A certificate of analysis (COA) states which tests a laboratory carried out on one specific batch and what the results were. For synthetic peptides, two measurements matter most: HPLC, which gives the purity as a percentage, and mass spectrometry (MS), which shows whether the right molecule is present. A COA only tells you anything about your product if the batch number matches and you can verify which lab performed the analysis.
What a COA should contain
- The product name and the batch or lot number, matching the number on the label.
- The date of the analysis.
- The name of the laboratory that performed the measurement, not just the name of the seller.
- The method, for example reversed-phase HPLC with UV detection, and the wavelength.
- The purity as a percentage, preferably with the chromatogram attached.
- The measured mass alongside the theoretical mass of the peptide.
- Often also the appearance (for example ‘white powder’) and sometimes the water or peptide content.
- A signature, verification code or other means of checking the certificate with the lab.
HPLC: what ‘99% purity’ means
In HPLC (high-performance liquid chromatography), the dissolved sample is pumped through a column. The substances in the sample leave the column at different times and a UV detector records them as peaks. Peptides are usually measured at around 210 to 215 nm, where the peptide bond absorbs light. Researchers at Ghent University used the same approach when they tested 98 research peptides [2].
The purity is the area of the main peak as a percentage of the total peak area. This is known as area normalisation [2]. ‘99%’ therefore means that, of everything the detector recorded at that wavelength, 99% fell under the main peak. What it does not mean:
- It does not tell you which molecule the main peak represents; that requires MS.
- Substances that do not absorb UV light, or that leave the column at the same time as the main peak, are not counted, or not counted separately.
- It is not a measure of content. Peptide powder also contains water and counterions, such as trifluoroacetate (TFA) from synthesis and purification [1][3]. A powder with 99% HPLC purity is therefore not 99% peptide.
On the chromatogram, look for one clear main peak, a stable baseline and the small peaks beside it. Labs only report small peaks above a threshold; in the Ghent study, that reporting threshold was 0.1% of the main peak [2].
Mass spectrometry: checking it is the right peptide
A mass spectrometer measures the mass of molecules, expressed as the mass-to-charge ratio (m/z). Electrospray ionisation (ESI) is often used for peptides. With this technique, a single peptide produces several peaks, because the molecule can carry different charges. The mass is calculated from these peaks and should match the theoretical mass derived from the amino acid sequence.
A difference equal to exactly one amino acid is a well-known warning sign. Solid-phase synthesis, the standard production method, readily produces deletion sequences, in which an amino acid is missing, and sometimes insertions with one extra amino acid [1]. In the Ghent study, 74% of the identified impurities were missing at least one amino acid. In one sample, the main substance even turned out to have a different structure from the peptide that had been ordered [2]. HPLC alone would not have revealed this.
Why a COA is not always reliable
The study by Verbeke and colleagues shows why it pays to read critically. All 98 peptides were delivered with a supplier COA stating a purity of at least 95%. When the researchers checked them, only 43 met that threshold [2]. They conclude that blindly trusting the supplier’s certificate can distort research results [2].
A COA is therefore a starting point, and it becomes more convincing the more you can verify: who performed the measurement, whether the lab confirms the certificate and whether the batch number really belongs to your pack.
Red flags
- No batch number, or a number that is not on the label.
- The same certificate for different products or batches.
- Only a percentage, without a chromatogram or method.
- No MS result, or no theoretical mass to compare it with.
- No lab name, or a lab that cannot be found or contacted.
- An analysis date that is inconsistent with the production of your batch.
What a standard COA does not measure
HPLC and MS say nothing about microbiological contamination, endotoxins or heavy metals; separate tests exist for those. Peptide content (how much of the powder is actually peptide) also requires a separate determination. If such a test is not on the certificate, assume it has not been carried out. A COA also reflects only the moment of analysis; how subsequent storage affects quality is explained in Storing peptides. For a pre-filled pen, what matters is the filled solution, not the powder it was made from.
Have a question about the analysis of a product you ordered from us? Please contact us and include your order number. Information about ordering and shipping is available in the FAQ.
Products
Every Clean Peptides vial and pen carries a batch number on the label. The full range is available in the shop, including:
Further reading
- Purity, endotoxins and heavy metals: what is tested in peptides?
- What are peptides? Explanation and key terms
- How do you store peptides so they stay stable?
- Retatrutide pen or vial: what are the differences?
- Knowledge base: peptides and research materials explained
Sources
- D’Hondt M, Bracke N, Taevernier L, et al. Related impurities in peptide medicines. Journal of Pharmaceutical and Biomedical Analysis 2014;101:2–30. doi:10.1016/j.jpba.2014.06.012
- Verbeke F, Wynendaele E, Braet S, et al. Quality evaluation of synthetic quorum sensing peptides used in R&D. Journal of Pharmaceutical Analysis 2015;5(3):169–181. doi:10.1016/j.jpha.2014.12.002
- Bachem. Handling and Storage Guidelines for Peptides. bachem.com (accessed 30 September 2026)
For laboratory research use only. Clean Peptides products are not intended for use in humans or animals. This article provides general information and is not medical advice.
