A certificate of analysis is the only objective evidence a buyer has about what is inside a sealed vial. It is also the document most often skimmed, because the numbers look reassuring and the methods look technical. Read properly, a certificate tells you the purity, the identity, how much peptide you are actually paying for, and whether the figures belong to your vial at all.
This guide walks through each section of a typical peptide certificate and explains what the figures mean in practice. Every lot we release is documented this way - you can see the certificates alongside the compounds themselves in the catalogue.
Lot number: does the certificate describe your vial?
Start here, because it determines whether anything else on the page applies to you. A lot-specific certificate carries the same lot number printed on the vial in your hand, and the analysis was performed on material drawn from that batch.
A representative or typical certificate is a different thing entirely: it shows results from some previous batch of the same compound, offered as an indication of what to expect. It is not evidence about your material. If the lot number on the certificate does not match the vial, treat the document as marketing rather than data.
HPLC purity: the main-peak area
Reverse-phase HPLC separates the target peptide from truncated sequences, deletion products and process residues, and the purity figure is the target peak's area as a percentage of total peak area. A figure of 99.2% means 0.8% of the detected material eluted somewhere other than the main peak.
Two details are worth checking. The detection wavelength - typically 214 nm for the peptide bond - determines what the detector can see at all, and the run time determines whether late-eluting impurities had a chance to appear. A short gradient can flatter a sample by never letting the hydrophobic impurities off the column.
Mass spectrometry: identity, not purity
HPLC tells you how much of the sample is one thing. Mass spectrometry tells you whether that thing is the peptide you ordered. The certificate should state the theoretical monoisotopic or average mass alongside the observed mass, and the two should agree within a few tenths of a Dalton.
A certificate with a purity figure but no mass confirmation is incomplete. It establishes that the sample is homogeneous without establishing what it is - and a homogeneous sample of the wrong sequence is the worst possible outcome for a reference standard.
Net peptide content: what you are actually buying
The label says 10 mg, but a lyophilised peptide vial also contains counter-ions - usually trifluoroacetate or acetate - and residual water. Net peptide content, established by nitrogen determination or amino acid analysis, states how much of the fill weight is peptide.
For qualitative work the distinction rarely matters. For anything quantitative it matters a great deal: use the gross label mass to calculate concentration and your standard curve is systematically wrong by however much the salt and water contribute.
Appearance, water content and the analysing laboratory
Supporting fields fill in the picture. Appearance should read as a white to off-white lyophilised powder or cake; discolouration in a fresh lot is a flag. Water content by Karl Fischer titration, where reported, predicts how well the cake will hold up in storage.
Finally, look at who ran the analysis. Testing performed by an independent laboratory rather than the manufacturer removes the obvious conflict of interest. Our certificates come from an independent partner laboratory, and each one is issued against a single released lot.
Residual solvents, water content and counter-ions
Purity and identity dominate the first read of a certificate, but the remaining figures explain what the rest of the vial contains. Residual solvent testing covers acetonitrile and trifluoroacetic acid carried through from purification, water content is usually determined by Karl Fischer titration, and the counter-ion is whatever salt form the peptide was lyophilised as.
These numbers matter for two reasons. They account for the gap between the label mass and the net peptide content, and they occasionally matter to the assay itself, because trifluoroacetate is cytotoxic in some cell-based systems and acetate salts are preferred where that is a concern.
- Water content by Karl Fischer, typically a few percent
- Counter-ion identity, usually acetate or trifluoroacetate
- Residual acetonitrile and trifluoroacetic acid from purification
- Appearance and solubility notes for the lot
Reading the chromatogram, not just the number
A purity percentage is a summary of a chromatogram, and the chromatogram carries information the summary discards. Look at whether the main peak is symmetrical, whether impurity peaks cluster immediately around it, and whether the baseline returns cleanly at the end of the gradient.
Peaks eluting very close to the target usually represent closely related sequences such as deletion or oxidation products, which are the hardest impurities to remove and the most likely to behave similarly in an assay. A cluster of late-eluting peaks suggests hydrophobic process residues. A rising baseline at the end of a run suggests material that never came off the column at all.
What a certificate does not tell you
A certificate describes the material as analysed, at the moment it was analysed. It says nothing about how the vial was stored afterwards, nothing about biological activity, and nothing about sterility unless a sterility test is explicitly reported.
It also cannot tell you whether the sample submitted for analysis was representative of the whole batch. That is a question about the supplier's process rather than the document, and it is the reason lot-level analysis and traceable documentation matter more than any single headline figure.
- Not a statement of biological activity
- Not a sterility or endotoxin result unless separately reported
- Not a guarantee of condition after shipping and storage
- Not applicable to any lot other than the one named
A five-minute checking routine
Reading a certificate properly does not need to be slow. A consistent routine catches the things that matter and takes less time than unpacking the box the vial arrived in.
- Match the lot number on the document to the vial in your hand
- Check the analysis date sits before your receipt date
- Read purity together with the detection wavelength and gradient length
- Confirm observed mass agrees with theoretical mass
- Note the net peptide content and use it for every calculation
- File the certificate against the lot, not against the compound
Everything described here relates to unlicensed reference standards supplied for in-vitro laboratory research by qualified professionals. Nothing we sell is a medicine, and nothing on this page is medical guidance. See our research use disclaimer.
Frequently asked
- What purity should I expect from a research peptide?
- For a reference standard, 98% or better by reverse-phase HPLC is the reasonable expectation, and most well-made short sequences land above 99%. Longer or more complex sequences legitimately sit slightly lower. A figure below 95% belongs in process material, not a reference vial.
- Is 99% purity by HPLC the same as 99% peptide in the vial?
- No, and conflating them is the most common misreading of a certificate. HPLC purity describes the proportion of detected peptide material that is the target sequence. Net peptide content describes how much of the vial's total mass is peptide at all, after counter-ions and water. Both figures matter and they answer different questions.
- Why does the certificate list a partner laboratory?
- Because independent analysis is more meaningful than self-certification. Sending material to a third-party laboratory means the purity figure was produced by an organisation with no commercial interest in the result.
- Is 99% purity meaningfully better than 98%?
- Sometimes. For qualitative screening the difference is rarely material. For quantitative reference work the identity of the missing one or two percent matters more than its size, since a closely related deletion sequence can behave very differently in an assay to an inert process residue.
- Why do different suppliers report different figures for the same compound?
- Because purity is method-dependent. The gradient, column, run length and detection wavelength all shape the number, and two honest laboratories using different methods will produce different figures for the same vial. This is why the method parameters printed on the certificate matter as much as the percentage.
- Should I keep certificates after the vial is used up?
- Yes. The certificate is the provenance record for any data generated with that lot, and questions about a result frequently arrive long after the material is gone. File them by lot number so the link between the data and the material survives.
