All products are supplied strictly for laboratory and research use only. Not for human or veterinary use.
A Certificate of Analysis (CoA) is the document that tells you what is actually in a vial of peptide how pure it is, whether it’s the right compound, and how much of the powder is peptide at all.
Most people look at one number, the purity percentage, and stop there. That’s the most common mistake in reading a CoA, and it can mean a researcher’s calculations are off by 20% or more without realising it.
This guide walks through each section of a peptide CoA, explains the difference between purity and peptide content, and covers the red flags that suggest a certificate shouldn’t be trusted.
What Is a Certificate of Analysis?
A Certificate of Analysis is a document issued by a testing laboratory confirming the results of analytical tests carried out on a specific batch of material.
For peptides, a proper CoA does three jobs:
- Confirms identity — that the compound is what the label says it is
- Measures purity — how much of the peptide material is the target peptide rather than related impurities
- Documents traceability — ties the results to one specific production batch
The key word is specific. A CoA describes one batch. It is not a general product specification, and a certificate that isn’t tied to a batch number isn’t really a Certificate of Analysis at all.
You can see the certificates for every batch we supply on our Certificates of Analysis page.
What a Peptide CoA Should Include
A complete peptide CoA will typically contain most of the following:
| Section | What it tells you |
|---|---|
| Product name and batch number | Which compound, and which production run the results apply to |
| Test date | When the analysis was performed |
| Molecular formula and weight | The theoretical chemical identity of the compound |
| Appearance | Physical description — usually a white lyophilised (freeze-dried) powder |
| HPLC purity | Percentage of the peptide material that is the target peptide |
| Mass spectrometry (MS) | Confirms the compound’s identity by measuring its molecular mass |
| Net peptide content | How much of the total powder weight is actually peptide |
| Testing laboratory | Who performed the analysis |
Not every certificate includes every line. But the more that’s missing, the less the document can actually tell you.
Purity vs Net Peptide Content: The Most Misread Figure
This is the part most people get wrong, and it matters.
HPLC purity answers the question: of the peptide material in this vial, how much is the target peptide rather than a related impurity? A 99% purity result means 99% of the peptide fraction is the correct sequence.
Net peptide content answers a different question: of the total powder in the vial, how much is peptide at all?
These are not the same number, and they are usually far apart.
The reason is that a lyophilised peptide powder is never pure peptide. It also contains:
- Counterions: Synthetic peptides purified by HPLC are usually obtained as salts, most commonly with trifluoroacetate (TFA). These counterions bind to the peptide’s charged groups and add weight.
- Residual water peptides are often hygroscopic, meaning they absorb moisture, and some remains even after freeze-drying.
- Trace residues from the purification process.
Here’s the detail that explains why the two figures diverge. TFA and water are UV-inactive, so standard analytical HPLC—which detects compounds by UV absorption—doesn’t see them. HPLC purity is calculated only from what the detector can see, which is the peptide material. The non-peptide mass in the vial is effectively invisible to that test.
So a vial can show 99% HPLC purity while the powder itself is well under 100% peptide by weight.
A worked example. AAPPTEC gives a clear illustration: a synthetic peptide with a molecular weight of 1,000 that carries two TFA counterions (each with a molecular weight of 114) has a theoretical net peptide content of:
1,000 ÷ (1,000 + 2 × 114) = 1,000 ÷ 1,228 = 81%
And that’s before accounting for water. In practice, actual net peptide content is determined by amino acid analysis or elemental (nitrogen) analysis rather than calculation.
Why this matters for research. If a protocol assumes that 10 mg of powder contains 10 mg of peptide, and the net peptide content is 80%, every concentration calculated from that assumption is off by 20%. For sensitive experiments, that’s a significant error, and it’s invisible if you only read the purity line.
A low net peptide content isn’t necessarily a sign of poor quality, either. Bachem notes that peptides containing a large proportion of basic amino acids can show low net peptide content even when they are extremely pure, simply because of salt formation.
Every batch we supply is independently third-party tested. Our certificates are published so you can check them before you buy.
How to Read an HPLC Result
HPLC (high-performance liquid chromatography) separates a sample into its components and measures each one as it passes a detector. The output is a chromatogram, a graph with peaks.
