Why would VendorInvestigate report 97.9% where the supplier certificate says something higher?

The specifics, since they change the answer: VendorInvestigate · 97.9%.

An unexpected observation, and I would like a differential rather than reassurance.

The conditions were within what I understood to be the acceptable range, which is why I am asking.

What would you check first, and what would you conclude from each outcome?

Concretely, identity and purity are orthogonal, and a high purity says almost nothing about whether the peak is actually what you think it is.

The fraction of your main peak that is actually your target versus isomers, fragments or related sequences is invisible without complementary identity testing.

In practice, temperature affects the dynamics of molecular conformation, and if a peptide has proline residues that interconvert on the chromatographic timescale, the peak will split or shoulder at low temperature and collapse at high temperature.

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.

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

The part that matters: read the chromatogram before you read the number, because the number without the trace is not a measurement, it is a claim.

Retention time is sequence-specific and method-specific, so comparing your result to a supplier value using a different method is meaningless without method documentation.

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 caveat is that purity without identity is only half an answer — a high purity does not mean the peak is actually what you think it is.

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

Worth being precise here: start from what the detector sees, because that tells you what the number means.

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.

In practice, 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.

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

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

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.

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.

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

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

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

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

One qualification: achieving purity above roughly 98 per cent on a 30-residue peptide is fighting the chemistry of synthesis, not the quality of the purification.

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