A certificate of analysis is a laboratory's report on one production lot. Read properly it answers three questions: is this the compound named on the label, how much of the sample is that compound, and what is the rest of it.
The header: lot number and date
Everything else on the page is conditional on this. A COA describes one lot. If the lot number is absent, redacted or does not match the vial you hold, the document is describing something other than what you have.
The date matters for a different reason: it tells you whether the certificate was produced for this production run or carried over from an earlier one.
The purity figure and the method
Purity on a peptide COA is almost always reported as HPLC peak area percentage. That is a relative measurement: it says the main peak accounts for that share of everything the detector saw. It does not say the main peak is the compound you ordered, and it does not account for anything the method cannot detect.
This is why 99% purity by HPLC and confirmed identity are different claims. The first is a proportion, the second is an identification.
Mass spectrometry: the identity check
An MS trace reports observed molecular weight, which is compared against the theoretical weight for the sequence. When the observed and theoretical figures agree, that is evidence the material is the named compound rather than a different molecule that happens to elute at a similar time.
A COA with HPLC and no MS gives you a proportion without an identity. That is not useless, but it is half the picture, and the half that is missing is the one that catches substitution.
What the rest of the sample is
Peptides supplied as lyophilised powder are rarely pure compound by mass. Residual solvent, counter-ions such as acetate or trifluoroacetate, and water content all contribute. A thorough COA reports these. A thin one omits them and lets the purity percentage imply a mass that is not there.
Net peptide content, where it is reported, is the figure that reconciles the two.
Appearance, solubility and storage
These read as boilerplate and occasionally are not. Appearance that does not match the description is the earliest visible sign that something is wrong with a lot. Stated solubility tells you which solvent the material was characterised in.
Red flags
- No lot number, or a lot number that does not match the vial
- No issuing laboratory named
- A purity percentage with no assay method stated
- The same certificate reused across every lot of a compound
- An image of a COA that cannot be enlarged enough to read the fields
- Identity claimed without any mass spectrometry data
A supplier that publishes complete, lot-matched certificates before you order is making a claim that can be checked. That is the entire value of the document, and it is why an unreadable or generic COA is worse than none: it looks like evidence without being evidence.
Questions and answers
Does 99% purity by HPLC mean the vial contains the compound ordered?
No. Purity on a peptide certificate is almost always HPLC peak area percentage, which is a relative measurement: the main peak accounts for that share of everything the detector saw. It does not establish that the main peak is the compound you ordered. Purity and confirmed identity are two different claims.
Why does a certificate need mass spectrometry as well as HPLC?
A mass spectrometry trace reports observed molecular weight and compares it against the theoretical weight for the sequence. Agreement is evidence the material is the named compound rather than a different molecule that happens to elute at a similar time. HPLC with no MS gives a proportion without an identity, and identity is the half that catches substitution.
If a peptide is 99% pure, is the vial 99% peptide by mass?
Usually not. Peptides supplied as lyophilised powder are rarely pure compound by mass: residual solvent, counter-ions such as acetate or trifluoroacetate, and water content all contribute. Net peptide content, where it is reported, is the figure that reconciles the purity percentage with the mass actually in the vial.
What are the red flags on a peptide certificate of analysis?
No lot number, or one that does not match the vial. No issuing laboratory named. A purity percentage with no assay method stated. The same certificate reused across every lot of a compound. An image that cannot be enlarged enough to read the fields. Identity claimed with no mass spectrometry data.