How to Read a Peptide Certificate of AnalysisHow to Read a Peptide Certificate of Analysis

Every peptide conversation eventually reaches the same wall: you cannot reason about a dose you cannot verify. This is a practical guide to reading a certificate of analysis without a chemistry degree.

Purity and content are two different numbers

A vial can be 99% pure by HPLC and still contain far less peptide than the label claims. Chromatographic purity describes what fraction of the peptide material is the target sequence. Net peptide content describes how much of the powder in the vial is peptide at all, with the remainder being counterions, residual water and salts. Both numbers are needed to know your actual dose.

Reading the chromatogram

1. Find the main peak and confirm the retention time matches the reference method.
2. Look for shoulder peaks, these are usually deletion sequences that failed a coupling step.
3. Check the y-axis scaling. A trace zoomed out far enough hides small impurity peaks by design.
4. Confirm the integration table reports every peak above 0.1%, not just the largest three.

Mass spectrometry is the identity check

HPLC tells you how homogeneous the material is. It does not tell you what the material is. Mass spec does. Compare the observed molecular weight against the theoretical monoisotopic mass of the sequence; a mismatch of one amino acid residue is usually visible as an 18 to 130 dalton offset depending on the substitution.