Most certificates of analysis (COAs) lean on two tests: high-performance liquid chromatography (HPLC) and mass spectrometry (MS). They measure different things. Knowing the difference lets you read a COA critically instead of treating it as a rubber stamp.
What HPLC Measures: Purity
HPLC separates the components of a sample by pushing it through a column under high pressure. Each component travels at a slightly different speed depending on how strongly it interacts with the column material. The detector records a peak for each one, and the area under those peaks gives the relative proportion of the substance of interest compared to everything else in the sample.
The result is usually reported as a purity percentage, for example "≥98% purity by HPLC." In plain terms: roughly 98% of the detected material is the target compound, and the remaining ~2% is something else. Solvent residues, degradation products, synthesis by-products, stray peptide fragments.
HPLC does not confirm that the main peak is the compound you ordered. A sample can be 99% pure and still be 99% of the wrong molecule.
What Mass Spectrometry Measures: Identity
Mass spectrometry ionizes the sample and measures the mass-to-charge ratio of the resulting ions. For peptides, that produces a characteristic molecular weight fingerprint. Researchers compare the observed mass against the theoretical molecular weight of the expected compound.
When the masses match within the instrument's tolerance, MS confirms the detected molecule has the correct molecular weight. That is identity confirmation: the sample is likely what it claims to be.
What MS does not tell you is how much of the sample is that compound. A vial could hold a tiny amount of the correct peptide diluted in inert filler and still return a positive MS result.
Why a Complete COA Needs Both
The two tests answer two separate questions:
| Test | Primary question answered | What it does NOT tell you |
|---|---|---|
| HPLC | How pure is the sample? | Whether the main compound is correctly identified |
| MS | Is the molecular identity correct? | How much of the sample is that compound |
| HPLC + MS combined | Is this the right compound, and how pure is it? | — |
Independent labs used by the research peptide community report both. Janoshik Analytical is the one cited most often, and its COAs typically carry HPLC purity and MS identity on the same document. According to Janoshik, each report carries a unique laboratory report number that anyone can check against the lab's records to confirm the result is genuine. A document with only one of the two tests, or one that cannot be verified with the issuing lab, deserves a closer look.
Aggregator platforms add a second layer on top of those lab reports. Finnrick, by its own account, does not run a lab. It commissions testing at commercial labs with no ties to the vendors, often using crowdsourced anonymized samples, then publishes the resulting COAs. Peptigrity maintains a database of independent COA images and, per its stated policy, accepts third-party laboratory data only (not in-house vendor testing) when scoring vendors. Both let you check a vendor's own paperwork against independently sourced results.
Bachem and other pharmaceutical-grade peptide manufacturers follow ICH and global regulatory expectations that call for multiple orthogonal analytical methods. Bachem's own quality-control guide describes HPLC (with purity assessed by UV detection at 210–220 nm) and mass spectrometry as standard release tests, backed by additional methods such as amino acid analysis for net peptide content.
Reading a COA in Practice
When evaluating a COA for a research peptide, researchers and reviewers tend to look for:
- HPLC purity reported as a percentage, with the method and wavelength specified (a common UV detection range for peptides is 210–220 nm).
- MS result confirming the observed molecular weight matches the theoretical value, often written as [M+H]⁺ or similar ionization notation.
- Date and sample ID linking the document to a specific batch.
- Issuing lab. An independent third-party lab carries more weight than an in-house result, and a report number that can be verified with the issuing lab carries more still.
Research peptides are sold for laboratory research use and are not approved for human consumption. The analytical standards described here are drawn from pharmaceutical and academic literature and apply to research-context quality assessment.
Sources
- https://www.janoshik.com
- https://www.finnrick.com/blog/independent-peptide-testing
- https://peptigrity.com
- https://www.bachem.com/knowledge-center/peptide-guide/quality-control-of-amino-acids-and-peptides/
- https://www.usp.org