How to read a peptide certificate of analysis

A certificate of analysis is the only direct evidence you have about what is in the vial. Most buyers glance at the purity figure and stop. The purity figure is the least informative number on the page.

Here is what is actually on a COA, in the order it usually appears, and what each line does and does not establish.

The header: identity and traceability

Product name and sequence

The one-letter or three-letter amino acid sequence should be printed, not just the trade name. A sequence is checkable; a name is not. If the certificate names the compound but omits the sequence, you cannot confirm that the mass spec result further down corresponds to the molecule you ordered.

Lot or batch number

This is the single most important field, and the one most often quietly wrong. The lot number on the certificate must match the lot number printed on the vial you received. A supplier who sends the same PDF to every customer for a year is showing you a document about material you do not have.

Date of analysis, and who performed it

A named laboratory with an address, not “our QC department.” A date within the current lot’s life, not two years ago. If the testing lab is the same entity as the seller, you are reading a self-assessment — which is not worthless, but is a different kind of evidence.

The identity section: mass spectrometry

Usually reported as calculated molecular weight versus observed (or found) molecular weight, often with an ESI-MS or MALDI-TOF trace attached.

What to check: the observed mass should be within roughly 1 Da of the calculated mass for a peptide of typical size. Larger deviations suggest the wrong sequence, a modification you did not order, or incomplete deprotection during synthesis.

What it establishes: that the major species present has the right mass. What it does not establish: how much of it there is, or whether isomers with identical mass are present. Mass spec answers “what,” not “how much.”

The purity section: HPLC

Reported as a percentage, typically from reverse-phase HPLC at a stated wavelength — 214 nm is standard for peptides because it detects the amide backbone, 220 nm and 280 nm also appear.

What the percentage actually means: the area of your target peak as a fraction of the total area of all peaks detected. It is a ratio between the peptide you wanted and the peptide-like impurities alongside it — deletion sequences, truncations, oxidation products, diastereomers.

Three things follow from that definition, and they are the whole reason this section exists:

It is relative, not absolute. Anything that does not absorb at the detection wavelength is invisible to the calculation. Water, salts and counterions contribute no peak and therefore do not reduce the purity figure at all.
The gradient matters. A short, steep gradient co-elutes closely-related impurities into the main peak and inflates the number. A well-run method uses a shallow gradient over 20–30 minutes. If the certificate includes the chromatogram, look at the baseline and the peak width, not just the number.
It says nothing about mass. Which brings us to the field most certificates omit.

The field that matters most, and is missing most often: peptide content

Also called net peptide content or peptide assay. It is the fraction of the vial’s total mass that is peptide, as opposed to everything else that came along with it.

A lyophilised peptide is not pure peptide by weight. It carries:

Residual water — lyophilised solids are hygroscopic; 3–10% by mass is normal, measured by Karl Fischer titration or loss on drying
Counterions — most commonly trifluoroacetate (TFA) from reverse-phase purification, which binds to basic residues. A peptide with several basic residues can carry 10–20% of its mass as TFA
Residual salts from synthesis and buffer exchange

Put together: a vial that honestly reports 99% HPLC purity may be 75–85% peptide by mass. Both figures are accurate. They answer different questions. A supplier reporting only the first is not necessarily deceiving you, but you are not seeing the number that determines how much peptide you received.

Peptide content is measured by amino acid analysis, quantitative NMR, or nitrogen determination. If a certificate reports it, that tells you something about the supplier beyond the number itself.

The remaining fields

Field	Typical value	What it tells you
Water content	<10%	Karl Fischer or loss on drying. High values mean a shorter practical shelf life and a mass you are partly paying for in water.
Counterion	TFA or acetate	Acetate is generally preferred for cell-based work; TFA is cytotoxic at sufficient concentration. Many certificates omit it entirely.
Appearance	White to off-white lyophilised powder	Low information, but a colour deviation is worth querying.
Solubility	Solvent and concentration	Practical value for reconstitution planning.
Storage conditions	−20 °C, desiccated, protected from light	Should match what you’re told at point of sale.
Endotoxin	<1 EU/mg	Only relevant for cell culture work. Rarely tested for research-grade material; say so rather than implying it was.

The four-minute check

In order, and you can stop at the first failure:

Does the lot number on the certificate match the lot number on the vial? If not, nothing else on the page is about your material.
Is the testing laboratory named, independent, and dated within this lot’s life?
Is there a mass spec result, and does observed match calculated?
Is the HPLC chromatogram attached, not just the number? A number without a trace is an assertion. A trace is evidence.

Then, if all four pass, read peptide content and water content to understand what you actually bought.

Common red flags

A purity figure with no chromatogram, no wavelength and no method stated
The same certificate served for every lot of a product, or no lot number at all
“Tested to 99%+” in marketing copy with no certificate available before purchase
A testing laboratory that cannot be found to exist
Identity “confirmed” by HPLC alone, with no mass spectrometry

None of these is proof of bad material. All of them are reasons to ask a question before ordering.

Looking for research material? Browse lyophilized research peptides — every lot is third-party tested and ships with a lot-matched certificate of analysis.

Quantum Peptides publishes a third-party certificate of analysis for every lot, tested by an independent US laboratory, with the lot number on the certificate matching the vial. Products are supplied for in-vitro and preclinical laboratory research only and are not for human or veterinary use.