Two acronyms dominate peptide certificates of analysis: HPLC and MS. They answer different questions, and the strongest CoAs report both. Confusing them is the most common way a buyer over-reads a certificate.
HPLC answers: how pure?
High-performance liquid chromatography (HPLC) separates the components of a sample as they pass through a column, producing a chromatogram of peaks. The main peak's area, as a percentage of the total, is reported as purity — e.g. "99.0% by HPLC". A tall, clean main peak with little else means few impurities. What HPLC does not tell you is what that main peak is.
MS answers: is it the right molecule?
Mass spectrometry (MS) measures the mass-to-charge ratio of the molecule, letting the lab confirm its molecular weight matches the target peptide. This is an identity check: it distinguishes the correct peptide from a different compound of similar purity. A sample can be 99% pure and still be 99% pure of the wrong thing — only MS catches that.
Why the best CoAs show both
| Method | Question | What a good result looks like |
|---|---|---|
| HPLC | How pure is it? | A high main-peak percentage with the chromatogram shown. |
| MS | Is it the right molecule? | An observed mass matching the theoretical mass of the target peptide. |
On PeptideTrust, the "identity + purity methods" criterion scores HPLC + MS highest, HPLC only in the middle, and anything else lower — because purity without identity is only half the picture.
A common marketing gap
Many vendors market "HPLC and LC-MS testing" but publish CoAs that only show an HPLC chromatogram, with no mass spectrum. When we score a vendor, we credit what the document actually shows, not the marketing copy around it. If you only see a chromatogram, treat identity as unconfirmed.
See which vendors publish full HPLC+MS certificates on the transparency scoreboard.