How to read a Certificate of Analysis

A Certificate of Analysis reports what a laboratory found in a specific batch. The two numbers that matter are HPLC purity, which is the percentage of total peak area attributable to the target compound, and mass spectrometry, which confirms the molecule is the one on the label. The most common thing people miss is that the milligram figure on a vial is usually gross weight, not net peptide content, and those are different numbers.

By Better Baseline · Last updated 13 September 2026

Most people never open the COA. The ones who do usually read the purity percentage, see a number above 98, and stop. That number is the least interesting thing on the page.

Here is how to read the rest, and what a good one looks like against a bad one.

The two tests that actually matter

HPLC, high performance liquid chromatography. The sample is pushed through a column that separates its components, and a detector records each as a peak. Purity is reported as the target compound's peak area as a percentage of total peak area.

What it tells you: how much of what is in the vial is the thing you wanted, relative to everything else the method detected.

What it does not tell you: what the impurities actually are. A 99% purity figure says 1% is something else. It does not say whether that something else is a harmless synthesis by-product or something you would care about.

MS, mass spectrometry. The molecule is ionised and its mass-to-charge ratio measured, giving an observed molecular weight compared against the theoretical weight for that peptide sequence.

What it tells you: identity. That the compound is what the label claims.

HPLC without MS is a purity figure for an unidentified substance. MS without HPLC is an identity check with no idea how much else is in there. A COA with only one of the two is half a document.

The thing almost nobody checks

A vial labelled 10mg usually contains 10mg of lyophilised powder. That powder is not pure peptide. It includes counterions such as acetate or trifluoroacetate, residual water, and any excipients.

Net peptide content is the actual mass of peptide, and it is typically somewhere around 70 to 85% of gross weight depending on the compound and the synthesis.

A thorough COA reports net peptide content separately. Most do not, which means the milligram figure people compare across vendors is frequently not comparing the same thing at all. Two vials both labelled 10mg can differ by a couple of milligrams of actual peptide.

This is the single biggest source of apples-to-oranges price comparison in this market.

The fields that tell you whether to trust the document

Work down this list. It takes two minutes.

Batch or lot number, and whether it matches the vial in front of you. This is the whole point. A COA for a batch you do not have is a document about someone else's product. If the vial has no lot number printed on it, the COA cannot be tied to it at all.

Date of analysis. Peptides degrade. A COA from three years ago describes a batch that no longer exists in that state.

The laboratory's name, and whether it is independent. In-house testing is not worthless, but it is not third-party.

Who submitted the sample. This field is the one people argue about most. A COA submitted by the manufacturer tells you the manufacturer had it tested. A COA submitted by the seller tells you the seller had it tested. Both are legitimate; they are answering different questions.

A chromatogram, not just a number. A real HPLC result comes with the trace. The trace shows you the peaks, including the ones that are not the target. A purity percentage typed into a table with no chromatogram behind it is an assertion, not a result.

Whether it is a real document or a picture. A COA that is an image with no selectable text, no lab letterhead and no contact details is trivial to manufacture.

Contaminant and safety testing

Purity and identity are not safety. A separate set of tests covers that, and most vendors do not publish them:

• Endotoxin testing, usually by LAL assay, for bacterial endotoxin
• Sterility
• Heavy metals
• Residual solvents from synthesis
• Adulterant screening, which in this market increasingly includes fentanyl analogues, driven by contamination found in other unregulated supply chains

A vendor publishing HPLC and MS is doing the normal thing. A vendor publishing endotoxin and adulterant screening is doing more than the normal thing.

The questions to ask a supplier

If you take one thing from this article, take these four.

1. Does the lot number on my vial appear on a COA you can send me?
2. Does the COA include both HPLC and MS, with the chromatogram?
3. Is net peptide content reported, or is that a gross weight?
4. Who submitted the sample to the lab?

Any supplier that cannot answer all four quickly is telling you something.

FAQ

What does 99% purity on a peptide COA mean?

That the target compound accounted for 99% of total peak area by HPLC. It does not identify the remaining 1%, and it says nothing about sterility or contaminants.

What is the difference between HPLC and mass spectrometry on a COA?

HPLC measures how much of the sample is the target compound. Mass spectrometry confirms the compound's identity by molecular weight. You want both.

Why is the actual peptide weight lower than the label?

Most labels report gross lyophilised powder weight, which includes counterions and residual water. Net peptide content is typically around 70 to 85% of that.

How do I know a COA is for my batch?

The lot number on the certificate must match the lot number on the vial. If the vial carries no lot number, the two cannot be connected.

Is a manufacturer's COA as good as a third-party one?

They answer different questions. A manufacturer COA shows the producer tested the batch. An independent COA commissioned by the seller shows the seller verified it. Neither is fake; the submitting party is the thing to read.

Sources

• Standard practice guidance on reversed-phase HPLC purity determination by peak area normalisation.
• USP and pharmacopoeial guidance on net peptide content and the reporting of peptide salt forms.
• Bacterial endotoxins test, LAL assay methodology.

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