LC-MS vs HPLC for peptide testing

If a Certificate of Analysis only shows one of these tests, you only have half the picture. This guide explains what LC-MS and HPLC each prove, and why a peptide CoA without both is incomplete.

The short answer

LC-MS (Liquid Chromatography-Mass Spectrometry) answers "is this the right molecule?" by measuring the peptide's mass and matching it to the theoretical mass on the label. HPLC (High-Performance Liquid Chromatography) answers "how pure is it, and how much is in the vial?" by separating components and quantifying them. You need both. One without the other is incomplete.

What LC-MS actually does

The sample is ionised and pushed through a mass spectrometer, which sorts ions by mass-to-charge ratio. The output is a spectrum with a peak at the molecule's measured mass. For a peptide labelled as retatrutide (theoretical mass 4731.4 Da), the LC-MS result should fall within a few daltons of that value. If the mass doesn't match, the vial doesn't contain the labelled peptide, regardless of how "pure" the powder is.

LC-MS is the only way to detect counterfeits where a vendor has substituted a cheaper peptide. About 1 in 6 samples LabDoc has tested from Australian buyers have failed identity. Most would have passed an HPLC-only check.

What HPLC actually does

HPLC pushes the sample through a column that separates components by their interaction with the stationary phase. A detector records each component as a peak on a chromatogram. Two related but different measurements come from HPLC:

• Purity (%): the labelled peptide's peak as a percentage of all peaks. Research-grade peptides are typically 97-99% pure.
• Peptide content (mg/vial): uses a calibration standard to quantify how many mg of peptide are actually in the vial. The remainder is mannitol, salts, and moisture. A vial can be 99% pure yet contain only 60% of the labelled mg.

Why you need both

HPLC alone can tell you the vial contains 98% of something, but not whether that something is the peptide on the label. LC-MS alone confirms identity but doesn't tell you whether the powder is mostly peptide or mostly mannitol. The two tests check different failure modes, and both failure modes are common in the grey-market peptide supply chain Australian buyers source from.

What a complete CoA looks like

A complete peptide CoA, like the ones LabDoc publishes, includes:

• LC-MS spectrum showing the measured mass within a few daltons of theoretical.
• HPLC chromatogram showing the purity peak and any impurities.
• Quantitative peptide content in mg per vial.
• Batch number, manufacture date, and the testing laboratory's name and verifiable credentials.

If any of these are missing, the CoA is incomplete, see how to read a peptide CoA for what to look for line by line.

How LabDoc tests peptides

LabDoc is independent. We don't sell peptides. Samples shipped to our Australian intake address are routed to an independent Australian partner laboratory that runs LC-MS for identity and HPLC for purity and quantitative content. Results are published on labdoc.org (anonymously if you choose) so other Australian buyers can verify the same batch. See our methodology page for the full protocol.