A certificate of analysis is the only document that tells you what is actually in the vial. Most suppliers will send you one. Very few explain what is on it, which leaves a document that looks authoritative and is difficult to use.

This walks through a peptide certificate section by section, in the order worth reading it.

Start with the batch reference, not the purity

The purity figure is the number everyone looks at first and it is not where to start. Start at the top of the sheet with the batch or lot reference, and check it against the number printed on the label of the vial in front of you.

If those two do not match, nothing else on the certificate applies to what you are holding. This is the single most common problem we get asked about, and it is almost never deliberate. Suppliers reuse a certificate from a previous lot because the new one has not come back yet, and the mismatch goes unnoticed until someone checks.

If you cannot match a certificate to a batch reference on the vial, treat the compound as uncharacterised.

Product name and stated identity

The certificate should name the compound and, for a peptide, give its sequence in three letter or one letter code. Check the sequence against the compound you ordered rather than the name alone, because a lot of research peptides trade under several names and some of those names cover more than one molecule.

SS-31, elamipretide and MTP-131 are the same peptide. Epitalon and Epithalon are the same tetrapeptide. TB-500 is a fragment of thymosin beta-4 and not the full protein, and a certificate that names it as thymosin beta-4 is describing something else.

The chromatogram

The HPLC trace is usually the largest thing on the page and the part most people skip. It is worth thirty seconds.

What you want to see is a single dominant peak with a flat baseline either side of it. The horizontal axis is retention time, the vertical is detector response, and the target compound is the tall one.

Things worth noticing:

Several peaks of similar height. The sample contains several things in meaningful quantities. A high purity figure alongside a trace like this usually means the integration window was set generously.
A noisy or sloping baseline. Makes the integration less reliable, and small impurity peaks disappear into the noise.
A shoulder on the main peak. Two compounds eluting close together, often a related impurity, and they may have been integrated as one.
No trace at all. A certificate quoting a purity figure with no chromatogram is asking you to take the number on trust.

The purity figure

Usually given as a percentage against HPLC, with a detection wavelength stated. It is the area under the main peak as a proportion of total integrated peak area.

What it means: of the material the detector saw, that percentage was the target compound.

What it does not mean:

That the remaining percentage is inert. It is unidentified, not harmless.
That the vial is that percentage compound by mass. Peptides carry residual water, counterion and sometimes solvent, none of which appear in an HPLC purity figure. Net peptide content is a separate measurement and is rarely supplied.
That two certificates quoting the same figure are equivalent. Purity depends on the method, the column, the gradient and the detection wavelength.

For most laboratory work the headline figure is sufficient. If you are working at low concentrations or your assay is sensitive to related impurities, ask what the remaining percentage consists of before you order.

Mass spectrometry

The chromatogram tells you how much of one thing is present. It does not tell you what that thing is. Mass spectrometry does.

The certificate should give a theoretical molecular weight and an observed one. For a peptide they should agree closely, usually within a fraction of a unit for a monoisotopic mass. A significant discrepancy means the material is not what the label says, however clean the chromatogram looks.

A pure sample of the wrong compound will produce an excellent purity figure. This is why both tests matter and why a certificate carrying only one of them is incomplete.

Physical and handling data

Appearance, solubility, storage conditions and shelf life. These are the sections that get copied between certificates without being checked, so read them against what actually arrived.

If the certificate says white lyophilised powder and you have a blue one, either the certificate is wrong or you have a different compound. The one legitimate exception in most catalogues is GHK-Cu, which is blue because of the copper complex, and a certificate for it should say so.

Dates

Two dates matter: date of manufacture and date of analysis. Shelf life runs from manufacture.

A long gap between manufacture and analysis is worth a question. It usually means the batch was tested some time after it was made, which tells you less about its current state than a recent test would.

What a certificate cannot tell you

It describes the material at the moment it was tested, in the laboratory that tested it. It says nothing about what happened between that laboratory and your bench.

A peptide that spent a weekend in an unrefrigerated depot has a perfectly valid certificate and may no longer match it. This is a supply chain question rather than an analytical one, and it is where most real world degradation happens. The relevant questions are how the compound was shipped, at what temperature, and how long it was in transit.

A short checklist

Batch reference matches the vial label
Compound name and sequence match what you ordered
Chromatogram shows one dominant peak on a flat baseline
Purity figure states a method and a detection wavelength
Observed mass agrees with theoretical mass
Appearance on the certificate matches what is in the vial
Manufacture and analysis dates are close together and recent

Seven checks, about two minutes, and they catch almost everything that goes wrong.

Questions worth asking a supplier

Can I see the certificate before I order. Is it for the batch I will receive or a previous one. What happens to a batch that fails. Is net peptide content available. How is the compound shipped and at what temperature.

A supplier who answers those quickly is telling you something. So is one who does not.