When reading one:
- The main peak is the target peptide. It should be large and clearly dominant.
- Smaller peaks are impurities — typically related peptides from the synthesis process, such as truncated sequences or sequences missing an amino acid.
- Purity is calculated as the area of the main peak divided by the total area of all peaks.
A good CoA includes the chromatogram itself, not just the resulting percentage. The chromatogram lets you see how the number was reached. A bare figure with no trace behind it is much harder to trust.
Mass Spectrometry: Confirming It’s the Right Compound
HPLC tells you how pure something is. It doesn’t tell you what it is.
This is a genuine gap. A sample could be 99% pure — and 99% pure of the wrong peptide. HPLC alone wouldn’t catch it.
Mass spectrometry closes that gap. It measures the molecular mass of the compound and compares it against the theoretical mass for the correct sequence. If the two match within an acceptable tolerance, identity is confirmed.
On a CoA, look for:
- Theoretical mass — what the correct compound should weigh
- Observed mass — what the test actually measured
- Confirmation that the two are consistent
A CoA with HPLC purity but no mass spectrometry confirms purity but not identity. Ideally you want both.
Red Flags on a Certificate of Analysis
These are the signs that a CoA may not be reliable:
No batch number. If the certificate isn’t tied to a specific batch, it can’t tell you anything about the vial you have.
Batch number doesn’t match the vial. The number on the certificate should match the number on the product. If it doesn’t, the certificate describes a different batch.
No chromatogram. A purity percentage with no supporting trace is an unverifiable claim.
No mass spectrometry. Purity without identity confirmation leaves the most basic question unanswered.
No laboratory named. A certificate should identify who carried out the testing.
The same certificate used across products or batches. Every batch should have its own certificate with its own results.
Suspiciously round numbers. Real analytical results rarely come out at exactly 99.00%.
Purity presented as if it were content. A certificate that implies 99% purity means 99% of the vial is peptide is either confused or misleading.
Third-Party vs In-House Testing
Some suppliers test their material in-house. Others send each batch to an independent laboratory.
In-house testing isn’t meaningless, but it has an obvious limitation: the party selling the product is also the party verifying it. Independent third-party testing removes that conflict. The laboratory has no stake in the result.
That’s the standard we work to. Every batch we supply is independently third-party tested, and the certificate for each one is published so it can be checked before purchase rather than after.
View our published Certificates of Analysis
Third-party tested, batch-specific Certificate of Analysis, same working day UK dispatch.
Frequently Asked Questions
What is a Certificate of Analysis for peptides?
A Certificate of Analysis is a document from a testing laboratory confirming the analytical results for one specific batch of peptide. It typically covers identity (via mass spectrometry), purity (via HPLC), and often net peptide content, tied to a batch number.
What is the difference between purity and net peptide content?
HPLC purity measures how much of the peptide material is the target peptide rather than related impurities. Net peptide content measures how much of the total powder is peptide at all, as opposed to counterions such as TFA, water, and other residues. A peptide can show 99% purity while its net peptide content is considerably lower.
Why doesn’t HPLC detect counterions and water?
Standard analytical HPLC detects compounds by UV absorption. TFA and water are UV-inactive, so they don’t register. Purity is therefore calculated only from the peptide material, and the non-peptide mass in the vial isn’t reflected in the purity figure.
What does mass spectrometry show on a CoA?
Mass spectrometry confirms the compound’s identity by measuring its molecular mass and comparing it against the theoretical mass of the correct sequence. HPLC confirms purity; mass spectrometry confirms that the compound is the right one.
How do I know if a CoA is genuine?
Check that it carries a batch number matching the product, names the testing laboratory, includes the HPLC chromatogram rather than just a percentage, and includes mass spectrometry results. Be cautious of certificates reused across batches or products, or with suspiciously round figures.
Is third-party testing better than in-house testing?
Independent third-party testing removes the conflict of interest that exists when a supplier verifies its own product. The testing laboratory has no stake in the result.
References
- Bachem. Quality Control of Amino Acids and Peptides: A Guide.
- AAPPTEC. Peptide Quality — FAQ.
- Iris Biotech. Net content and purity, two key parameters in peptide synthesis.
All products are supplied strictly for laboratory and research use only. Not for human or veterinary use.
