see our breakdown of what the PCAC vote actually changed for the full regulatory picture. Whatever the regulatory outcome, the operators with a documented, lot-level quality file will be the ones who can demonstrate diligence. The ones with a folder of PDFs nobody read will not.
Frequently asked questions
What is a good HPLC purity percentage for peptides?
Most legitimate suppliers report 95–99% by HPLC area percent. Purity claims above 99.9% are rare and worth double-checking rather than treating as a selling point — see the red flags above.
What's the difference between peptide purity and net peptide content?
Purity (HPLC) describes how clean the peptide is relative to other substances in the sample. Net peptide content describes what percentage of the vial's total powder weight is actually peptide, once water and counterions are accounted for. A sample can be highly pure and still have net content well under 100%.
Do I need a third-party COA if the manufacturer already provides one?
Yes, for anything where identity and purity matter to your business or your patients. A manufacturer's own COA is a claim about its own product; only an accredited independent lab testing a received sample counts as verification.
APA members can access the vendor due-diligence forms library and put sourcing questions to regulatory counsel through the Compliance Corner.