How do I reconcile 99.4% from VendorInvestigate with 98.4% from the supplier?

Conditions: 99.4% · VendorInvestigate · 98.4%.

I have two candidate explanations and no way to distinguish them.

The same procedure has worked without incident several times previously, which argues against technique.

Is this recoverable, and how would I tell?

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.

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 part that matters: mass on column affects detector linearity and peak overlap — overloading broadens peaks and hides neighbours, while underloading improves resolution but loses sensitivity.

Proline conformer interconversion kinetics are well-characterised and the half-life is of the same order as the chromatographic peak width at room temperature.

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

Read the chromatogram before you read the number, because the number without the trace is not a measurement, it is a claim.

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

The underlying point is that 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.

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

Gradient slope is the most powerful parameter and almost nobody mentions it, which is why two reports on the same material disagree by a point.

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.

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

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

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

The single most important distinction is between what purity measures — the fraction of detected material that is your target — and what you actually want to know — how much of the material in the vial is your target.

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.

Published side-by-side method comparisons show that a two-point difference in purity on the same vial is easily explained by method choice alone.

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

edited 7 Sept 2024 by retest_please — added a caveat about sampling