Disclosure first: I work for Peptriva Research (research-use-only compounds), and I can't help with anything use-related. Testing questions are fair game though.
The way I explain this to people: mass spec and HPLC are answering two different questions, and vendors love to blur them together.
LC-MS tells you whether the molecule is what the label claims. It matches the molecular weight against the expected sequence, and that's it. A passing mass spec says nothing about how much of the vial is actually that molecule.
The purity % everyone quotes comes from HPLC, which is basically asking how much of the chromatogram is the main peak. Thing is, stuff like endotoxin doesn't show up there at all, which is why a decent COA lists LAL and microbial as separate tests instead of hiding behind one purity number.
So if a COA only shows one of these, you're getting half an answer. You want identity, purity, the contaminant screens, and a lot number that matches your vial. If you've got a specific COA you're squinting at, post it or DM me and I'll walk through it.