HPLC purity
Also called: HPLC testing
Clinical reviewer: Jacob Moore, MD · Last checked September 22, 2026
What does peptide purity percentage mean?
HPLC purity is the share of a chromatography signal attributed to the target peptide, measured against everything else the method detects, such as impurities, degradation products and aggregates. It is a manufacturing quality check, not a measure of sterility or endotoxin content, which require separate tests. A high percentage on a label does not guarantee either.
How is an HPLC purity percentage calculated?
A purity percentage is the share of the chromatographic signal the method attributes to the target peptide, versus everything else it detects [1]. Chromatography methods such as reversed-phase HPLC are standard in the pharmaceutical industry for judging whether a peptide matches its intended structure, considering impurities, degradation products and the extent of aggregation [1]. Liquid chromatography-mass spectrometry can further identify impurities down to structural isomers and stereoisomers, with thresholds set by current regulatory guidance [2].
What does a purity percentage not tell you?
Not sterility, and not endotoxin content. FDA's review of one peptide's compounding nominations found certificates of analysis that lacked tests for impurities, aggregates, and microbial and bacterial endotoxins, even though sterility, a bacterial endotoxins test and foreign particulates are critical quality attributes for an injectable [3]. Nor does purity by itself establish how much material is in the vial: a 2024 study of semaglutide bought from online pharmacies reported content and purity separately, and found endotoxin in every sample tested regardless of what the label claimed [4].
How low can real-world purity be?
Lower than labels claim. A 2024 study of vials purchased from illegal online pharmacies measured semaglutide purity between 7.7% and 14.37%, against a 99% claim on the product label, using liquid chromatography with mass spectrometry [4]. All three vials were considered probable substandard and falsified products [4]. The number also depends on the method: many variables affect a peptide's separation, recovery and stability during analysis [1].
Frequently asked questions
Does a 99% purity claim mean a peptide is safe to inject?+−
No. Purity describes the chromatography signal, not sterility or endotoxin content. Those need their own separate tests, which a purity percentage does not include.
What else should a certificate of analysis show?+−
Checks for impurities, aggregates, and microbial and bacterial endotoxins, which FDA found missing from the certificates of analysis in one peptide's compounding nominations.
Related terms
Sources
- Sharma N et al. Synthetic pharmaceutical peptides characterization by chromatography principles and method development. Journal of Separation Science, 2022.
- Lian Z et al. Characterization of Synthetic Peptide Therapeutics Using Liquid Chromatography-Mass Spectrometry, Challenges, Solutions, Pitfalls, and Future Perspectives. Journal of the American Society for Mass Spectrometry, 2021.
- FDA — Semax-related bulk drug substances briefing document, Pharmacy Compounding Advisory Committee meeting, July 23-24, 2026
- Ashraf AR et al. Multifactor Quality and Safety Analysis of Semaglutide Products Sold by Online Sellers Without a Prescription. Journal of Medical Internet Research, 2024.
This entry is for education and is not medical advice. Talk with a licensed clinician about your own situation before starting, stopping, or changing any treatment.
