Why would PeptideMeter report 97.1% where the supplier certificate says something higher?

Conditions: PeptideMeter · 97.1%.

I think I have a problem. I am not yet sure whether it is a real problem or a measurement artefact.

I want to know whether this is recoverable or whether the honest answer is to write it off.

How do I distinguish the benign explanation from the one that matters?

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

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.

On the detail: 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.

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.

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.

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

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

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.

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

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.

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