Reading a Certificate of Analysis: HPLC, MS and counter-ion checks
A practical walkthrough of the analytical sections of a peptide Certificate of Analysis and what each measurement tells you about a reference standard.
A Certificate of Analysis (COA) is the document that ties a vial in your freezer to a set of measurements. This guide walks through the analytical sections of a peptide COA and what each one tells you about a reference standard.
HPLC purity
The headline figure is reversed-phase HPLC purity, reported as the main-peak area as a percentage of total peak area, usually at 220 nm.
- Check the wavelength and method are stated — a purity number without a method is not interpretable.
- A single dominant peak with small, well-resolved impurities is what you want to see.
- The reported value should match the lot, not a generic product specification.
Mass-spec confirmation
Mass spectrometry confirms identity by matching the observed mass to the theoretical monoisotopic or average mass of the sequence.
- Expect the observed mass to agree with the calculated value within instrument tolerance.
- MALDI-TOF and ESI are both common; the method should be named.
Counter-ion content
Synthetic peptides are typically isolated as salts. The counter-ion report (for example acetate or trifluoroacetate) tells you how much of the vial mass is peptide versus salt and water, which matters when you calculate concentration.
Always reconcile the COA lot number with the lot printed on the vial before using a reference standard in quantitative work.
Research use only. All products and content are intended strictly for in-vitro laboratory research and analytical use. Not for human or veterinary use, not for consumption, and not for any diagnostic or therapeutic purpose.