How to read a peptide certificate of analysis

A certificate of analysis (COA) is the only objective record of what is actually in a vial. For a research peptide, two tests matter: reverse-phase HPLC (RP-HPLC) for purity, and electrospray mass spectrometry (ESI-MS) for identity. They answer two different questions, and a certificate missing either one is only telling you half the story.

RP-HPLC separates the contents of a sample by how they interact with the column's stationary phase, then measures each fraction by UV absorbance. The result is a chromatogram: one tall peak for the target peptide and smaller peaks for related substances — truncated sequences, oxidised forms, or synthesis by-products. Purity is reported as the main peak's share of the total peak area, typically at 214–220 nm. A main peak reported at 99% means the other 1% is everything else in the vial, not that the peptide is 99% "active" in any functional sense — HPLC purity is a chemical measurement, not a biological one.

ESI-MS answers a different question: is this even the right molecule? HPLC purity alone cannot rule out that a sample is 99% pure and 100% the wrong peptide. Mass spectrometry ionises the sample and measures its mass-to-charge ratio; the observed mass is then compared against the theoretical mass calculated from the peptide's sequence. A tolerance (usually a few Daltons) accounts for instrument precision. Identity confirmed by mass alone is good; identity confirmed by mass with a result that also matches the expected fragmentation pattern is better, where the certificate provides it.

What to actually check on a certificate: the lot number printed on your vial should match the lot number on the certificate — not the product name, not the order date. Certificates are lot-specific because manufacturing runs vary; a certificate for a different lot of the same compound tells you nothing about the vial in front of you. Second, check that both tests are present, with method and acceptance criteria stated, not just a purity percentage with no method named.

If a supplier can't produce a certificate for the specific lot you received, treat that as a data gap, not a detail. See our certificate of analysis page for the full test table we use, and ask any supplier for the lot certificate before relying on a compound for research work.