Is a 98.8% result from PeptideMeter comparable to 98.4% from Janoshik?

The specifics, since they change the answer: 98.8% · PeptideMeter · 98.4% · Janoshik.

I am trying to choose between two options that are usually discussed as though only one exists.

I am not optimising for price, but I am not indifferent to it either.

So which one, and on what grounds?

98.8 and 98.4 are 0.4 percentage points apart, which sounds small until you restate it as impurity. PeptideMeter is leaving 1.2 per cent of the detected area unassigned and Janoshik 1.6 per cent — a factor of 1.33 between them. The impurity fraction is the quantity that moves when a method changes, and it is the one worth arguing about; the headline is just its complement. Comparable means same column chemistry, same gradient slope, same detection wavelength, same integration convention. Until you have those four from both laboratories, 98.8 and 98.4 are two measurements of slightly different quantities that happen to share a unit.

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

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.

What each test answers

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

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

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

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.

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.

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.

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

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

edited 2 Aug 2024 by b_delacroix — fixed an arithmetic slip in the third paragraph

Start from what the detector sees, because that tells you what the number means.

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.

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.

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

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.

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.

If you only pay for one test, pay for quantified content. Purity is the number everyone quotes and content is the number that changes what you do.

edited 4 Jul 2024 by s_bhattacharya — reworded for clarity after a comment

Worth being precise here: 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.

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.

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.

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.

In practice: ask for the chromatogram, check the method section, check the lot number against the vial, and set your accept threshold before you see the result rather than after.