Purity, retention time, mass spectra. What matters, what does not, what suppliers hide.
A Certificate of Analysis is not a marketing document, though many suppliers treat it as one. It is a data sheet — HPLC purity, mass spectrometry identity, and a handful of physical measurements. Everything else is decoration.
Start with the HPLC trace. You want a single sharp peak at the expected retention time, with a purity figure of ≥ 98% by area. Multiple peaks mean impurities. A single peak with a long tail means degradation. A purity number without a chromatogram means nothing at all.
Then the mass spec. The observed monoisotopic mass should match the theoretical mass of the intact peptide within 1 Da. If the supplier only shows an ESI-MS with no deconvolution, they may be hiding a truncation product that shares a similar retention time.
Water content, endotoxin, and acetate content are the sleepers. High water content shortens shelf life. Endotoxin above 5 EU/mg makes a peptide useless for any cell-based assay. High acetate — a leftover from TFA-to-acetate exchange — can skew mass measurements and irritate tissue in animal work.
If a COA does not include chromatograms, mass spectra, and endotoxin numbers, it is not a COA. It is a receipt with a percentage printed on it.