How to Read a Peptide Certificate of Analysis (COA)

A Certificate of Analysis is the single most important document a peptide supplier can hand over, and it’s also the most commonly skimmed. Most buyers glance at a “Purity: 99%+” line and move on. That number is real, but it’s derived from specific tests, and understanding those tests tells you far more than the headline figure alone.

The two questions a COA answers

A proper COA answers two separate questions:

1. Is this the right molecule? (Identity)
2. How much of the vial is that molecule, versus impurities, water, and counter-ions? (Purity)

Suppliers sometimes report only one of these. A COA that shows purity but no mass-spec identity confirmation hasn’t actually proven the vial contains the peptide it claims to — it has only proven that whatever is in the vial is fairly homogeneous.

HPLC purity: what the chromatogram shows

High-performance liquid chromatography (HPLC) separates the contents of a sample by how they interact with a column as they’re pushed through it, producing a chromatogram — a plot of detector signal against time. The peptide of interest should show up as one large, well-resolved peak; the area under that peak, divided by the total area under all peaks, gives the purity percentage.

What to check beyond the summary number:

• Peak shape. A sharp, symmetric peak indicates a clean, homogeneous sample. A broad or tailing peak can indicate degradation products or a mix of closely related sequences (e.g., truncated or deamidated variants).
• Baseline noise. Excess baseline noise or small satellite peaks close to the main peak are often trimmed out of a summary purity calculation but are worth a look — they can indicate related-substance impurities from incomplete synthesis.
• Retention time. This isn’t meaningful in isolation, but a supplier who publishes retention time alongside a reference standard’s retention time is giving you a reproducibility anchor — useful if you’re comparing multiple batches over time.

Mass spectrometry: identity confirmation

Mass spec (typically MALDI-TOF or ESI-MS for peptides) measures the mass-to-charge ratio of the ionized sample. For identity confirmation, the observed molecular weight should match the theoretical molecular weight of the target sequence within a small tolerance (commonly within 0.1–0.5%, depending on the method and instrument).

A COA that lists “MW confirmed by MS: 4813.5 Da (theoretical: 4813.2 Da)” is telling you the lab put the actual molecule under a mass spectrometer and matched it against the expected structure — a meaningfully stronger claim than an HPLC purity number alone, which only characterizes the sample’s internal consistency, not its identity.

Batch and lot information

A COA should be tied to a specific lot number, not issued as a generic template reused across shipments. Look for:

• Lot/batch number matching the vial label
• Test date (ideally close to the ship date — a COA run a year before shipment tells you less about the vial in your hand)
• The testing lab’s name, and whether testing was done in-house or by an independent third party

Third-party testing is a meaningful signal. It doesn’t guarantee accuracy, but it removes the incentive problem of a manufacturer grading its own product.

What a COA does not tell you

A COA characterizes a specific tested sample from a specific lot — not necessarily every vial you receive, and not the compound’s stability over time in your storage conditions. It also typically does not test for endotoxins, heavy metals, or residual solvents unless those are explicitly listed as separate line items. If your application is sensitive to any of these, confirm they’re included rather than assuming a purity COA covers them.

A short checklist

• Purity percentage plus a viewable chromatogram (not just the number)
• Mass spec identity confirmation with observed vs. theoretical MW
• Lot number matching the physical vial
• Recent test date
• Named testing lab, ideally third-party
• Confirmation of what was and wasn’t tested (endotoxins, heavy metals, solvents)

Reading past the summary line takes an extra two minutes per COA. It’s the cheapest quality-control step available to a buyer who doesn’t have in-house analytical equipment.