How do I reconcile 97.1% from Janoshik with 96.8% from the supplier?

Numbers first: 97.1% · Janoshik · 96.8%.

Before I write this off, I want to check whether it is a known failure mode.

I have the lot number, the certificate and the date, and I am happy to compare them against anything.

What is the most likely explanation, and how would I confirm it?

Purity is a method-dependent figure, and that is not a limitation of the measurement, it is a property of what the measurement actually answers.

Gradient slope controls resolution, and gentler slopes resolve co-eluting impurities into separate peaks — so the better method reports the worse purity number.

The part that matters: column pore size affects mass transfer — a 100 Angstrom packing on a 5 kDa peptide restricts diffusion, broadening the peak and potentially hiding small impurities in the shoulders.

The practical summary: ask for the chromatogram and the method, and ignore the headline number until you have both.

Reporting threshold is convention and not chemistry, which is why two certificates with different thresholds disagree by a tenth of a point or more.

Tailing factor measures peak shape, and a badly tailing peak spreads into the region where small impurities live, forcing tangent-skim integration that assigns tail area to the main peak.

Integration of the shoulder — whether you use perpendicular drop or tangent skim — determines what area gets assigned to the main peak versus the impurity table.

I would be careful about over-reading a single measurement — treat it as a data point, not as ground truth.

Compare purity within a single laboratory on the same method, never across laboratories.

The honest answer is that the achievable range of plausible purity figures for a given vial is wider than most people expect.

Mobile phase additive choice affects ionisation and peak shape — TFA gives sharp peaks but suppresses mass spectrometry signal, formic acid gives worse peaks but preserves signal.

Mass on column affects detector linearity and peak overlap — overloading broadens peaks and hides neighbours, while underloading improves resolution but loses sensitivity.

Inter-laboratory studies on identical peptide material routinely find half-a-per-cent to a full-per-cent spreads in reported purity on the same sample.

Worth noting that method standardisation is poor in the research-grade space compared to pharmaceutical work, so identical-looking methods can produce different results.

If you are ranking vendors, specify a method and have all samples tested at the same place.

More usefully, the short answer is that two competent laboratories on identical material will disagree, and the disagreement is almost always explainable by method differences.

Sample solvent strength affects peak shape — if you inject in strong solvent on a gradient starting in weak solvent, the solvent peak can distort your main peak or create a false shoulder.

The practical summary: ask for the chromatogram and the method, and ignore the headline number until you have both.

Specifically, understanding purity requires separating the chemistry from the method from the reporting convention, and the three are not independent.

Buffer versus acid in the mobile phase changes the ionisation state of basic and acidic residues, shifting retention and selectivity — same vial, potentially different separation.

The Arrhenius relationship for peptide degradation is the basis of accelerated stability testing and also governs how quickly methods drift with temperature.

The limitation is that single-digit micro-impurities become invisible at typical reporting thresholds, so "no impurities detected" means "none above one in two thousand."

Compare purity within a single laboratory on the same method, never across laboratories.