How to read a certificate of analysis

A certificate of analysis is a record of measurements performed on one specific batch of material. It is not a description of a product line, and it says nothing about any other batch. That is the entire reason lot numbers exist: a certificate belongs to the material in front of you, or it belongs to nothing.

A useful certificate answers four questions. Is this molecule the one named on the label? How much of the sample is that molecule? What else is in the vial? And which batch was measured? Every section below is one of those four questions in more detail.

Mass spectrometry measures molecular weight. A peptide of known sequence has a known theoretical mass, and the certificate should show the observed mass beside it. When the two agree closely, the molecule is the one named.

This is the first thing to read, and it is the check most often missing. A purity figure describes how much of a sample is a single substance. It says nothing whatsoever about which substance. A sample can be 99% pure and still be entirely the wrong compound.

HPLC separates a sample into its components and reports each as a percentage of total detector response, usually as area percent at a stated wavelength.

Two consequences follow, and both are routinely misread:

This is the distinction that separates a certificate written for chemists from one written for marketing.

Purity describes the peptide fraction of the sample: of the peptide present, how much is the target sequence. Net peptide content describes something different — how much of the vial's total mass is peptide at all. The remainder is counterion, residual water and salts left over from synthesis and purification.

A vial can be 99% pure and 78% net peptide at the same time, and both figures can be perfectly honest. They measure different things. A certificate that reports purity and omits net peptide content has told you the material is clean without telling you how much material there is.

Peptides are generally isolated as salts. Trifluoroacetate — TFA — is the counterion that most commonly survives purification. Acetate is the usual alternative, produced by an additional exchange step.

The salt form is worth reading for two reasons. It is part of the mass that is not peptide, so it bears directly on net peptide content. And the two are not interchangeable across every experimental context, since residual TFA is itself detectable in some assays. A thorough certificate states which salt form was isolated. Many state neither.

Lyophilized material retains residual moisture. Karl Fischer titration measures how much.

Water matters twice over. It is mass that is not peptide, and it is the principal driver of degradation during storage. A high moisture figure predicts a shorter shelf life regardless of how clean the initial chromatogram looked, which is why this number belongs beside the purity figure rather than in a footnote.

Two screens appear on thorough certificates and are absent from most.

Bacterial endotoxin is measured by LAL assay and reported in endotoxin units. Endotoxin is a residue of bacterial growth during production. It is heat-stable and is not removed by filtration, so a sterile result does not imply a low endotoxin result — they are separate measurements answering separate questions.

Heavy metals are measured by ICP-MS. A broad elemental screen catches catalyst and equipment residues that a purity figure cannot show by definition, because those elements do not appear as chromatographic peaks at all.

Last, the record-keeping — which is where fabricated certificates most often fall apart.

A certificate should carry a lot number, a date of analysis, the identity of the laboratory that performed the work, and instrument-generated output rather than figures transcribed into a template. The lot number should match the one printed on the vial. A certificate that cannot be tied to the specific container it arrived with is documenting somebody else's material.

No single omission proves anything. A pattern of them is informative, and these are the ones worth noticing: