What’s in the Other 1%? Peptide Impurities, Explained

The story below is a composite of real experiences; details changed.

Owen Hart, 41, spends his workday with calipers in his hand. He runs quality control at a machine shop. No part leaves his bench until he’s measured it.

For the last year, he’s spent his evenings reading peptide research. Every supplier site shows him the same badge: 99% pure.

To Owen, a number without a spec sheet is a sales pitch. In his shop, a part nobody can check doesn’t ship.

So he asks what he’d ask about any part: What’s in the other 1%, and how would I know?

Good question. Here’s what’s in the other 1%, why “99% pure” can still mean 90% peptide, and what a complete certificate of analysis (COA) should list.

How a peptide is built, and where errors creep in

Most synthetic peptides are built one amino acid at a time on a resin, then cut free and purified using an acid called TFA. (Pharmaceuticals, 2020) Every step can misfire:

• A failed step leaves a chain missing an amino acid. Too much reagent can add an extra one.
• Some amino acids flip into their mirror-image form.
• Chemical “protecting groups” used during building can be left behind.
• After synthesis, peptides can oxidize or break down during manufacturing and storage.
• Solvents and other process chemicals can remain.

Detecting them is the hard part. FDA says these impurities “are typically similar in structure to the target peptide and may be difficult to identify and quantify without sophisticated analytical methods.” (FDA)

Why “99% pure” can still be 90% peptide

HPLC purity answers one question: of the peptide material, how much is the right peptide? It “does not include any water and trifluoroacetate salt.” (AltaBioscience)

How much of the powder is peptide at all is a different number, called net peptide content. One manufacturer puts the typical range at 70 to 90%.

Here’s what that gap looks like. In a 2020 study, a synthetic glucagon came with a reported purity of 983.72 mg/g. Researchers measured everything else in it and subtracted.

The real figure was 896.36 mg/g, or about 90%, not 98%. TFA made up about a tenth of the weight, and water about 5%. (Scientific Reports)

Purity tells you what kind of peptide is there. It doesn’t tell you how much. For the line-by-line version, read how to read a peptide COA.

Why impurities matter in research

A review of peptide impurities warns that they can greatly influence early lab studies, “possibly resulting in erroneous conclusions.” Two examples show how.

TFA. In bone-cell cultures, tiny amounts of TFA slowed cell growth. When peptides were tested as TFA salts, researchers either missed a real growth effect or saw a false anti-growth effect. The authors’ fix was to switch the peptide to a different salt before testing. (Am J Physiol, 1999)

TFA isn’t even consistent: in another cell type, it stimulated growth. (Pharmaceuticals)

Endotoxin. A protein once looked like it switched on an inflammation signal in immune cells. That effect turned out to be “entirely due to the contaminating LPS,” a bacterial endotoxin. (J Biol Chem, 2003)

That was a protein, not a synthetic peptide, but the lesson carries. Endotoxin is hard to remove once it’s there, and it can fake the very inflammation signals researchers measure. (FDA)

What FDA flagged about popular research peptides

• On its compounding safety page, FDA says BPC-157 “may have complexities with regard to peptide-related impurities” and possible immune reactions. It notes similar concerns for TB-500 and injectable GHK-Cu, including aggregation. (FDA)
• Thin paperwork. In July 2026, FDA reviewers wrote that “most CoAs for BPC-157 (free base) only contain purity testing results.” (FDA) For TB-500, “assay, impurities, bacterial endotoxins, and aggregates are not tested or controlled.” One TB-500 certificate allowed a single impurity of up to 1.0%. (FDA)
• The medicine benchmark. For generic peptide drugs, FDA expects every impurity at 0.10% or more to be identified. It treats a new one above 0.5% as a possible immune-reaction concern. That’s a standard for medicines, not a rule for research chemicals. It shows how closely the pros look. (FDA guidance, 2021)
• Spot checks back this up. Researchers bought semaglutide from online sellers that used “research”-style disclaimers. All three vials that arrived contained endotoxin, and the peptide content ran 29% to 39% above the label. (J Med Internet Res, 2024)

For a researcher, the reason is simple: you can’t interpret a result if you don’t know what was in the vial.

What a complete COA should list

Owen’s spec sheet

Owen builds a sheet: one row per supplier, one column per test. Most rows have a lot of empty cells.

It’s the rule from his bench: no data, no sign-off. He isn’t looking for a badge anymore. He’s looking for data he can check.

A purity badge answers one question. A complete COA answers the rest.

Your next step: take the next COA you see and check it against the four core lines above. Mark every line it leaves blank.

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Owen is a composite, drawn from the kinds of questions careful readers ask. The details are illustrative. Research compounds are sold for laboratory research only. Nothing here is medical advice or a recommendation to use any compound.